Inducing Cellular Immune Responses to Plasmodium Falciparum Using Peptide and Nucleic Acid Compositions

- Epimmune Inc.

This invention uses our knowledge of the mechanisms by which antigen is recognized by T cells to identify and prepare Plasmodium falciparum epitopes, and to develop epitope-based vaccines directed towards malaria. More specifically, this application communicates our discovery of pharmaceutical compositions and methods of use in the prevention and treatment of malaria. In particular, this application discloses isolated peptides comprising oligopeptides, for example the oligopeptides LLACAGLAY, FLIFFDLFLV, FMKAVCVEV, VLAGLLGNV, GLIMVLSFL, KILSVFFLA, GLLGNVSTV, VLLGGVGLVL, ILSVSSFLFV, QTNFKSLLR, LACAGLAYK, ALFFIIFNK, LLACAGLAYK, HVLSHNSYEK, FILVNLLIFH, FQDEENIGIY, PSDGKCNLY, YYIPHQSSL, FYFILVNLL, KYLVIVFLI and KYKLATSVL, or isolated peptides conjugated with T helper peptides that are used as antigens in epitope-based vaccines to prevent and/or treat malaria.

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Description
CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 09/390,061, filed Sep. 3, 1999, wherein U.S. application Ser. No. 09/390,061 is a continuation-in-part of U.S. application Ser. No. 09/017,743, filed Feb. 3, 1998 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/821,739, filed Mar. 20, 1997 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/452,843, filed May 30, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/454,033, filed May 26, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); said Ser. No. 09/017,743 (abandoned) is a continuation-in-part of U.S. application Ser. No. 08/753,615, filed Nov. 23, 1996 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/590,298, filed Jan. 23, 1996 (abandoned); which is a continuation-in-part of said Ser. No. 08/452,843, filed May 30, 1995 (abandoned); which is a continuation-in-part of said Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/278,634, filed Jul. 21, 1994 (abandoned); said Ser. No. 08/821,739 (abandoned) claims the benefit of U.S. Provisional Application No. 60/013,833, filed Mar. 21, 1996 (now inactive); and is a continuation-in-part of U.S. application Ser. No. 08/451,913, filed May 26, 1995 (abandoned).

This application is related to U.S. Ser. No. 09/189,702 filed Nov. 10, 1998, now U.S. Pat. No. 7,252,829, which is a CIP of U.S. Ser. No. 08/205,713 filed Mar. 4, 1994 (abandoned), which is a CIP of Ser. No. 08/159,184 filed Nov. 29, 1993 and now abandoned, which is a CIP of Ser. No. 08/073,205 filed Jun. 4, 1993 and now abandoned, which is a CIP of Ser. No. 08/027,146 filed Mar. 5, 1993 and now abandoned. The present application is also related to U.S. Ser. No. 09/226,775 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/815,396, which claims benefit of abandoned U.S. Ser. No. 60/013,113 filed Mar. 21, 1996. Furthermore, the present application is related to U.S. Ser. No. 09/017,735 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/589,108; U.S. Ser. No. 08/454,033 (abandoned); and U.S. Ser. No. 08/349,177 (abandoned). The present application is also related to U.S. Ser. No. 09/017,524 (abandoned), U.S. Ser. No. 08/821,739 (abandoned), which claims benefit of abandoned U.S. Ser. No. 60/013,833 filed Mar. 21, 1996; and U.S. Ser. No. 08/347,610 (abandoned), which is a CIP of U.S. Ser. No. 08/159,339, now U.S. Pat. No. 6,037,135, which is a CIP of abandoned U.S. Ser. No. 08/103,396, which is a CIP of abandoned U.S. Ser. No. 08/027,746, which is a CIP of abandoned U.S. Ser. No. 07/926,666. The present application is also related to U.S. Ser. No. 09/017,743 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/590,298; and U.S. Ser. No. 08/452,843 (abandoned), which is a CIP of U.S. Ser. No. 08/344,824 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/278,634. The present application is also related to PCT application PCT/US99/12066 filed May 28, 1999 which claims benefit of provisional U.S. Ser. No. 60/087,192, filed May 29, 1998 (now inactive), and U.S. Ser. No. 09/009,953 (abandoned), which is a CIP of abandoned U.S. Ser. No. 60/036,713 and abandoned U.S. Ser. No. 60/037,432. In addition, the present application is related to U.S. Ser. No. 09/098,584 (abandoned), U.S. Ser. No. 09/239,043 now U.S. Pat. No. 6,689,363, and to Provisional U.S. Patent Application 60/117,486 filed Jan. 27, 1999 (now inactive). The present application is also related to Ser. No. 09/350,401 filed Jul. 8, 1999, and U.S. Ser. No. 09/357,737 filed Jul. 19, 1999. All of the above applications are incorporated herein by reference.

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was funded, in part, by the United States government under grants with the National Institutes of Health. The U.S. government has certain rights in this invention.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing (Name: 2473 0510005_SeqListing_ST25.txt, Size: 962,033 bytes; and Date of Creation: Dec. 21, 2015) filed herewith was originally filed with U.S. application Ser. No. 09/390,061 and is incorporated herein by reference in its entirety.

INDEX I. Background of the Invention II. Summary of the Invention III. Brief Description of the Figures IV. Detailed Description of the Invention

    • A. Definitions
    • B. Stimulation of CTL and HTL responses
    • C. Binding Affinity of Peptide Epitopes for HLA Molecules
    • D. Peptide Epitope Binding Motifs and Supermotifs
      • 1. HLA-A1 supermotif
      • 2. HLA-A2 supermotif
      • 3. HLA-A3 supermotif
      • 4. HLA-A24 supermotif
      • 5. HLA-B7 supermotif
      • 6. HLA-B27 supermotif
      • 7. HLA-B44 supermotif
      • 8. HLA-B58 supermotif
      • 9. HLA-B62 supermotif
      • 10. HLA-A1 motif
      • 11. HLA-A2.1 motif
      • 12. HLA-A3 motif
      • 13. HLA-A11 motif
      • 14. HLA-A24 motif
      • 15. HLA-DR-1-4-7 supermotif
      • 16. HLA-DR3 motifs
    • E. Enhancing Population Coverage of the Vaccine
    • F. Immune Response-Stimulating Peptide Epitope Analogs
    • G. Computer Screening of Protein Sequences from Disease-Related Antigens for Supermotif- or Motif-Containing Epitopes
    • H. Preparation of Peptide Epitopes
    • I. Assays to Detect T-Cell Responses
    • J. Use of Peptide Epitopes for Evaluating Immune Responses
    • K. Vaccine Compositions
      • 1. Minigene Vaccines
      • 2. Combinations of CTL Peptides with Helper Peptides
    • L. Administration of Vaccines for Therapeutic or Prophylactic Purposes
    • M. Kits

V. Examples VI. Claims VII. Abstract I. BACKGROUND OF THE INVENTION

Malaria, which is caused by infection with the parasite Plasmodium falciparum (PF), represents a major world health problem. Approximately 500 million people in the world are at risk from the disease, with approximately 200 million people actually harboring the parasites. An estimated 1 to 2 million deaths occur each year due to malaria. (Miller et al., Science 234:1349, 1986).

Fatal outcomes are not confined to first infections, and constant exposure is apparently a prerequisite for maintaining immunity. Naturally acquired sterile immunity is rare, if it exists at all. Accordingly, major efforts to develop an efficacious malaria vaccine have been undertaken.

Human volunteers injected with irradiated PF sporozoites are resistant to subsequent sporozoite challenges, which demonstrates that development of a malaria vaccine is indeed immunologically feasible. Furthermore, these immune individuals developed a vigorous response, including antibodies, and cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) components, directed against multiple antigens. Reproducing the breadth and multiplicity of this response in a vaccine, however, is a task of large proportions. The epitope approach, as described herein, may represent a solution to this challenge, in that it allows the incorporation of various antibody, CTL and HTL epitopes, from various proteins, in a single vaccine composition.

Anti-sporozoite antibodies are by themselves, in general, not completely efficacious in clearing the infection (Egan et al., Science 236:453, 1987). However, high concentrations of antibodies directed against the repeated region of the major B cell antigen of the sporozoite/circumsporozoite protein (CSP) have been shown to prevent liver cell infection in certain experimental models (Egan et al., Science 236:453, 1987; Potocnjak, P. et al., Science 207:71, 1980). The present inventors have shown that constructs encompassing CSP-repeat B cell epitopes and the optimized helper epitope PADRE™ (San Diego, Calif.) are highly immunogenic, and can protect in vitro against sporozoite invasion in both mouse and human liver cells, and protect mice in vivo against live sporozoite challenge (Franke et al., Vaccine 17:1201-1205, 1999)

PF-specific CD4+ T cells also have a role in malarial immunity beyond providing help for B cell and CTL responses. Experiments by Renia et al. (Renia, et al., Proc. Natl. Acad. Sci. USA 88:7963, 1991) demonstrated that HTLs directed against the Plasmodium yoelli CS protein could in fact adoptivley transfer protection against malaria.

Considerable data implicate CTLs in protection against pre-erythrocytic-stage malaria. CD8+ CTLs can eliminate Plasmodium berghei- or Plasmodium yoelii-infected mouse hepatocytes from in vitro culture in a major histocompatibility complex (MHC)-restricted and antigen-restricted manner (Hoffman et al., Science 244:1078-1081, 1989; Weiss et al., J. Exp. Med. 171:763-773, 1990). Further, it has also been shown that the immunity that developed in mice vaccinated with irradiated sporozoites is also dependent upon the present of CD8+ T cells. These T cells accumulate in inflammatory liver infiltrates subsequent to challenge. Passive transfer of circumsporozoite (CSP)-specific CTL clones as long as three hours after inoculation of sporozoites (i.e., after the parasites have left the bloodstream and infected liver cells) were capable of protecting animals against infection (Romero et al., Nature 341:323, 1989).

It is notable that CTL-restricted responses directed against a single antigen are insufficient to protect mice with different MHC alleles, and a combination of multiple antigens was required even to protect mice from the most common laboratory strains of Plasmodium. These data indicate that a combination of epitopes form several antigens is necessary to elicit a protective CTL response.

Indirect evidence that CTLs are important in protective immunity against Pf in humans has also accumulated. It has been reported that cytotoxic CD8+ T cells can be identified in humans immunized with PF sporozoites (Moreno, et al., Int. Immunol. 3:997, 1991). Further, humans immunized with irradiated sporozoites or naturally exposed to malaria can generate a CTL response to the pre-erythrocytic-stage antigens, CSP, sporozoite surface protein 2 (SSP2), liver-stage antigen-1 (LSA-1), and exported protein-1 (Exp-1) (see, e.g. Malik et al., Proc. Natl. Acad. Sci. USA 88, 3300-3304, 1991; Doolan et al., Int. Immunol. 3:511-516, 1991; Hill et al., Nature 360:434-439, 1992). Additionally, there is evidence that the polymorphism within the CSP may be the result of selection by CTLs of parasites that express variant forms (MCutchan and Water, Immunol. Lett. 25:23-26, 1990). This is based on the observation that the variation is nonsynonymous at the nucleotide level, thereby indicating selective pressure at the protein level. The polymorphism primarily maps to identified CTL and T helper epitopes (Doolan et al., Int. Immunol. 5:27-46, 1993); and CTL responses to some of the parasite variants do not cross-react (Hill et al., supra). Finally, the MHC class I human leukocyte antigen (HLA)-Bw53 has been associated with resistance to severe malaria in The Gambia, and CTLs to a conserved epitope restricted by the HLA-Bw53 allele have been identified on P. falciparum LSA-1 (Hill et al., Nature 352:595-600, 1991; Hill et al., Nature 340:434-439, 1992). Since HLA-Bw53 is found in 15%-40% of the population of sub-Saharan Africa but in less than 1% of Caucasians and Asians, these data suggest evolutionary selection on the basis of protection against severe malaria.

Thus, antibody, and both HLA class I and class II restricted responses directed against multiple sporozoite antigens appear to be involved in generating protective immunity to malaria. Furthermore, several important antigenic epitopes against which humoral and cellular immunity is focused have already been exactly delineated.

HLA class I molecules are expressed on the surface of almost all nucleated cells. Following intracellular processing of antigens, epitopes from the antigens are presented as a complex with the HLA class I molecules on the surface of such cells. CTL recognize the peptide-HLA class I complex, which then results in the destruction of the cell bearing the HLA-peptide complex directly by the CTL and/or via the activation of non-destructive mechanisms e.g., the production of interferon.

In view of the heterogeneous immune response observed with PF infection, induction of a multi-specific cellular immune response directed simultaneously against multiple PF epitopes appears to be important for the development of an efficacious vaccine against PF. There is a need, however, to establish vaccine embodiments that elicit immune responses that correspond to responses seen in patients that clear PF infection.

The information provided in this section is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, information in this section is not intended, in any way, to delineate the priority date for the invention.

II. SUMMARY OF THE INVENTION

This invention applies our knowledge of the mechanisms by which antigen is recognized by T cells, for example, to develop epitope-based vaccines directed towards PF. More specifically, this application communicates our discovery of specific epitope pharmaceutical compositions and methods of use in the prevention and treatment of PF infection.

Upon development of appropriate technology, the use of epitope-based vaccines has several advantages over current vaccines, particularly when compared to the use of whole antigens in vaccine compositions. There is evidence that the immune response to whole antigens is directed largely toward variable regions of the antigen, allowing for immune escape due to mutations. The epitopes for inclusion in an epitope-based vaccine are selected from conserved regions of antigens of pathogenic organisms or tumor-associated antigens, which thereby reduces the likelihood of escape mutants. Furthermore, immunosuppressive epitopes that may be present in whole antigens can be avoided with the use of epitope-based vaccines.

An additional advantage of an epitope-based vaccine approach is the ability to combine selected epitopes (CTL and HTL), and further, to modify the composition of the epitopes, achieving, for example, enhanced immunogenicity. Accordingly, the immune response can be modulated, as appropriate, for the target disease. Similar engineering of the response is not possible with traditional approaches.

Another major benefit of epitope-based immune-stimulating vaccines is their safety. The possible pathological side effects caused by infectious agents or whole protein antigens, which might have their own intrinsic biological activity, is eliminated.

An epitope-based vaccine also provides the ability to direct and focus an immune response to multiple selected antigens from the same pathogen. Thus, patient-by-patient variability in the immune response to a particular pathogen may be alleviated by inclusion of epitopes from multiple antigens from that pathogen in a vaccine composition. A “pathogen” may be an infectious agent or a tumor associated molecule.

One of the most formidable obstacles to the development of broadly efficacious epitope-based immunotherapeutics, however, has been the extreme polymorphism of HLA molecules. To date, effective non-genetically biased coverage of a population has been a task of considerable complexity; such coverage has required that epitopes be used that are specific for HLA molecules corresponding to each individual HLA allele; impractically large numbers of epitopes would therefore have to be used in order to cover ethnically diverse populations. Thus, there has existed a need for peptide epitopes that are bound by multiple HLA antigen molecules for use in epitope-based vaccines. The greater the number of HLA antigen molecules bound, the greater the breadth of population coverage by the vaccine.

Furthermore, as described herein in greater detail, a need has existed to modulate peptide binding properties, e.g., so that peptides that are able to bind to multiple HLA antigens do so with an affinity that will stimulate an immune response. Identification of epitopes restricted by more than one HLA allele at an affinity that correlates with immunogenicity is important to provide thorough population coverage, and to allow the elicitation of responses of sufficient vigor to prevent or clear an infection in a diverse segment of the population. Such a response can also target a broad array of epitopes. The technology disclosed herein provides for such favored immune responses.

In a preferred embodiment, epitopes for inclusion in vaccine compositions of the invention are selected by a process whereby protein sequences of known antigens are evaluated for the presence of motif or supermotif-bearing epitopes. Peptides corresponding to a motif- or supermotif-bearing epitope are then synthesized and tested for the ability to bind to the HLA molecule that recognizes the selected motif. Those peptides that bind at an intermediate or high affinity i.e., an IC50 (or a KD value) of 500 nM or less for HLA class I molecules or an IC50 of 1000 nM or less for HLA class II molecules, are further evaluated for their ability to induce a CTL or HTL response. Immunogenic peptide epitopes are selected for inclusion in vaccine compositions.

Supermotif-bearing peptides may additionally be tested for the ability to bind to multiple alleles within the HLA supertype family. Moreover, peptide epitopes may be analogued to modify binding affinity and/or the ability to bind to multiple alleles within an HLA supertype.

The invention also includes embodiments comprising methods for monitoring or evaluating an immune response to PF in patient having a known HLA-type. Such methods comprise incubating a T cell sample from the patient with a peptide composition comprising an PF epitope consisting essentially of an amino acid sequence described in Tables VII to Table XX or Table XXII which binds the product of at least one HLA allele present in the patient, and detecting for the presence of a T cell that binds to the peptide. A CTL peptide epitope may, for example, be used as a component of a tetrameric complex for such an analysis.

An alternative modality for defining the peptide epitopes in accordance with the invention is to recite the physical properties, such as length; primary structure; or charge, which are correlated with binding to a particular allele-specific HLA molecule or group of allele-specific HLA molecules. A further modality for defining peptide epitopes is to recite the physical properties of an HLA binding pocket, or properties shared by several allele-specific HLA binding pockets (e.g. pocket configuration and charge distribution) and reciting that the peptide epitope fits and binds to said pocket or pockets.

As will be apparent from the discussion below, other methods and embodiments are also contemplated. Further, novel synthetic peptides produced by any of the methods described herein are also part of the invention.

III. BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 provides a graph of total frequency of genotypes as a function of the number of PF candidate epitopes bound by HLA-A and B molecules, in an average population.

 IV. DETAILED DESCRIPTION OF THE INVENTION

The peptide epitopes and corresponding nucleic acid compositions of the present invention are useful for stimulating an immune response to PF by stimulating the production of CTL or HTL responses. The peptide epitopes, which are derived directly or indirectly from native PF protein amino acid sequences, are able to bind to HLA molecules and stimulate an immune response to PF. The complete sequence of the PF proteins to be analyzed can be obtained from Genbank. Peptide epitopes and analogs thereof can also be readily determined from sequence information that may subsequently be discovered for heretofore unknown variants of PF, as will be clear from the disclosure provided below.

The peptide epitopes of the invention have been identified in a number of ways, as will be discussed below. Also discussed in greater detail is that analog peptides have been derived and the binding activity for HLA molecules modulated by modifying specific amino acid residues to create peptide analogs exhibiting altered immunogenicity. Further, the present invention provides compositions and combinations of compositions that enable epitope-based vaccines that are capable of interacting with HLA molecules encoded by various genetic alleles to provide broader population coverage than prior vaccines.

IV.A. DEFINITIONS

The invention can be better understood with reference to the following definitions, which are listed alphabetically:

A “computer” or “computer system” generally includes: a processor; at least one information storage/retrieval apparatus such as, for example, a hard drive, a disk drive or a tape drive; at least one input apparatus such as, for example, a keyboard, a mouse, a touch screen, or a microphone; and display structure. Additionally, the computer may include a communication channel in communication with a network. Such a computer may include more or less than what is listed above.

“Cross-reactive binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is degenerate binding.

A “cryptic epitope” elicits a response by immunization with an isolated peptide, but the response is not cross-reactive in vitro when intact whole protein which comprises the epitope is used as an antigen.

A “dominant epitope” is an epitope that induces an immune response upon immunization with a whole native antigen (see, e.g., Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993). Such a response is cross-reactive in vitro with an isolated peptide epitope.

With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues which is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor (TCR) proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vivo or in vitro, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, TCR or HLA molecule. Throughout this disclosure epitope and peptide are often used interchangeably. It is to be appreciated, however, that isolated or purified protein or peptide molecules larger than and comprising an epitope of the invention are still within the bounds of the invention.

“Human Leukocyte Antigen” or “HLA” is a human class I or class II MHC protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994).

An “HLA supertype or family”, as used herein, describes sets of HLA molecules grouped on the basis of shared peptide-binding specificities. HLA class I molecules that share somewhat similar binding affinity for peptides bearing certain amino acid motifs are grouped into HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecules (where xx denotes a particular HLA type), are synonyms.

Throughout this disclosure, results are expressed in terms of “IC50's.” IC50 is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (i.e., limiting HLA proteins and labeled peptide concentrations), these values approximate KD values. Assays for determining binding are described in detail, e.g., in PCT publications WO 94/20127 and WO 94/03205. It should be noted that IC50 values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC50 of a given ligand.

Alternatively, binding is expressed relative to a reference peptide. Although as a particular assay becomes more, or less, sensitive, the IC50's of the peptides tested may change somewhat, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC50 of the reference peptide increases 10-fold, the IC50 values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC50, relative to the IC50 of a standard peptide.

Binding may also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392, 1989; Christnick et al., Nature 352:67, 1991; Busch et al., Immunol. 2:443, 1990; Hill et al., J. Immunol. 147:189, 1991; del Guercio et al., J. Immunol. 154:685, 1995), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069, 1991), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et al., J. Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al., EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476, 1990; Schumacher et al., Cell 62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J. Immunol. 149:1896, 1992).

As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC50, or KD value, of 50 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an IC50 or KD value of 100 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 100 and about 1000 nM.

The terms “identical” or percent “identity,” in the context of two or more peptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.

An “immunogenic peptide” or “peptide epitope” is a peptide that comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL and/or HTL response. Thus, immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and thereafter inducing a cytotoxic T cell response, or a helper T cell response, to the antigen from which the immunogenic peptide is derived.

The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.

“Major Histocompatibility Complex” or “MHC” is a cluster of genes that plays a role in control of the cellular interactions responsible for physiologic immune responses. In humans, the MHC complex is also known as the HLA complex. For a detailed description of the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3RD ED., Raven Press, New York, 1993.

The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

A “negative binding residue” or “deleterious residue” is an amino acid which, if present at certain positions (typically not primary anchor positions) in a peptide epitope, results in decreased binding affinity of the peptide for the peptide's corresponding HLA molecule.

The term “peptide” is used interchangeably with “oligopeptide” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the alpha-amino and carboxyl groups of adjacent amino acids. The preferred CTL-inducing peptides of the invention are 13 residues or less in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. The preferred HTL-inducing peptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between about 12 and 25, and often between about 15 and 20 residues.

“Pharmaceutically acceptable” refers to a non-toxic, inert, and physiologically compatible composition.

A “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding grooves of an HLA molecule, with their side chains buried in specific pockets of the binding grooves themselves. In one embodiment, for example, the primary anchor residues are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 9-residue peptide epitope in accordance with the invention. The primary anchor positions for each motif and supermotif are set forth in Table 1. For example, analog peptides can be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to modulate the binding affinity of a peptide comprising a particular motif or supermotif.

“Promiscuous recognition” is where a distinct peptide is recognized by the same T cell clone in the context of various HLA molecules. Promiscuous recognition or binding is synonymous with cross-reactive binding.

A “protective immune response” or “therapeutic immune response” refers to a CTL and/or an HTL response to an antigen derived from an infectious agent or a tumor antigen, which prevents or at least partially arrests disease symptoms or progression. The immune response may also include an antibody response which has been facilitated by the stimulation of helper T cells.

The term “residue” refers to an amino acid or amino acid mimetic incorporated into an oligopeptide by an amide bond or amide bond mimetic.

A “secondary anchor residue” is an amino acid at a position other than a primary anchor position in a peptide which may influence peptide binding. A secondary anchor residue occurs at a significantly higher frequency amongst bound peptides than would be expected by random distribution of amino acids at one position. The secondary anchor residues are said to occur at “secondary anchor positions.” A secondary anchor residue can be identified as a residue which is present at a higher frequency among high or intermediate affinity binding peptides, or a residue otherwise associated with high or intermediate affinity binding. For example, analog peptides can be created by altering the presence or absence of particular residues in these secondary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.

A “subdominant epitope” is an epitope which evokes little or no response upon immunization with whole antigens which comprise the epitope, but for which a response can be obtained by immunization with an isolated peptide, and this response (unlike the case of cryptic epitopes) is detected when whole protein is used to recall the response in vitro or in vivo.

A “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Preferably, a supermotif-bearing peptide is recognized with high or intermediate affinity (as defined herein) by two or more HLA antigens.

“Synthetic peptide” refers to a peptide that is not naturally occurring, but is man-made using such methods as chemical synthesis or recombinant DNA technology.

The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in a peptide epitope they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal end of the epitope, or the peptide or protein of which it may be a part. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. Symbols for the amino acids are shown below.

Single Letter Three Letter Amino Symbol Symbol Acids A Ala Alanine C Cys Cysteine D Asp Aspartic Acid E Glu Glutamic Acid F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine K Lys Lysine L Leu Leucine M Met Methionine N Asn Asparagine P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan Y Tyr Tyrosine

IV.B. STIMULATION OF CTL AND HTL RESPONSES

The mechanism by which T cells recognize antigens has been delineated during the past ten years. Based on our understanding of the immune system we have developed efficacious peptide epitope vaccine compositions that can induce a therapeutic or prophylactic immune response to PF in a broad population. For an understanding of the value and efficacy of the claimed compositions, a brief review of immunology-related technology is provided.

A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are described herein and are set forth in Tables I, II, and III (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via web at: http://134.2.96.221/scripts.hlaserver.d11/home.htm; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics, in press, 1999).

Furthermore, x-ray crystallographic analysis of HLA-peptide complexes has revealed pockets within the peptide binding cleft of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that have the potential of binding particular HLA antigen(s).

The present inventors have found that the correlation of binding affinity with immunogenicity, which is disclosed herein, is an important factor to be considered when evaluating candidate peptides. Thus, by a combination of motif searches and HLA-peptide binding assays, candidates for epitope-based vaccines have been identified. After determining their binding affinity, additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, antigenicity, and immunogenicity.

Various strategies can be utilized to evaluate immunogenicity, including:

1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998); This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells.

2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997); In this method, peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

3) Demonstration of recall T cell responses from immune individuals who have effectively been vaccinated, recovered from infection, and/or from chronically infected patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). In applying this strategy, recall responses are detected by culturing PBL from subjects that have been naturally exposed to the antigen, for instance through infection, and thus have generated an immune response “naturally”, or from patients who were vaccinated against the infection. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays for T cell activity including 51Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

The following describes the peptide epitopes and corresponding nucleic acids of the invention.

IV.C. BINDING AFFINITY OF PEPTIDE EPITOPES FOR HLA MOLECULES

As indicated herein, the large degree of HLA polymorphism is an important factor to be taken into account with the epitope-based approach to vaccine development. To address this factor, epitope selection encompassing identification of peptides capable of binding at high or intermediate affinity to multiple HLA molecules is preferably utilized, most preferably these epitopes bind at high or intermediate affinity to two or more allele-specific HLA molecules.

CTL-inducing peptides of interest for vaccine compositions preferably include those that have an IC50 or binding affinity value for class I HLA molecules of 500 nM or better (i.e., the value is ≦500 nM). HTL-inducing peptides preferably include those that have an IC50 or binding affinity value for class II HLA molecules of 1000 nM or better, (i.e., the value is ≦1,000 nM). For example, peptide binding is assessed by testing the capacity of a candidate peptide to bind to a purified HLA molecule in vitro. Peptides exhibiting high or intermediate affinity are then considered for further analysis. Selected peptides are tested on other members of the supertype family. In preferred embodiments, peptides that exhibit cross-reactive binding are then used in cellular screening analyses or vaccines.

As disclosed herein, higher HLA binding affinity is correlated with greater immunogenicity. Greater immunogenicity can be manifested in several different ways. Immunogenicity corresponds to whether an immune response is elicited at all, and to the vigor of any particular response, as well as to the extent of a population in which a response is elicited. For example, a peptide might elicit an immune response in a diverse array of the population, yet in no instance produce a vigorous response. In accordance with these principles, close to 90% of high binding peptides have been found to be immunogenic, as contrasted with about 50% of the peptides which bind with intermediate affinity. Moreover, higher binding affinity peptides leads to more vigorous immunogenic responses. As a result, less peptide is required to elicit a similar biological effect if a high affinity binding peptide is used. Thus, in preferred embodiments of the invention, high affinity binding epitopes are particularly useful.

The relationship between binding affinity for HLA class I molecules and immunogenicity of discrete peptide epitopes on bound antigens has been determined for the first time in the art by the present inventors. The correlation between binding affinity and immunogenicity was analyzed in two different experimental approaches (see, e.g., Sette, et al., J. Immunol. 153:5586-5592, 1994). In the first approach, the immunogenicity of potential epitopes ranging in HLA binding affinity over a 10,000-fold range was analyzed in HLA-A*0201 transgenic mice. In the second approach, the antigenicity of approximately 100 different hepatitis B virus (HBV)-derived potential epitopes, all carrying A*0201 binding motifs, was assessed by using PBL from acute hepatitis patients. Pursuant to these approaches, it was determined that an affinity threshold value of approximately 500 nM (preferably 50 nM or less) determines the capacity of a peptide epitope to elicit a CTL response. These data are true for class I binding affinity measurements for naturally processed peptides and for synthesized T cell epitopes. These data also indicate the important role of determinant selection in the shaping of T cell responses (see, e.g., Schaeffer et al. Proc. Natl. Acad. Sci. USA 86:4649-4653, 1989).

An affinity threshold associated with immunogenicity in the context of HLA class II DR molecules has also been delineated (see, e.g., Southwood et al. J. Immunology 160:3363-3373,1998, and U.S. Ser. No. 09/009,953 filed Jan. 21, 1998, now U.S. Pat. No. 6,413,517). In order to define a biologically significant threshold of DR binding affinity, a database of the binding affinities of 32 DR-restricted epitopes for their restricting element (i.e., the HLA molecule that binds the motif) was compiled. In approximately half of the cases (15 of 32 epitopes), DR restriction was associated with high binding affinities, i.e. binding affinity values of 100 nM or less. In the other half of the cases (16 of 32), DR restriction was associated with intermediate affinity (binding affinity values in the 100-1000 nM range). In only one of 32 cases was DR restriction associated with an IC50 of 1000 nM or greater. Thus, 1000 nM can be defined as an affinity threshold associated with immunogenicity in the context of DR molecules.

The binding affinity of peptides for HLA molecules can be determined as described in Example 1, below.

IV.D. PEPTIDE EPITOPE BINDING MOTIFS AND SUPERMOTIFS

Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues required for allele-specific binding to HLA molecules have been identified. The presence of these residues correlates with binding affinity for HLA molecules. The identification of motifs and/or supermotifs that correlate with high and intermediate affinity binding is an important issue with respect to the identification of immunogenic peptide epitopes for the inclusion in a vaccine. Kast et al. (J. Immunol. 152:3904-3912, 1994) have shown that motif-bearing peptides account for 90% of the epitopes that bind to allele-specific HLA class I molecules. In this study all possible peptides of 9 amino acids in length and overlapping by eight amino acids (240 peptides), which cover the entire sequence of the E6 and E7 proteins of human papillomavirus type 16, were evaluated for binding to five allele-specific HLA molecules that are expressed at high frequency among different ethnic groups. This unbiased set of peptides allowed an evaluation of the predictive value of HLA class I motifs. From the set of 240 peptides, 22 peptides were identified that bound to an allele-specific HLA molecule with high or intermediate affinity. Of these 22 peptides, 20 (i.e. 91%) were motif-bearing. Thus, this study demonstrates the value of motifs for the identification of peptide epitopes for inclusion in a vaccine: application of motif-based identification techniques will identify about 90% of the potential epitopes in a target antigen protein sequence.

Such peptide epitopes are identified in the Tables described below.

Peptides of the present invention may also comprise epitopes that bind to MEW class II DR molecules. A greater degree of heterogeneity in both size and binding frame position of the motif, relative to the N and C termini of the peptide, exists for class II peptide ligands. This increased heterogeneity of HLA class II peptide ligands is due to the structure of the binding groove of the HLA class II molecule which, unlike its class I counterpart, is open at both ends. Crystallographic analysis of HLA class II DRB*0101-peptide complexes showed that the major energy of binding is contributed by peptide residues complexed with complementary pockets on the DRB*0101 molecules. An important anchor residue engages the deepest hydrophobic pocket (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587, 1995) and is referred to as position 1 (P1). P1 may represent the N-terminal residue of a class II binding peptide epitope, but more typically is flanked towards the N-terminus by one or more residues. Other studies have also pointed to an important role for the peptide residue in the 6th position towards the C-terminus, relative to P1, for binding to various DR molecules.

In the past few years evidence has accumulated to demonstrate that a large fraction of HLA class I and class II molecules can be classified into a relatively few supertypes, each characterized by largely overlapping peptide binding repertoires, and consensus structures of the main peptide binding pockets. Thus, peptides of the present invention are identified by any one of several HLA-specific amino acid motifs (see, e.g., Tables or if the presence of the motif corresponds to the ability to bind several allele-specific HLA antigens, a supermotif. The HLA molecules that bind to peptides that possess a particular amino acid supermotif are collectively referred to as an HLA “supertype.”

The peptide motifs and supermotifs described below, and summarized in Tables I-III, provide guidance for the identification and use of peptide epitopes in accordance with the invention.

Examples of peptide epitopes bearing a respective supermotif or motif are included in Tables as designated in the description of each motif or supermotif below. The Tables include a binding affinity ratio listing for some of the peptide epitopes. The ratio may be converted to IC50 by using the following formula: IC50 of the standard peptide/ratio=IC50 of the test peptide (i.e., the peptide epitope). The IC50 values of standard peptides used to determine binding affinities for Class I peptides are shown in Table IV. The IC50 values of standard peptides used to determine binding affinities for Class II peptides are shown in Table V. The peptides used as standards for the binding assays described herein are examples of standards; alternative standard peptides can also be used when performing binding analyses.

To obtain the peptide epitope sequences listed in each Table, protein sequence data for four P. falciparum antigens were evaluated for the presence of the designated supermotif or motif. These antigens are: EXP-1, LSA-1, SSP2, and CSP. Nineteen sequences were available for CSP, 10 sequences were available for SSP, and one sequence each was available for EXP-1 and LSA-1. Peptide epitopes were additionally evaluated on the basis of their conservancy among the protein sequences for the PF antigens for which multiple sequences were available. A criterion for conservancy requires that the entire sequence of an HLA class I binding peptide be totally (i.e., 100%) conserved in 79% of the sequences available for a specific protein. Similarly, a criterion for conservancy requires that the entire 9-mer core region of an HLA class II binding peptide be totally conserved in 79% of the sequences available for a specific protein. The percent conservancy of the selected peptide epitopes is indicated on the Tables. The frequency, i.e. the number of sequences of the PF protein antigen in which the totally conserved peptide sequence was identified, is also shown. The “pos” (position) column in the Tables designates the amino acid position in the PF protein that corresponds to the first amino acid residue of the epitope. The “number of amino acids” indicates the number of residues in the epitope sequence.

HLA Class I Motifs Indicative of CTL Inducing Peptide Epitopes:

The primary anchor residues of the HLA class I peptide epitope supermotifs and motifs delineated below are summarized in Table I. The HLA class I motifs set out in Table I(a) are those most particularly relevant to the invention claimed here. Primary and secondary anchor positions are summarized in Table II. Allele-specific HLA molecules that comprise HLA class I supertype families are listed in Table VI. In some cases, peptide epitopes may be listed in both a motif and a supermotif Table. The relationship of a particular motif and respective supermotif is indicated in the description of the individual motifs.

IV.D.1. HLA-A1 SUPERMOTIF

The HLA-A1 supermotif is characterized by the presence in peptide ligands of a small (T or S) or hydrophobic (L, I, V, or M) primary anchor residue in position 2, and an aromatic (Y, F, or W) primary anchor residue at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A1 supermotif (i.e., the HLA-A1 supertype) is comprised of at least A*0101, A*2601, A*2602, A*2501, and A*3201 (see, e.g., DiBrino, M. et al., J. Immunol. 151:5930, 1993; DiBrino, M. et al., J. Immunol. 152:620, 1994; Kondo, A. et al., Immunogenetics 45:249, 1997). Other allele-specific HLA molecules predicted to be members of the A1 supertype are shown in Table VI. Peptides binding to each of the individual HLA proteins can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A1 supermotif are set forth on the attached Table VII.

IV.D.2. HLA-A2 Supermotif

Primary anchor specificities for allele-specific HLA-A2.1 molecules (see, e.g., Falk et al., Nature 351:290-296, 1991; Hunt et al., Science 255:1261-1263, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992; Ruppert et al., Cell 74:929-937, 1993) and cross-reactive binding among HLA-A2 and -A28 molecules have been described. (See, e.g., Fruci et al., Human Immunol. 38:187-192, 1993; Tanigaki et al., Human Immunol. 39:155-162, 1994; Del Guercio et al., J. Immunol. 154:685-693, 1995; Kast et al., J. Immunol. 152:3904-3912, 1994 for reviews of relevant data.) These primary anchor residues define the HLA-A2 supermotif; which presence in peptide ligands corresponds to the ability to bind several different HLA-A2 and -A28 molecules. The HLA-A2 supermotif comprises peptide ligands with L, I, V, M, A, T, or Q as a primary anchor residue at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope.

The corresponding family of HLA molecules (i.e., the HLA-A2 supertype that binds these peptides) is comprised of at least: A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*0209, A*0214, A*6802, and A*6901. Other allele-specific HLA molecules predicted to be members of the A2 supertype are shown in Table VI. As explained in detail below, binding to each of the individual allele-specific HLA molecules can be modulated by substitutions at the primary anchor and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise an A2 supermotif are set forth on the attached Table VIII. The motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein.

IV.D.3. HLA-A3 Supermotif

The HLA-A3 supermotif is characterized by the presence in peptide ligands of A, L, I, V, M, S, or, T as a primary anchor at position 2, and a positively charged residue, R or K, at the C-terminal position of the epitope, e.g., in position 9 of 9-mers (see, e.g., Sidney et al., Hum. Immunol. 45:79, 1996). Exemplary members of the corresponding family of HLA molecules (the HLA-A3 supertype) that bind the A3 supermotif include at least A*0301, A*1101, A*3101, A*3301, and A*6801. Other allele-specific HLA molecules predicted to be members of the A3 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions of amino acids at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A3 supermotif are set forth on the attached Table IX.

IV.D.4. HLA-A24 Supermotif

The HLA-A24 supermotif is characterized by the presence in peptide ligands of an aromatic (F, W, or Y) or hydrophobic aliphatic (L, I, V, M, or T) residue as a primary anchor in position 2, and Y, F, W, L, I, or M as primary anchor at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A24 supermotif (i.e., the A24 supertype) includes at least A*2402, A*3001, and A*2301. Other allele-specific HLA molecules predicted to be members of the A24 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the A24 supermotif are set forth on the attached Table X.

IV.D.5. HLA-B7 Supermotif

The HLA-B7 supermotif is characterized by peptides bearing proline in position 2 as a primary anchor, and a hydrophobic or aliphatic amino acid (L, I, V, M, A, F, W, or Y) as the primary anchor at the C-terminal position of the epitope. The corresponding family of HLA molecules that bind the B7 supermotif (i.e., the HLA-B7 supertype) is comprised of at least twenty six HLA-B proteins including: B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601, B*5602, B*6701, and B*7801 (see, e.g., Sidney, et al., J. Immunol. 154:247, 1995; Barber, et al., Curr. Biol. 5:179, 1995; Hill, et al., Nature 360:434, 1992; Rammensee, et al., Immunogenetics 41:178, 1995 for reviews of relevant data). Other allele-specific HLA molecules predicted to be members of the B7 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B7 supermotif are set forth on the attached Table XI.

IV.D.6. HLA-B27 Supermotif

The HLA-B27 supermotif is characterized by the presence in peptide ligands of a positively charged (R, H, or K) residue as a primary anchor at position 2, and a hydrophobic (F, Y, L, W, M, I, A, or V) residue as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B27 supermotif (i.e., the B27 supertype) include at least B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2706, B*3801, B*3901, B*3902, and B*7301. Other allele-specific HLA molecules predicted to be members of the B27 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B27 supermotif are set forth on the attached Table XII.

IV.D.7. HLA-B44 Supermotif

The HLA-B44 supermotif is characterized by the presence in peptide ligands of negatively charged (D or E) residues as a primary anchor in position 2, and hydrophobic residues (F, W, Y, L, I, M, V, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney et al., Immunol. Today 17:261, 1996). Exemplary members of the corresponding family of HLA molecules that bind to the B44 supermotif (i.e., the B44 supertype) include at least: B*1801, B*1802, B*3701, B*4001, B*4002, B*4006, B*4402, B*4403, and B*4006. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the supermotif.

IV.D.8. HLA-B58 Supermotif

The HLA-B58 supermotif is characterized by the presence in peptide ligands of a small aliphatic residue (A, S, or T) as a primary anchor residue at position 2, and an aromatic or hydrophobic residue (F, W, Y, L, I, V, M, or A) as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999 for reviews of relevant data). Exemplary members of the corresponding family of HLA molecules that bind to the B58 supermotif (i.e., the B58 supertype) include at least: B*1516, B*1517, B*5701, B*5702, and B*5801. Other allele-specific HLA molecules predicted to be members of the B58 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B58 supermotif are set forth on the attached Table XIII.

IV.D.9. HLA-B62 Supermotif

The HLA-B62 supermotif is characterized by the presence in peptide ligands of the polar aliphatic residue Q or a hydrophobic aliphatic residue (L, V, M, I, or P) as a primary anchor in position 2, and a hydrophobic residue (F, W, Y, M, I, V, L, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B62 supermotif (i.e., the B62 supertype) include at least: B*1501, B*1502, B*1513, and B5201. Other allele-specific HLA molecules predicted to be members of the B62 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Representative peptide epitopes that comprise the B62 supermotif are set forth on the attached Table XIV.

IV.D.10. HLA-A1 Motif

The HLA-A1 motif is characterized by the presence in peptide ligands of T, S, or M as a primary anchor residue at position 2 and the presence of Y as a primary anchor residue at the C-terminal position of the epitope. An alternative allele-specific A1 motif is characterized by a primary anchor residue at position 3 rather than position 2. This motif is characterized by the presence of D, E, A, or S as a primary anchor residue in position 3, and a Y as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., J. Immunol., 152:620, 1994; Kondo et al., Immunogenetics 45:249, 1997; and Kubo et al., J. Immunol. 152:3913, 1994 for reviews of relevant data). Peptide binding to HLA A1 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise either A1 motif are set forth on the attached Table XV. Those epitopes comprising T, S, or M at position 2 and Y at the C-terminal position are also included in the listing of HLA-A1 supermotif-bearing peptide epitopes listed in Table VII, as these residues are a subset of the A1 supermotif primary anchors.

IV.D.11. HLA-A*0201 Motif

An HLA-A2*0201 motif was determined to be characterized by the presence in peptide ligands of L or M as a primary anchor residue in position 2, and L or V as a primary anchor residue at the C-terminal position of a 9-residue peptide (see, e.g., Falk et al., Nature 351:290-296, 1991) and was further found to comprise an I at position 2 and I or A at the C-terminal position of a nine amino acid peptide (see, e.g., Hunt et al., Science 255:1261-1263, Mar. 6, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992). The A*0201 allele-specific motif has also been defined by the present inventors to additionally comprise V, A, T, or Q as a primary anchor residue at position 2, and M or T as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kast et al., J. Immunol. 152:3904-3912, 1994). Thus, the HLA-A*0201 motif comprises peptide ligands with L, I, V, M, A, T, or Q as primary anchor residues at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope. The preferred and tolerated residues that characterize the primary anchor positions of the HLA-A*0201 motif are identical to the residues describing the A2 supermotif. (For reviews of relevant data, see, e.g., Del Guercio et al., J. Immunol. 154:685-693, 1995; Ruppert et al., Cell 74:929-937, 1993; Sidney et al., Immunol. Today 17:261-266, 1996; Sette and Sidney, Curr. Opin. in Immunol. 10:478-482, 1998). Secondary anchor residues that characterize the A*0201 motif have additionally been defined (see, e.g., Ruppert et al., Cell 74:929-937, 1993). These are shown in Table II. Peptide binding to HLA-A*0201 molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise an A*0201 motif are set forth on the attached Table VIII. The A*0201 motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein

IV.D.12. HLA-A3 Motif

The HLA-A3 motif is characterized by the presence in peptide ligands of L, M, V, I, S, A, T, F, C, G, or D as a primary anchor residue at position 2, and the presence of K, Y, R, H, F, or A as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., Proc. Natl. Acad. Sci USA 90:1508, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A3 motif are set forth on the attached Table XVI. Those peptide epitopes that also comprise the A3 supermotif are also listed in Table IX. The A3 supermotif primary anchor residues comprise a subset of the A3- and A11-allele specific motif primary anchor residues.

IV.D.13. HLA-A11 Motif

The HLA-A11 motif is characterized by the presence in peptide ligands of V, T, M, L, I, S, A, G, N, C, D, or F as a primary anchor residue in position 2, and K, R, Y, or H as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Zhang et al., Proc. Natl. Acad. Sci USA 90:2217-2221, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A11 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A11 motif are set forth on the attached Table XVII; peptide epitopes comprising the A3 allele-specific motif are also present in this Table because of the extensive overlap between the A3 and A11 motif primary anchor specificities. Further, those peptide epitopes that comprise the A3 supermotif are also listed in Table IX.

IV.D.14. HLA-A24 Motif

The HLA-A24 motif is characterized by the presence in peptide ligands of Y, F, W, or M as a primary anchor residue in position 2, and F, L, I, or W as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kondo et al., J. Immunol. 155:4307-4312, 1995; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A24 molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the motif.

Representative peptide epitopes that comprise the A24 motif are set forth on the attached Table XVIII. These epitopes are also listed in Table X, which sets forth HLA-A24-supermotif-bearing peptide epitopes, as the primary anchor residues characterizing the A24 allele-specific motif comprise a subset of the A24 supermotif primary anchor residues.

Motifs Indicative of Class II HTL Inducing Peptide Epitopes

The primary and secondary anchor residues of the HLA class II peptide epitope supermotifs and motifs delineated below are summarized in Table III.

IV.D.15. HLA DR-1-4-7 Supermotif

Motifs have also been identified for peptides that bind to three common HLA class II allele-specific HLA molecules: HLA DRB1*0401, DRB1*0101, and DRB1*0701 (see, e.g., the review by Southwood et al. J. Immunology 160:3363-3373,1998). Collectively, the common residues from these motifs delineate the HLA DR-1-4-7 supermotif. Peptides that bind to these DR molecules carry a supermotif characterized by a large aromatic or hydrophobic residue (Y, F, W, L, I, V, or M) as a primary anchor residue in position 1, and a small, non-charged residue (S, T, C, A, P, V, I, L, or M) as a primary anchor residue in position 6 of a 9-mer core region. Allele-specific secondary effects and secondary anchors for each of these HLA types have also been identified (Southwood et al., supra). These are set forth in Table III. Peptide binding to HLA-DRB1*0401, DRB1*0101, and/or DRB1*0701 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

Conserved 9-mer core regions (i.e., sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis), comprising the DR-1-4-7 supermotif, wherein position 1 of the supermotif is at position 1 of the nine-residue core, are set forth in Table XIXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in section “a” of the Table. Cross-reactive binding data for exemplary 15-residue supermotif-bearing peptides are shown in Table XIXb.

IV.D.16. HLA DR3 Motifs

Two alternative motifs (i.e., submotifs) characterize peptide epitopes that bind to HLA-DR3 molecules (see, e.g., Geluk et al., J. Immunol. 152:5742, 1994). In the first motif (submotif DR3A) a large, hydrophobic residue (L, I, V, M, F, or Y) is present in anchor position 1 of a 9-mer core, and D is present as an anchor at position 4, towards the carboxyl terminus of the epitope. As in other class II motifs, core position 1 may or may not occupy the peptide N-terminal position.

The alternative DR3 submotif provides for lack of the large, hydrophobic residue at anchor position 1, and/or lack of the negatively charged or amide-like anchor residue at position 4, by the presence of a positive charge at position 6 towards the carboxyl terminus of the epitope. Thus, for the alternative allele-specific DR3 motif (submotif DR3B): L, I, V, M, F, Y, A, or Y is present at anchor position 1; D, N, Q, E, S, or T is present at anchor position 4; and K, R, or H is present at anchor position 6. Peptide binding to HLA-DR3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

Conserved 9-mer core regions (i.e., those sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis) corresponding to a nine residue sequence comprising the DR3A submotif (wherein position 1 of the motif is at position 1 of the nine residue core) are set forth in Table XXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in Table XXa. Table XXb shows binding data of exemplary DR3 submotif A-bearing peptides.

Conserved 9-mer core regions (i.e., those that are 100% conserved in at least 79% conserved in the PF antigen protein sequences used for the analysis) comprising the DR3B submotif and respective exemplary 15-mer peptides comprising the DR3 submotif-B epitope are set forth in Table XXc. Table XXd shows binding data of exemplary DR3 submotif B-bearing peptides.

Each of the HLA class I or class II peptide epitopes set out in the Tables herein are deemed singly to be an inventive aspect of this application. Further, it is also an inventive aspect of this application that each peptide epitope may be used in combination with any other peptide epitope.

IV.E. ENHANCING POPULATION COVERAGE OF THE VACCINE

Vaccines that have broad population coverage are preferred because they are more commercially viable and generally applicable to the most people. Broad population coverage can be obtained using the peptides of the invention (and nucleic acid compositions that encode such peptides) through selecting peptide epitopes that bind to HLA alleles which, when considered in total, are present in most of the population. Table XXI lists the overall frequencies of the HLA class I supertypes in various ethnicities (Table XXIa) and the combined population coverage achieved by the A2-, A3-, and B7-supertypes (Table XXIb). The A2-, A3-, and B7 supertypes are each present on the average of over 40% in each of these five major ethnic groups. Coverage in excess of 80% is achieved with a combination of these supermotifs. These results suggest that effective and non-ethnically biased population coverage is achieved upon use of a limited number of cross-reactive peptides. Although the population coverage reached with these three main peptide specificities is high, coverage can be expanded to reach 95% population coverage and above, and more easily achieve truly multispecific responses upon use of additional supermotif or allele-specific motif bearing peptides.

The B44-, A1-, and A24-supertypes are present, on average, in a range from 25% to 40% in these major ethnic populations (Table XXIa). While less prevalent overall, the B27-, B58-, and B62 supertypes are each present with a frequency >25% in at least one major ethnic group (Table XXIa). Table XXIb summarizes the estimated prevalence of combinations of HLA supertypes that have been identified in five major ethnic groups. The incremental coverage obtained by the inclusion of A1-, A24-, and B44-supertypes with the A2, A3, and B7 coverage and coverage obtained with all of the supertypes described herein, is shown.

The data presented herein, together with the previous definition of the A2-, A3-, and B7-supertypes, indicates that all antigens, with the possible exception of A29, B8, and B46, can be classified into a total of nine HLA supertypes. By including epitopes from the six most frequent supertypes, an average population coverage of 99% is obtained for five major ethnic groups.

IV.F. IMMUNE RESPONSE-STIMULATING PEPTIDE ANALOGS

In general, CTL and HTL responses are not directed against all possible epitopes. Rather, they are restricted to a few “immunodominant” determinants (Zinkernagel, et al., Adv. Immunol. 27:5159, 1979; Bennink, et al., J. Exp. Med. 168:19351939, 1988; Rawle, et al., J. Immunol. 146:3977-3984, 1991). It has been recognized that immunodominance (Benacerraf, et al., Science 175:273-279, 1972) could be explained by either the ability of a given epitope to selectively bind a particular HLA protein (determinant selection theory) (Vitiello, et al., J. Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977), or to be selectively recognized by the existing TCR (T cell receptor) specificities (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OF SELFNONSELF DISCRIMINATION, John Wiley & Sons, New York, pp. 270-310, 1982). It has been demonstrated that additional factors, mostly linked to processing events, can also play a key role in dictating, beyond strict immunogenicity, which of the many potential determinants will be presented as immunodominant (Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993).

The concept of dominance and subdominance is relevant to immunotherapy of both infectious diseases and cancer. For example, in the course of chronic infectious disease, recruitment of subdominant epitopes can be important for successful clearance of the infection, especially if dominant CTL or HTL specificities have been inactivated by functional tolerance, suppression, mutation of viruses and other mechanisms (Franco, et al., Curr. Opin. Immunol. 7:524-531, 1995). In the case of cancer and tumor antigens, CTLs recognizing at least some of the highest binding affinity peptides might be functionally inactivated. Lower binding affinity peptides are preferentially recognized at these times, and may therefore be preferred in therapeutic or prophylactic anti-cancer vaccines.

In particular, it has been noted that a significant number of epitopes derived from known non-viral tumor associated antigens (TAA) bind HLA class I with intermediate affinity (IC50 in the 50-500 nM range). For example, it has been found that 8 of 15 known TAA peptides recognized by tumor infiltrating lymphocytes (TIL) or CTL bound in the 50-500 nM range. (These data are in contrast with estimates that 90% of known viral antigens were bound by HLA class I molecules with IC50 of 50 nM or less, while only approximately 10% bound in the 50-500 nM range (Sette, et al., J. Immunol., 153:558-5592, 1994). In the cancer setting this phenomenon is probably due to elimination or functional inhibition of the CTL recognizing several of the highest binding peptides, presumably because of T cell tolerization events.

Without intending to be bound by theory, it is believed that because T cells to dominant epitopes may have been clonally deleted, selecting subdominant epitopes may allow existing T cells to be recruited, which will then lead to a therapeutic or prophylactic response. However, the binding of HLA molecules to subdominant epitopes is often less vigorous than to dominant ones. Accordingly, there is a need to be able to modulate the binding affinity of particular immunogenic epitopes for one or more HLA molecules, and thereby to modulate the immune response elicited by the peptide, for example to prepare analog peptides which elicit a more vigorous response. This ability would greatly enhance the usefulness of peptide epitope-based vaccines and therapeutic agents.

Although peptides with suitable cross-reactivity among all alleles of a superfamily are identified by the screening procedures described above, cross-reactivity is not always as complete as possible, and in certain cases procedures to increase cross-reactivity of peptides can be useful; moreover, such procedures can also be used to modify other properties of the peptides such as binding affinity or peptide stability. Having established the general rules that govern cross-reactivity of peptides for HLA alleles within a given motif or supermotif, modification (i.e., analoging) of the structure of peptides of particular interest in order to achieve broader (or otherwise modified) HLA binding capacity can be performed. More specifically, peptides which exhibit the broadest cross-reactivity patterns, can be produced in accordance with the teachings herein. The present concepts related to analog generation are set forth in greater detail in U.S. Ser. No. 09/226,775 filed Jan. 6, 1999, now abandoned.

In brief, the strategy employed utilizes the motifs or supermotifs which correlate with binding to certain HLA molecules. The motifs or supermotifs are defined by having primary anchors, and in many cases secondary anchors. Analog peptides can be created by substituting amino acid residues at primary anchor, secondary anchor, or at primary and secondary anchor positions. Generally, analogs are made for peptides that already bear a motif or supermotif. Preferred secondary anchor residues of supermotifs and motifs that have been defined for HLA class I and class II binding peptides are shown in Tables II and III, respectively.

For a number of the motifs or supermotifs in accordance with the invention, residues are defined which are deleterious to binding to allele-specific HLA molecules or members of HLA supertypes that bind the respective motif or supermotif (Tables II and III). Accordingly, removal of such residues that are detrimental to binding can be performed in accordance with the present invention. For example, in the case of the A3 supertype, when all peptides that have such deleterious residues are removed from the population of peptides used for the analysis, the incidence of cross-reactivity increased from 22% to 37% (see, e.g., Sidney, J. et al., Hu. Immunol. 45:79, 1996). Thus, one strategy to improve the cross-reactivity of peptides within a given supermotif is simply to delete one or more of the deleterious residues present within a peptide and substitute a small “neutral” residue such as Ala (that may not influence T cell recognition of the peptide). An enhanced likelihood of cross-reactivity is expected if, together with elimination of detrimental residues within a peptide, “preferred” residues associated with high affinity binding to an allele-specific HLA molecule or to multiple HLA molecules within a superfamily are inserted.

To ensure that an analog peptide, when used as a vaccine, actually elicits a CTL response to the native epitope in vivo (or, in the case of class II epitopes, elicits helper T cells that cross-react with the wild type peptides), the analog peptide may be used to immunize T cells in vitro from individuals of the appropriate HLA allele. Thereafter, the immunized cells' capacity to induce lysis of wild type peptide sensitized target cells is evaluated. It will be desirable to use as antigen presenting cells, cells that have been either infected, or transfected with the appropriate genes, or, in the case of class II epitopes only, cells that have been pulsed with whole protein antigens, to establish whether endogenously produced antigen is also recognized by the relevant T cells.

Another embodiment of the invention is to create analogs of weak binding peptides. Class I binding peptides exhibiting binding affinities of 500-5000 nM, and carrying an acceptable but suboptimal primary anchor residue at one or both positions can be “fixed” by substituting preferred anchor residues in accordance with the respective supertype. The analog peptides can then be tested for crossbinding activity.

Another embodiment for generating effective peptide analogs involves the substitution of residues that have an adverse impact on peptide stability or solubility in, e.g., a liquid environment. This substitution may occur at any position of the peptide epitope. For example, a cysteine (C) can be substituted out in favor of α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substituting α-amino butyric acid for C not only alleviates this problem, but actually improves binding and crossbinding capability in certain instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999). Substitution of cysteine with α-amino butyric acid may occur at any residue of a peptide epitope, i.e. at either anchor or non-anchor positions.

Representative analog peptides are set forth in Table XXII. The Table indicates the length and sequence of the analog peptide as well as the motif or supermotif, if appropriate. The information in the “Fixed Nomenclature” column indicates the residues substituted at the indicated position numbers for the respective analog.

IV.G. COMPUTER SCREENING OF PROTEIN SEQUENCES FROM DISEASE-RELATED ANTIGENS FOR SUPERMOTIF- OR MOTIF-BEARING PEPTIDES

In order to identify supermotif- or motif-bearing epitopes in a target antigen, a native protein sequence, e.g., a tumor-associated antigen, or sequences from an infectious organism, or a donor tissue for transplantation, is screened using a means for computing, such as an intellectual calculation or a computer, to determine the presence of a supermotif or motif within the sequence. The information obtained from the analysis of native peptide can be used directly to evaluate the status of the native peptide or may be utilized subsequently to generate the peptide epitope.

Computer programs that allow the rapid screening of protein sequences for the occurrence of the subject supermotifs or motifs are encompassed by the present invention; as are programs that permit the generation of analog peptides. These programs are implemented to analyze any identified amino acid sequence or operate on an unknown sequence and simultaneously determine the sequence and identify motif-bearing epitopes thereof; analogs can be simultaneously determined as well. Generally, the identified sequences will be from a pathogenic organism or a tumor-associated peptide. For example, the target molecules considered herein include, without limitation, the EXP1, LSA1, SSP2, and CSP1 proteins of PF.

In cases where the sequence of multiple variants of the same target protein are available, peptides may also be selected on the basis of their conservancy. A presently preferred criterion for conservancy defines that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide, be totally (i.e., 100%) conserved in at least 79% of the sequences evaluated for a specific protein. This definition of conservancy has been employed herein; although, as appreciated by those in the art, lower or higher degrees of conservancy can be employed as appropriate for a given antigenic target.

It is important that the selection criteria utilized for prediction of peptide binding are as accurate as possible, to correlate most efficiently with actual binding. Prediction of peptides that bind, for example, to HLA-A*0201, on the basis of the presence of the appropriate primary anchors, is positive at about a 30% rate (see, e.g., Ruppert, J. et al. Cell 74:929, 1993). However, by extensively analyzing peptide-HLA binding data disclosed herein, data in related patent applications, and data in the art, the present inventors have developed a number of allele-specific polynomial algorithms that dramatically increase the predictive value over identification on the basis of the presence of primary anchor residues alone. These algorithms take into account not only the presence or absence of primary anchors, but also consider the positive or deleterious presence of secondary anchor residues (to account for the impact of different amino acids at different positions). The algorithms are essentially based on the premise that the overall affinity (or AG) of peptide-HLA interactions can be approximated as a linear polynomial function of the type:


ΔG=a1i×a2i×a3i . . . ×ani

where aji is a coefficient that represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. An important assumption of this method is that the effects at each position are essentially independent of each other. This assumption is justified by studies that demonstrated that peptides are bound to HLA molecules and recognized by T cells in essentially an extended conformation. Derivation of specific algorithm coefficients has been described, for example, in Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997.

Additional methods to identify preferred peptide sequences, which also make use of specific motifs, include the use of neural networks and molecular modeling programs (see, e.g., Milik et al., Nature Biotechnology 16:753, 1998; Altuvia et al., Hum. Immunol. 58:1, 1997; Altuvia et al, J. Mol. Biol. 249:244, 1995; Buus, S. Curr. Opin. Immunol. 11:209-213, 1999; Brusic, V. et al., Bioinformatics 14:121-130, 1998; Parker et al., J. Immunol. 152:163, 1993; Meister et al., Vaccine 13:581, 1995; Hammer et al., J. Exp. Med. 180:2353, 1994; Sturniolo et al., Nature Biotechnol. 17:555 1999).

For example, it has been shown that in sets of A*0201 motif-bearing peptides containing at least one preferred secondary anchor residue while avoiding the presence of any deleterious secondary anchor residues, 69% of the peptides will bind A*0201 with an IC50 less than 500 nM (Ruppert, J. et al. Cell 74:929, 1993). These algorithms are also flexible in that cut-off scores may be adjusted to select sets of peptides with greater or lower predicted binding properties, as desired.

In utilizing computer screening to identify peptide epitopes, a protein sequence or translated sequence may be analyzed using software developed to search for motifs, for example the “FINDPATTERNS’ program (Devereux, et al. Nucl. Acids Res. 12:387-395, 1984) or MotifSearch 1.4 software program (D. Brown, San Diego, Calif.) to identify potential peptide sequences containing appropriate HLA binding motifs. The identified peptides can be scored using customized polynomial algorithms to predict their capacity to bind specific HLA class I or class II alleles. As appreciated by one of ordinary skill in the art, a large array of computer programming software and hardware options are available in the relevant art which can be employed to implement the motifs of the invention in order to evaluate (e.g., without limitation, to identify epitopes, identify epitope concentration per peptide length, or to generate analogs) known or unknown peptide sequences.

In accordance with the procedures described above, PF peptide epitopes and analogs thereof that are able to bind HLA supertype groups or allele-specific HLA molecules have been identified (Tables VII-XX; Table XXII).

IV.H. PREPARATION OF PEPTIDE EPITOPES

Peptides in accordance with the invention can be prepared synthetically, by recombinant DNA technology or chemical synthesis, or from natural sources such as native tumors or pathogenic organisms. Peptide epitopes may be synthesized individually or as polyepitopic peptides. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides may be synthetically conjugated to native fragments or particles.

The peptides in accordance with the invention can be a variety of lengths, and either in their neutral (uncharged) forms or in forms which are salts. The peptides in accordance with the invention are either free of modifications such as glycosylation, side chain oxidation, or phosphorylation; or they contain these modifications, subject to the condition that modifications do not destroy the biological activity of the peptides as described herein.

Desirably, the peptide epitope will be as small as possible while still maintaining substantially all of the immunologic activity of the native protein. When possible, it may be desirable to optimize HLA class I binding peptide epitopes of the invention to a length of about 8 to about 13 amino acid residues, preferably 9 to 10. HLA class II binding peptide epitopes may be optimized to a length of about 6 to about 30 amino acids in length, preferably to between about 13 and about 20 residues. Preferably, the peptide epitopes are commensurate in size with endogenously processed pathogen-derived peptides or tumor cell peptides that are bound to the relevant HLA molecules.

The identification and preparation of peptides of other lengths can also be carried out using the techniques described herein. Moreover, it is preferred to identify native peptide regions that contain a high concentration of class I and/or class II epitopes. Such a sequence is generally selected on the basis that it contains the greatest number of epitopes per amino acid length. It is to be appreciated that epitopes can be present in a frame-shifted manner, e.g. a 10 amino acid long peptide could contain two 9 amino acid long epitopes and one 10 amino acid long epitope; upon intracellular processing, each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. This larger, preferably multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source.

The peptides of the invention can be prepared in a wide variety of ways. For the preferred relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. (See, for example, Stewart & Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co., 1984). Further, individual peptide epitopes can be joined using chemical ligation to produce larger peptides that are still within the bounds of the invention.

Alternatively, recombinant DNA technology can be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant polypeptides which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope.

The nucleotide coding sequence for peptide epitopes of the preferred lengths contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981). Peptide analogs can be made simply by substituting the appropriate and desired nucleic acid base(s) for those that encode the native peptide sequence; exemplary nucleic acid substitutions are those that encode an amino acid defined by the motifs/supermotifs herein. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast, insect or mammalian cell hosts may also be used, employing suitable vectors and control sequences.

IV.I. ASSAYS TO DETECT T-CELL RESPONSES

Once HLA binding peptides are identified, they can be tested for the ability to elicit a T-cell response. The preparation and evaluation of motif-bearing peptides are described in PCT publications WO 94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from a particular antigen are synthesized and tested for their ability to bind to the appropriate HLA proteins. These assays may involve evaluating the binding of a peptide of the invention to purified HLA class I molecules in relation to the binding of a radioiodinated reference peptide. Alternatively, cells expressing empty class I molecules (i.e. lacking peptide therein) may be evaluated for peptide binding by immunofluorescent staining and flow microfluorimetry. Other assays that may be used to evaluate peptide binding include peptide-dependent class I assembly assays and/or the inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule, typically with an affinity of 500 nM or less, are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with selected target cells associated with a disease. Corresponding assays are used for evaluation of HLA class II binding peptides. HLA class II motif-bearing peptides that are shown to bind, typically at an affinity of 1000 nM or less, are further evaluated for the ability to stimulate HTL responses.

Conventional assays utilized to detect T cell responses include proliferation assays, lymphokine secretion assays, direct cytotoxicity assays, and limiting dilution assays. For example, antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells. Alternatively, mutant non-human mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides and that have been transfected with the appropriate human class I gene, may be used to test for the capacity of the peptide to induce in vitro primary CTL responses.

Peripheral blood mononuclear cells (PBMCs) may be used as the responder cell source of CTL precursors. The appropriate antigen-presenting cells are incubated with peptide, after which the peptide-loaded antigen-presenting cells are then incubated with the responder cell population under optimized culture conditions. Positive CTL activation can be determined by assaying the culture for the presence of CTLs that kill radio-labeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed forms of the antigen from which the peptide sequence was derived.

More recently, a method has been devised which allows direct quantification of antigen-specific CTLs by staining with Fluorescein-labelled HLA tetrameric complexes (Altman, J. D. et al., Proc. Natl. Acad. Sci. USA 90:10330, 1993; Altman, J. D. et al., Science 274:94, 1996). Other relatively recent technical developments include staining for intracellular lymphokines, and interferon release assays or ELISPOT assays. Tetramer staining, intracellular lymphokine staining and ELISPOT assays all appear to be at least 10-fold more sensitive than more conventional assays (Lalvani, A. et al., J. Exp. Med. 186:859, 1997; Dunbar, P. R. et al., Curr. Biol. 8:413, 1998; Murali-Krishna, K. et al., Immunity 8:177, 1998).

HTL activation may also be assessed using such techniques known to those in the art such as T cell proliferation and secretion of lymphokines, e.g. IL-2 (see, e.g. Alexander et al., Immunity 1:751-761, 1994).

Alternatively, immunization of HLA transgenic mice can be used to determine immunogenicity of peptide epitopes. Several transgenic mouse models including mice with human A2.1, A11 (which can additionally be used to analyze HLA-A3 epitopes), and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed. Additional transgenic mouse models with other HLA alleles may be generated as necessary. Mice may be immunized with peptides emulsified in Incomplete Freund's Adjuvant and the resulting T cells tested for their capacity to recognize peptide-pulsed target cells and target cells transfected with appropriate genes. CTL responses may be analyzed using cytotoxicity assays described above. Similarly, HTL responses may be analyzed using such assays as T cell proliferation or secretion of lymphokines. Exemplary immunogenic peptide epitopes are set out in Table XXIII

IV.J. USE OF PEPTIDE EPITOPES AS DIAGNOSTIC AGENTS AND FOR EVALUATING IMMUNE RESPONSES

HLA class I and class II binding peptides as described herein can be used, in one embodiment of the invention, as reagents to evaluate an immune response. The immune response to be evaluated may be induced by using as an immunogen any agent that may result in the production of antigen-specific CTLs or HTLs that recognize and bind to the peptide epitope(s) to be employed as the reagent. The peptide reagent need not be used as the immunogen. Assay systems that may be used for such an analysis include relatively recent technical developments such as tetramers, staining for intracellular lymphokines and interferon release assays, or ELISPOT assays.

For example, a peptide of the invention may be used in a tetramer staining assay to assess peripheral blood mononuclear cells for the presence of antigen-specific CTLs following exposure to a pathogen or immunogen. The HLA-tetrameric complex is used to directly visualize antigen-specific CTLs (see, e.g., Ogg et al., Science 279:2103-2106, 1998; and Altman et al., Science 174:94-96, 1996) and determine the frequency of the antigen-specific CTL population in a sample of peripheral blood mononuclear cells. A tetramer reagent using a peptide of the invention may be generated as follows: A peptide that binds to an HLA molecule is refolded in the presence of the corresponding HLA heavy chain and β2-microglobulin to generate a trimolecular complex. The complex is biotinylated at the carboxyl terminal end of the heavy chain at a site that was previously engineered into the protein. Tetramer formation is then induced by the addition of streptavidin. By means of fluorescently labeled streptavidin, the tetramer can be used to stain antigen-specific cells. The cells may then be identified, for example, by flow cytometry. Such an analysis may be used for diagnostic or prognostic purposes.

Peptides of the invention may also be used as reagents to evaluate immune recall responses. (see, e.g., Bertoni et al., J. Clin. Invest. 100:503-513, 1997 and Penna et al., J. Exp. Med. 174:1565-1570, 1991.) For example, patient PBMC samples from individuals infected with PF may be analyzed for the presence of antigen-specific CTLs or HTLs using specific peptides. A blood sample containing mononuclear cells may be evaluated by cultivating the PBMCs and stimulating the cells with a peptide of the invention. After an appropriate cultivation period, the expanded cell population may be analyzed, for example, for CTL or for HTL activity.

The peptides may also be used as reagents to evaluate the efficacy of a vaccine. PBMCs obtained from a patient vaccinated with an immunogen may be analyzed using, for example, either of the methods described above. The patient is HLA typed, and peptide epitope reagents that recognize the allele-specific molecules present in that patient are selected for the analysis. The immunogenicity of the vaccine is indicated by the presence of PF epitope-specific CTLs and/or HTLs in the PBMC sample.

The peptides of the invention may also be used to make antibodies, using techniques well known in the art (see, e.g. CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY; and Antibodies A Laboratory Manual Harlow, Harlow and Lane, Cold Spring Harbor Laboratory Press, 1989), which may be useful as reagents to diagnose PF infection. Such antibodies include those that recognize a peptide in the context of an HLA molecule, i.e., antibodies that bind to a peptide-WIC complex.

IV.K. VACCINE COMPOSITIONS

Vaccines that contain an immunogenically effective amount of one or more peptides as described herein are a further embodiment of the invention. Once appropriately immunogenic epitopes have been defined, they can be sorted and delivered by various means, herein referred to as “vaccine” compositions. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptide(s). The peptide(s) can be individually linked to its own carrier; alternatively, the peptide(s) can exist as a homopolymer or heteropolymer of active peptide units. Such a polymer has the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition may be a naturally occurring region of an antigen or may be prepared, e.g., recombinantly or by chemical synthesis.

Furthermore, useful carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS).

As disclosed in greater detail herein, upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later infection, or at least partially resistant to developing an ongoing chronic infection, or derives at least some therapeutic benefit when the antigen was tumor-associated.

In some instances it may be desirable to combine the class I peptide vaccines of the invention with vaccines which induce or facilitate neutralizing antibody responses to the target antigen of interest, particularly to surface antigens. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a PADRE™ (Epimmune, San Diego, Calif.) molecule (described, for example, in U.S. Pat. No. 5,736,142). Furthermore, any of these embodiments can be administered as a nucleic acid mediated modality.

The vaccine compositions of the invention may also be used in combination with antiviral drugs such as interferon-α.

For therapeutic or prophylactic immunization purposes, the peptides of the invention can also be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a non-infected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL and/or HTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

Antigenic peptides are used to elicit a CTL and/or HTL response ex vivo, as well. Ex vivo administration is described, for example, in application U.S. Ser. No. 09/016,361 filed Jan. 30, 1998, now abandoned. The resulting CTL or HTL cells, can be used to treat chronic infections, or tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (an infected cell or a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells. Alternatively, dendritic cells are transfected, e.g., with a minigene construct in accordance with the invention, in order to elicit immune responses. Minigenes will be discussed in greater detail in a following section.

Vaccine compositions may also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

DNA or RNA encoding one or more of the peptides of the invention can also be administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. Exemplary epitopes that may be utilized in a vaccine to treat or prevent PF infection are set out in Tables XXXIII and XXXIV. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

It is preferred that each of the following principles are balanced in order to make the selection.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen (see e.g., Rosenberg et al., Science 278:1447-1450).

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.

3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

4.) When selecting epitopes from cancer-related antigens it is often preferred to select analogs because the patient may have developed tolerance to the native epitope. When selecting epitopes for infectious disease-related antigens it is preferable to select either native or analoged epitopes. Of particular relevance for infectious disease vaccines (but for cancer-related vaccines as well), are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.

When providing nested epitopes, it is preferable to provide a sequence that has the greatest number of epitopes per provided sequence. Preferably, one avoids providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, it is important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

5.) When creating a minigene, as disclosed in greater detail in the following section, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Furthermore, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis, that only exists because two discrete peptide sequences are encoded directly next to each other. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

IV.K.1. Minigene Vaccines

A growing body of experimental evidence demonstrates that a number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention. The use of multi-epitope minigenes is described below and in, e.g., application U.S. Ser. No. 09/311,784, now U.S. Pat. No. 6,534,482; Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding nine dominant HLA-A*0201- and A11-restricted epitopes derived from the polymerase, envelope, and core proteins of HBV and human immunodeficiency virus (HIV), the PADRE™ universal HTL epitope, and an endoplasmic reticulum-translocating signal sequence was engineered. Immunization of HLA transgenic mice with this plasmid construct resulted in strong CTL induction responses against the nine epitopes tested, similar to those observed with a lipopeptide of known immunogenicity in humans, and significantly greater than immunization in oil-based adjuvants. Moreover, the immunogenicity of DNA-encoded epitopes in vivo correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these data show that the minigene served to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes. A similar approach may be used to develop minigenes encoding PF epitopes.

For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). HTL epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids can also be used in the formulation; in addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) can also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987).

Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (IP) for lipid-complexed DNA).

Twenty-one days after immunization, splenocytes are harvested and restimulated for 1 week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, 51Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is evaluated in transgenic mice in an analogous manner.

Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

IV.K.2. Combinations of CTL Peptides with Helper Peptides

Vaccine compositions comprising the peptides of the present invention, or analogs thereof, which have immunostimulatory activity may be modified to provide desired attributes, such as improved serum half life, or to enhance immunogenicity.

For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. The use of T helper epitopes in conjunction with CTL epitopes to enhance immunogenicity is illustrated, for example, in applications U.S. Ser. No. 08/197,484, now U.S. Pat. No. 6,419,931, and U.S. Ser. No. 08/464,234, now abandoned.

Particularly preferred CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the CTL peptide may be linked to the T helper peptide without a spacer.

The CTL peptide epitope may be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated. The HTL peptide epitopes used in the invention can be modified in the same manner as CTL peptides. For instance, they may be modified to include D-amino acids or be conjugated to other molecules such as lipids, proteins, sugars and the like.

In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in the majority of the population. This can be accomplished by selecting amino acid sequences that bind to many, most, or all of the HLA class II molecules. These are known as “loosely HLA-restricted” or “promiscuous” T helper sequences. Examples of amino acid sequences that are promiscuous include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 3799), Plasmodium falciparum CS protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 3800), and Streptococcus 18 kD protein at positions 116 (GAVDSILGGVATYGAA; SEQ ID NO: 3801). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed to most preferrably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVWANTLKAAa (SEQ ID NO: 3802), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

HTL peptide epitopes can also be modified to alter their biological properties. For example, peptides comprising HTL epitopes can contain D-amino acids to increase their resistance to proteases and thus extend their serum half-life. Also, the epitope peptides of the invention can be conjugated to other molecules such as lipids, proteins or sugars, or any other synthetic compounds, to increase their biological activity. Specifically, the T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes cytotoxic T cells. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide. (See, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses to infection.

As noted herein, additional amino acids can be added to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide, particularly class I peptides. However, it is to be noted that modification at the carboxyl terminus of a CTL epitope may, in some cases, alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH2 acylation, e.g., by alkanoyl (C1-C20) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.

IV.L. ADMINISTRATION OF VACCINES FOR THERAPEUTIC OR PROPHYLACTIC PURPOSES

The peptides of the present invention and pharmaceutical and vaccine compositions of the invention are useful for administration to mammals, particularly humans, to treat and/or prevent malaria. Vaccine compositions containing the peptides of the invention are administered to an individual susceptible to, or otherwise at risk for, malaria or to a patient infected with PF to elicit an immune response against PF antigens and thus enhance the patient's own immune response capabilities. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective CTL and/or HTL response to the PF antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

The vaccine compositions of the invention may also be used purely as prophylactic agents. The level of expected exposure (e.g., a traveler versus a resident of an area where malaria is endemic) determines the magnitude of response that is desired to be achieved by the vaccination. Therefore, some vaccination regimens may employ higher doses of the vaccine compositions, or more doses may be administered.

Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine may be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.

As noted above, peptides comprising CTL and/or HTL epitopes of the invention induce immune responses when presented by HLA molecules and contacted with a CTL or HTL specific for an epitope comprised by the peptide. The manner in which the peptide is contacted with the CTL or HTL is not critical to the invention. For instance, the peptide can be contacted with the CTL or HTL either in vivo or in vitro. If the contacting occurs in vivo, the peptide itself can be administered to the patient, or other vehicles, e.g., DNA vectors encoding one or more peptides, viral vectors encoding the peptide(s), liposomes and the like, can be used, as described herein.

For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual who has not been infected with PF. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences.

The pharmaceutical compositions may also be used to treat individuals already infected with PF. Patients can be treated with the immunogenic peptide epitopes separately or in conjunction with other treatments, as appropriate.

For therapeutic use, administration should generally begin at the first diagnosis of PF infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. Loading doses followed by boosting doses may be required.

The peptide or other compositions used for prophylaxis or the treatment of PF infection can be used, e.g., in persons who are not manifesting symptoms of disease but who act as a disease vector. In this context, it is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.

The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. The peptides and compositions of the present invention may be employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

Thus, for treatment of a chronically infected individual, a representative dose is in the range disclosed above. Initial doses followed by boosting doses at established intervals, e.g., from four weeks to six months, may be required, possibly for a prolonged period of time to effectively immunize an individual. Administration should continue until at least clinical symptoms or laboratory tests indicate that the PF infection has been eliminated or substantially abated and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, intrathecal, or local administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

A human unit dose form of the peptide composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, preferably an aqueous carrier, and is administered in a volume of fluid that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985).

The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or to target selectively to infected cells, as well as to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.

For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

IV.M. KITS

The peptide and nucleic acid compositions of this invention can be provided in kit form together with instructions for vaccine administration. Typically the kit would include desired peptide compositions in a container, preferably in unit dosage form and instructions for administration. An alternative kit would include a minigene construct with desired nucleic acids of the invention in a container, preferably in unit dosage form together with instructions for administration. Lymphokines such as IL-2 or IL-12 may also be included in the kit. Other kit components that may also be desirable include, for example, a sterile syringe, booster dosages, and other desired excipients.

The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non-critical parameters that can be changed or modified to yield alternative embodiments in accordance with the invention.

V. EXAMPLES

The following examples illustrate identification, selection, and use of immunogenic Class I and Class II peptide epitopes for inclusion in vaccine compositions.

Example 1 HLA Class I and Class II Binding Assays

The following example of peptide binding to HLA molecules demonstrates quantification of binding affinities of HLA class I and class II peptides. Binding assays can be performed with peptides that are either motif-bearing or not motif-bearing.

Epstein-Barr virus (EBV)-transformed homozygous cell lines, fibroblasts, CIR, or 721.22 transfectants were used as sources of HLA class I molecules. These cells were maintained in vitro by culture in RPMI 1640 medium supplemented with 2 mM L-glutamine (GIBCO, Grand Island, N.Y.), 50 μM 2-ME, 100 μg/ml of streptomycin, 100 U/ml of penicillin (Irvine Scientific) and 10% heat-inactivated FCS (Irvine Scientific, Santa Ana, Calif.). Cells were grown in 225-cm2 tissue culture flasks or, for large-scale cultures, in roller bottle apparatuses. The specific cell lines routinely used for purification of MHC class I and class II molecules are listed in Table XXIV.

Cell lysates were prepared and HLA molecules purified in accordance with disclosed protocols (Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, cells were lysed at a concentration of 108 cells/ml in 50 mM Tris-HCl, pH 8.5, containing 1% Nonidet P-40 (Fluka Biochemika, Buchs, Switzerland), 150 mM NaCl, 5 mM EDTA, and 2 mM PMSF. Lysates were cleared of debris and nuclei by centrifugation at 15,000×g for 30 min.

HLA molecules were purified from lysates by affinity chromatography. Lysates prepared as above were passed twice through two pre-columns of inactivated Sepharose CL4-B and protein A-Sepharose. Next, the lysate was passed over a column of Sepharose CL-4B beads coupled to an appropriate antibody. The antibodies used for the extraction of HLA from cell lysates are listed in Table XXV. The anti-HLA column was then washed with 10-column volumes of 10 mM Tris-HCL, pH 8.0, in 1% NP-40, PBS, 2-column volumes of PBS, and 2-column volumes of PBS containing 0.4% n-octylglucoside. Finally, MHC molecules were eluted with 50 mM diethylamine in 0.15M NaCl containing 0.4% n-octylglucoside, pH 11.5. A 1/25 volume of 2.0M Tris, pH 6.8, was added to the eluate to reduce the pH to ˜8.0. Eluates were then be concentrated by centrifugation in Centriprep 30 concentrators at 2000 rpm (Amicon, Beverly, Mass.). Protein content was evaluated by a BCA protein assay (Pierce Chemical Co., Rockford, Ill.) and confirmed by SDS-PAGE.

A detailed description of the protocol utilized to measure the binding of peptides to Class I and Class II MEW has been published (Sette et al., Mol. Immunol. 31:813, 1994; Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998). Briefly, purified MHC molecules (5 to 500 nM) were incubated with various unlabeled peptide inhibitors and 1-10 nM 125I-radiolabeled probe peptides for 48 h in PBS containing 0.05% Nonidet P-40 (NP40) (or 20% w/v digitonin for H-2 IA assays) in the presence of a protease inhibitor cocktail. The final concentrations of protease inhibitors (each from CalBioChem, La Jolla, Calif.) were 1 mM PMSF, 1.3 nM 1.10 phenanthroline, 73 μM pepstatin A, 8 mM EDTA, 6 mM N-ethylmaleimide (for Class II assays), and 200 μM N alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK). All assays were performed at pH 7.0 with the exception of DRB1*0301, which was performed at pH 4.5, and DRB1*1601 (DR2w21β1) and DRB4*0101 (DRw53), which were performed at pH 5.0. pH was adjusted as described elsewhere (see Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998).

Following incubation, MHC-peptide complexes were separated from free peptide by gel filtration on 7.8 mm×15 cm TSK200 columns (TosoHaas 16215, Montgomeryville, Pa.), eluted at 1.2 mls/min with PBS pH 6.5 containing 0.5% NP40 and 0.1% NaN3. Because the large size of the radiolabeled peptide used for the DRB1*1501 (DR2w2β1) assay makes separation of bound from unbound peaks more difficult under these conditions, all DRB1*1501 (DR2w2β1) assays were performed using a 7.8 mm×30 cm TSK2000 column eluted at 0.6 mls/min. The eluate from the TSK columns was passed through a Beckman 170 radioisotope detector, and radioactivity was plotted and integrated using a Hewlett-Packard 3396A integrator, and the fraction of peptide bound was determined.

Radiolabeled peptides were iodinated using the chloramine-T method. Representative radiolabeled probe peptides utilized in each assay, and its assay specific IC50 nM, are summarized in Tables IV and V. Typically, in preliminary experiments, each MHC preparation was titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays were performed using these HLA concentrations.

Since under these conditions [label]<[HLA] and IC50≧[HLA], the measured IC50 values are reasonable approximations of the true KD values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC50 of a positive control for inhibition by the IC50 for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC50 nM values by dividing the IC50 nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation has proven to be the most accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

Because the antibody used for HLA-DR purification (LB3.1) is α-chain specific, β1 molecules are not separated from β3 (and/or β4 and β5) molecules. The β1 specificity of the binding assay is obvious in the cases of DRB1*0101 (DR1), DRB1*0802 (DR8w2), and DRB1*0803 (DR8w3), where no β3 is expressed. It has also been demonstrated for DRB1*0301 (DR3) and DRB3*0101 (DR52a), DRB1*0401 (DR4w4), DRB1*0404 (DR4w14), DRB1*0405 (DR4w15), DRB1*1101 (DR5), DRB1*1201 (DR5w12), DRB1*1302 (DR6w19) and DRB1*0701 (DR7). The problem of β chain specificity for DRB1*1501 (DR2w2β1), DRB5*0101 (DR2w2β2), DRB1*1601 (DR2w21β1), DRB5*0201 (DR51Dw21), and DRB4*0101 (DRw53) assays is circumvented by the use of fibroblasts. Development and validation of assays with regard to DRβ molecule specificity have been described previously (see, e.g., Southwood et al., J. Immunol. 160:3363-3373, 1998).

Binding assays as outlined above may be used to analyze supermotif and/or motif-bearing epitopes as, for example, described in Example 2.

Example 2 Identification of Conserved HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes

Vaccine compositions of the invention may include multiple epitopes that comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Additional experimental details that may be relevant to this example are found in Doolan, D. L. et al., Immunity 7:97, 1997. Calculation of population coverage was performed using the strategy described below.

Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes

Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs were performed as follows. All translated PF protein sequences were analyzed using a text string search software program, e.g., MotifSearch 1.4 (D. Brown, San Diego) to identify potential peptide sequences containing appropriate HLA binding motifs;

alternative programs are readily produced in accordance with information in the art in view of the motif/supermotif disclosure herein. Furthermore, such calculations can be made mentally. Identified A2-, A3-, and DR-supermotif sequences were scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms take into account both extended and refined motifs (that is, to account for the impact of different amino acids at different positions), and are essentially based on the premise that the overall affinity (or AG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:


“ΔG”=a1i×a2i×a3i×ani

where aji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide. This assumption is justified by studies from our laboratories that demonstrated that peptides are bound to MHC and recognized by T cells in essentially an extended conformation (data omitted herein).

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of ji. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

Selection of HLA-A2 Supertype Cross-Reactive Peptides

Complete protein sequences from PF antigens were aligned, then scanned, utilizing motif identification software, to identify conserved 9- and 10-mer sequences containing the HLA-A*0201-motif main anchor specificity. Following conservancy determination and algorithm analysis to take into account the influence of secondary anchors, 53 peptides containing the HLA-A*0201 of potential interest were identified and tested for their capacity to bind to purified HLA-A*0201 molecules in vitro. Fifteen peptides bound A*0201 with IC50 values ≦500 nM.

Fourteen of these peptides were subsequently tested for immunogenicity as described below. Of these, 5 scored positive both in primary in vitro CTL responses and in HLA transgenic mice.

The five immunogenic peptides were then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). The peptide SSP214-23, which was immunogenic in primary human CTL cultures and contains the SSP214-22 epitope (rather than SSP214-22 itself), was included in the analysis. In addition, the peptide Exp-183, which was positive in the murine CTL assays and the peptide CSP425 and SSP2230, were also analyzed for cross-reactive binding. As shown in Table XXVI, all eight of these peptides were found to be A2-supertype cross-reactive binders with six of these binding to three or more A2 supertype alleles.

Selection of HLA-A3 Supermotif-Bearing Epitopes

The PF protein sequences scanned above were also examined for the presence of conserved peptides with the HLA-A3 supermotif primary anchors. Further analysis using the A03 and A11 algorithms (see, e.g., Gulukota et al, J. Mol. Biol. 267:1258-1267, 1997 and Sidney et al, Human Immunol. 45:79-93, 1996) identified 203 conserved 9- or 10-mer motif-containing peptide sequences that scored high in either or both algorithms. Of these candidates, twenty five peptides were identified that bound A3 and/or A11 with binding affinities of ≦500 nM. These peptides were then tested for binding cross-reactivity to the other common A3-supertype alleles (A*3101, A*3301, and A*6801). Seven of them bound at least three of the five HLA-A3-supertype molecules tested. An eighth peptide, LSA-111 was also considered for further study because it bound strongly to two of the A3 supertype alleles and weakly to the other two A3 supertype alleles. (Table XXVII)

In summary, eight HLA-A3 supertype cross-reactive binding peptides derived from conserved regions of PF proteins were identified.

Selection of HLA-B7 Supermotif Bearing Epitopes

When the same PF target antigen protein sequences were also analyzed for the presence of conserved 9- or 10-mer peptides with the HLA-B7-supermotif, 26 sequences were identified. Of these 26, 24 corresponding peptides were synthesized and tested for binding to HLA-B*0702, the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Four of the peptides bound B*0702 with IC50 of ≦500 nM. These four peptides were then tested for binding to other common B7-supertype molecules (B*3501, B*51, B*5301, and B*5401). As shown in Table XXVIII, one peptide was capable of to four of the five B7 supertype alleles; another was found to bind three of the five alles.

Selection of A1 and A24 Motif-Bearing Epitopes

To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into potential vaccine constructs.

An analysis of the protein sequence data from the PF target antigens utilized above identified 40 A1- and 81 A24-motif-containing conserved sequences. Testing for binding to the appropriate HLA molecule (i.e., A1 or A24) was performed on a subset of those peptides. Four A1-motif peptides and four A24-motif peptides, shown in Table Table XXIX, were found to have binding capacities of 500 nM or less for the appropriate allele-specific HLA molecule.

Example 3 Confirmation of Immunogenicity Evaluation of A*0201 Immunogenicity

It has been shown that CTL induced in A*0201/Kb transgenic mice exhibit specificity similar to CTL induced in the human system (see, e.g., Vitiello et al., J Exp. Med. 173:1007-1015, 1991; Wentworth et al., Eur. J. Immunol. 26:97-101, 1996). Accordingly, these mice were used to evaluate the immunogenicity of the fourteen conserved A*0201 motif-bearing high affinity binding peptides identified in Example 2 above.

CTL induction in transgenic mice following peptide immunization has been described (Vitiello et al., J. Exp. Med. 173:1007-1015, 1991; Alexander et al.; J. Immunol. 159:4753-4761, 1997). In these studies, mice were injected subcutaneously at the base of the tail with each peptide (50 μg/mouse) emulsified in IFA in the presence of an excess of an IAb-restricted helper peptide (140 μg/mouse) (HBV core 128-140, Sette et al., J Immunol. 153:5586-5592, 1994). Eleven days after injection, splenocytes were incubated in the presence of peptide-loaded syngenic LPS blasts. After six days, cultures were assayed for cytotoxic activity using peptide-pulsed targets. The data indicated that 5 of the 14 peptides were capable of inducing primary CTL responses in A*0201/Kb transgenic mice. (For these studies, a peptide was considered positive if it induced CTL (L.U. 30/106 cells in at least two transgenic animals (Wentworth et al., Eur. Immunol. 26:97-101, 1996).

The fourteen peptides that bound to HLA-A*0201 with good affinity were also tested for immunogenicity with PBMCs from at least four malaria-naive human donors. The induction of primary CTL responses in vitro with PBMCs from normal naive humans requires a brief treatment of the antigen-presenting cells with acidic buffer and subsequent neutralization in the presence of excess B2-microglobulin and exogenous peptide (Wentworth et al., supra). By ensuring that the majority of the HLA class I molecules are occupied by exogenous peptide, these steps are essential for the induction of primary CTL responses. Such responses cannot be induced using methods developed for the induction of recall CTL responses. A peptide was considered positive if yielding more than 2 LU30/106 cells (lytic units 20% per 104 cells, where one lytic unit corresponds to the number of effector cells required to induce 30% 51Cr release from 10,000 target cells during a 6 hr assay.) or 15% peptide-specific lysis, respectively, in at least two different primary CTL cultures. The five peptides that were positive in HLA transgenic mice were also shown to induce primary CTL responses.

The HLA-A2 cross-reactive binding peptides were tested for their ability to elicit in vitro recall responses from PBMCs of six volunteers, each of whom had an HLA-A*0201 allele, immunized with irradiated sporozoites. The results demonstrated that all of the A2-binding peptides were recognized in association with HLA-A*0201.

In addition to investigating whether the peptides could be recognized as CTL epitopes, the ability of the peptides to induce specific cytokine responses was also measured. In particular, induction of interferon-γ and TNF-α were measured, both of which have been implicated in protective immunity against malaria. PBMC from irradiated sporozoite-immunized volunteers and PBMC from naturally exposed individuals were tested. The results indicate that significant peptide-induced cytokine responses were observed for all of the A2 supermotif-bearing peptides. (See Doolan et al., Immunity 7:97-112, 1997.)

Evaluation of A*03/A11 Immunogenicity

The immunogenicity of the eight supermotif-bearing peptides was also evaluated in recall responses using PBMC from volunteers bearing HLA-A3 supertype alleles who had previously been immunized with irradiated sporozoites. All the peptides were recognized in association with both A3 and A33. The fraction of individuals responding to each peptide varied for the supertype overall from 50% for one of the peptides to 100% for three of the peptides.

Immunogenicity was also evaluated using PBMCs of semi-immune or nonimmune individuals naturally exposed to malaria. In this population, recall CTL responses (percentage specific lysis greater than 10%) were detected for five of the eight A3-binding peptides.

Immunogenicity of A3 supermotif-bearing peptides can also be evaluated in transgenic mice that bear a human HLA-A11 allele using methodology analagous to that for immunogenicity studies using HLA-A2.1 transgenic mice.

Evaluation of B7 Immunogenicity

Immunogenicity of two B7 supermotif-bearing peptides, SSP2539 and the HLA-B-restricted peptide Pfs1677 was also examined in individuals who had been exposed to PF, either through immunization or natural exposure, as described for the evaluation of A2- and A3-supermotif-bearing peptides.

Both peptides were found to be capable of inducing CTL responses. The two peptides were recognized as CTL epitopes in the context of three of the five B7 supertype alleles.

Example 4 Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analogued, or “fixed” to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analog peptides that exhibit modulated binding affinity are set forth in this example.

Analoging at Primary Anchor Residues

The primary anchor residues are analogued to modulate binding activity. For example, peptide engineering strategies are implemented to further increase the cross-reactivity of the A3-supertype candidate epitopes identified above. On the basis of the data disclosed, e.g., in related and U.S. Ser. No. 09/226,775, now abandoned, the main anchors of A3-supermotif-bearing peptides are altered, for example, to introduce a preferred V, S, or M at position 2.

To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A3 supertype alleles A3 and A11; then, if binding capacity is maintained, for additional A3-supertype cross-reactivity.

Similarly, analogs of HLA-A2 supermotif-bearing epitopes may also be generated. For example, peptides binding to A2-supertype molecules may be engineered at primary anchor residues to possess a preferred residue (L, I, V, or M) at position 2 and/or a preferred I or V as a position 9 primary anchor residue.

The analog peptides are then tested for the ability to bind the A2 supermotif prototype allele, A*0201. Those peptides that demonstrate 500 nM binding capacity are then tested for A2-supertype cross-reactivity.

Similarly to the A2- and A3-motif bearing peptides, peptide binding to B7-supertype alleles may be improved, where possible, to achieve increased cross-reactive binding. B7 supermotif-bearing peptides may, for example, be engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).

Analoging at Secondary Anchor Residues

Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of an analog of the B7 supermotif-bearing peptide Pf SSP2126, representing a discreet single amino acid substitution at position one, is analyzed. The peptide may be substituted with an F at position 1, rather than and L. The peptide, which binds to 3 of 5 B7 supertype alles, is then analyzed for the ability to bind all five B7-supertype molecules with a good affinity.

Because so few B7-supertype cross-reactive epitopes were identified in the initial binding screen, results from previous binding evaluations may be analyzed to identify conserved (8-, 9-, 10-, or 11-mer) peptides which bind, minimally, 3/5 B7 supertype molecules with weak affinity (IC50 of 500 nM-5 μM). This analysis identifies additional candidate peptides that can be analogued. These peptides are tested for enhanced binding affinity and B7-supertype cross-reactivity.

Engineered analogs with sufficiently improved binding capacity or cross-reactivity are tested as described in Example 2 for the ability of the peptide to induce CTL responses using PBMC from individuals who had previously been exposed to Pf antigens. Immunogenicity may also be studied in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization.

In conclusion, these data demonstrate that by the use of even single amino acid substitutions, it is possible to increase the binding affinity and/or cross-reactivity of peptide ligands for HLA supertype molecules.

Example 5 Identification of Conserved PF-Derived Sequences with HLA-DR Binding Motifs

Peptide epitopes bearing an HLA class II supermotif or motif may also be identified as outlined below using methodology similar to that described in Examples 1-3.

Selection of HLA-DR-Supermotif-Bearing Epitopes

To identify PF-derived, HLA class II HTL epitopes, the protein sequences from the same four PF antigens used for the identification of HLA Class I supermotif/motif sequences were analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences were selected comprising a DR-supermotif, further comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total). It was also required that the 9-mer core sequence be 100% conserved in at least 79% of the sequences analyzed.

The conserved, PF-derived peptides identified above were tested for their binding capacity for various common HLA-DR molecules. All peptides were initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least 2 of these 3 DR molecules were then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least 2 of the 4 secondary panel DR molecules, and thus cumulatively at least 4 of 7 different DR molecules, were screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least 7 of the 10 DR molecules comprising the primary, secondary, and tertiary screening assays were considered cross-reactive DR binders. The composition of these screening panels, and the phenotypic frequency of associated antigens, are shown in Table XXX.

In conclusion, 8 cross-reactive DR-binding peptides derived from 6 independent regions were identified that bind 7 or more HLA DR alleles. Five other peptides were also identified that bound between 4 and 6 DR alleles (Table XXXI).

Selection of Conserved DR3 Motif Peptides

Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is an important criterion in the selection of HTL epitopes. However, data generated previously indicated that DR3 only rarely cross-reacts with other DR alleles (Sidney et al., J. Immunol. 149:2634-2640, 1992; Geluk et al., J. Immunol. 152:5742-5748, 1994; Southwood et al., J. Immunol. 160:3363-3373, 1998). This is not entirely surprising in that the DR3 peptide-binding motif appears to be distinct from the specificity of most other DR alleles.

To efficiently identify peptides that bind DR3, target proteins were analyzed for conserved sequences carrying one of the two DR3 specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). Peptides containing a DR3 motif were then synthesized and tested for their DR3 binding capacity. Three peptides were found to bind DR3 with an affinity of 1 μM or less (Table XXXI), and thereby qualify as HLA class II high affinity binders. On of these peptides was also identified above as a cross-reactive DR binding peptide.

DR3 binding epitopes identified in this manner that are found to induce immunological responses as in Example 6 below may then be included in vaccine compositions with DR supermotif-bearing peptide epitopes.

Example 6 Immunogenicity of PF-Derived HTL Epitopes

The immunogenicity of the HLA class II binding epitopes identified in Example 5 was evaluated in a study testing PBMC from either healthy volunteers previously immunized with an irradiated sporozoite vaccine, and thereby immune to malaria, or PBMC from naturally exposed individuals from the Irian Java (Indonesia) region where malaria is highly endemic. Vigorous responses were seen in volunteers vaccinated with whole irradiate sporozoites. All peptides were recognized in at least one immune individual, but not in either of the two individuals for which pre-immunization sample were available. All individuals recognized at least two, and up to nine different epitopes.

In the case of Irian Java population, PBMC from over 100 different individuals were screened for reactivity. Proliferation and secretion of various lymphokines has been measured. The results demonstrate that also in this semi-immune chronically exposed population, all peptides are recognized, with the percentage of individuals yielding positive responses ranging from 7% to 29% for IFN-γ, 36% to 51% for TNF-α and 12% to 2% for proliferative responses (Table XXII.

In conclusion, the immunogenicity of class II epitopes derived from conserved regions of the PF genome has been demonstrated.

Example 7 Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

In order to analyze population coverage, gene frequencies of HLA alleles were determined. Gene frequencies for each HLA allele were calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies were calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)2].

Where frequency data was not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies was assumed. To obtain total potential supertype population coverage no linkage disequilibrium was assumed, and only alleles confirmed to belong to each of the supertypes were included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations were made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).

Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups (see Table XXI). Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analagous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Summary of Candidate HLA Class I and Class II Epitopes

In summary, on the basis of the data presented in the above examples, candidate peptide epitopes derived from conserved regions of PF have been identified (Table XXXIII) These include eight HLA-A2 supermotif-bearing epitopes, eight HLA-A3 supermotif-bearing epitopes, and two HLA-B7 supermotif-bearing epitope, each capable of binding to multiple A2-, A3-, or B7-supertype molecules, and immunogenic in HLA transgenic mice or antigenic for human PBL. In addition four A1 motif-bearing and four A24 motif-bearing epitopes are also include candidate CTL epitopes for inclusion in a vaccine composition.

With these 26 CTL epitopes (as disclosed herein and from the art), average population coverage, (i.e., recognition of at least one PF epitope), is predicted to be, on average, greater than 95% (range of 90.6%-99.1%), in five major ethnic populations. The potential redundancy of coverage afforded by these epitopes can be estimated using the game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994). As shown in FIG. 1, it is estimated that 90% of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize 8 or more of the candidate epitopes described herein.

A list of PF-derived HTL epitopes that would be preferred for use in the design of minigene constructs or other vaccine formulations is summarized in Table XXXIV. As shown, 13 different peptide-binding regions have been identified which bind multiple HLA-DR molecules or bind HLA-DR3.

It is estimated that each of 10 common DR molecules recognizing the DR supermotif, and DR3, are covered by a minimum of 2 epitopes. Correspondingly, the total estimated population coverage represented by this panel of epitopes is, on average, in excess of 94% in each of the 5 major ethnic populations (Table XXXV).

Example 8 Recognition of Generation of Endogenous Processed Antigens after Priming

This example determines that CTL induced by native or analogued peptide epitopes identified and selected as described in Examples 1-6 recognize endogenously synthesized, i.e., native antigens.

Effector cells isolated from transgenic mice that are immunized with peptide epitopes as in Example 3, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/Kb target cells in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with PF expression vectors.

The result will demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized PF antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that is being evaluated. In addition to HLA-A*0201/Kb transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 9 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

This example illustrates the induction of CTLs and HTLs in transgenic mice by use of a PF CTL/HTL peptide conjugate whereby the vaccine composition comprises peptides administered to a PF-infected patient or an individual at risk for malaria. The peptide composition can comprise multiple CTL and/or HTL epitopes. This analysis demonstrates enhanced immunogenicity that can be achieved by inclusion of one or more HTL epitopes in a vaccine composition. Such a peptide composition can comprise a lipidated HTL epitope conjugated to a preferred CTL epitope containing, for example, at least one CTL epitope selected from Tables VII-XVIII, or an analog of that epitope. The HTL epitope is, for example, selected from Table XIX or XX.

Lipopeptide preparation: Lipopeptides are prepared by coupling the appropriate fatty acid to the amino terminus of the resin bound peptide. A typical procedure is as follows: A dichloromethane solution of a four-fold excess of a pre-formed symmetrical anhydride of the appropriate fatty acid is added to the resin and the mixture is allowed to react for two hours. The resin is washed with dichloromethane and dried. The resin is then treated with trifluoroacetic acid in the presence of appropriate scavengers [e.g. 5% (v/v) water] for 60 minutes at 20° C. After evaporation of excess trifluoroacetic acid, the crude peptide is washed with diethyl ether, dissolved in methanol and precipitated by the addition of water. The peptide is collected by filtration and dried.

Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/Kb mice, which are transgenic for the human HLA A2.1 allele and are useful for the assessment of the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, are primed subcutaneously (base of the tail) with 0.1 ml of peptide conjugate formulated in saline, or DMSO/saline. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)

In vitro CTL activation: One week after priming, spleen cells (30×106 cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×106 cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

Assay for cytotoxic activity: Target cells (1.0 to 1.5×106) are incubated at 37° C. in the presence of 200 μl of 51Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 104 51Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a 6 hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % 51Cr release data is expressed as lytic units/106 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a 6 hour 51Cr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide. For example, if 30% 51Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×105 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1/50,000)−(1/500,000)]×106=18 LU.

The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using the CTL epitope as outlined in Example 3. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures it is found that a CTL response is induced, and concomitantly that an HTL response is induced, upon administration of such compositions.

Example 10 Selection of CTL and HTL Epitopes for Inclusion in a PF-Specific Vaccine

This example illustrates the procedure for the selection of peptide epitopes for vaccine compositions of the invention. The peptides in the composition may be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or may be single and/or polyepitopic peptides.

The following principles are utilized when selecting an array of epitopes for inclusion in a vaccine composition. Each of the following principles are balanced in order to make the selection.

1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. In other words, it has been observed that patients who spontaneously clear PF generate an immune response to at least 3 epitopes on at least one PF antigen. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen.

2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.

3.) Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art and discussed herein, can be employed to assess breadth, or redundancy, of population coverage.

4.) When selecting epitopes for PF antigens it may be preferable to select native epitopes. Therefore, of particular relevance for infectious disease vaccines, are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.

When providing nested epitopes, a sequence that has the greatest number of epitopes per provided sequence is provided. A limitation on this principle is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, the sequence is screened in order to insure that it does not have pathological or other deleterious biological properties.

5.) When creating a minigene, as disclosed in greater detail in Example 11, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Additionally, however, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that epitope, which is not present in a native PF protein sequence. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

Peptide epitopes for inclusion in vaccine compositions are, for example, selected from those listed in Tables XXXIII and XXXIV. A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude of an immune response that clears an acute PF infection.

Example 11 Construction of Minigene Multi-Epitope DNA Plasmids

This example describes the design and construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of CTL and/or HTL epitopes or epitope analogs as described herein. Expression plasmids have been constructed and evaluated as described, for example, in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and in Ishioka et al., J. Immunol. 162:3915-3925, 1999.

A minigene expression plasmid may include multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. Preferred epitopes are identified, for example, in Tables XXXIII and XXXIV. HLA class I supermotif or motif-bearing peptide epitopes derived from multiple PF antigens, e.g., EXP-1, SSP2, CSP and LSA-1, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from multiple PF antigens to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

This example illustrates the methods to be used for construction of such a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

The minigene DNA plasmid contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

Overlapping oligonucleotides, for example eight oligonucleotides, averaging approximately 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

For the first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: Oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product for 25 additional cycles. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 12 The Plasmid Construct and the Degree to which it Induces Immunogenicity

The degree to which the plasmid construct prepared using the methodology outlined in Example 11 is able to induce immunogenicity is evaluated through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analysed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and Alexander et al., Immunity 1:751-761, 1994. To assess the capacity of the pMin minigene construct to induce CTLs in vivo, HLA-A11/Kb transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against the A3-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine. It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A3 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A2 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A2 and HLA-B7 motif or supermotif epitopes.

To assess the capacity of a class II epitope encoding minigene to induce HTLs in vivo, I-Ab restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant.

CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a 3H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al., Immunity 1:751-761, 1994). the results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

DNA minigenes, constructed as described in Example 11, may also be evaluated as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent may consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Reotroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).

For example, the efficacy of the DNA minigene may be evaluated in transgenic mice. In this example, A2.1/Kb transgenic mice are immunized IM with 100 μg of the DNA minigene encoding the immunogenic peptides. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 107 pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an IFN-y ELISA. It is found that the minigene utilized in a prime-boost mode elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis is also performed using other HLA-A11 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes.

Example 13 Peptide Composition for Prophylactic Uses

Vaccine compositions of the present invention are used to prevent PF infection in persons who are at risk for such infection. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in Examples 9 and/or 10, which are also selected to target greater than 80% of the population, is administered to individuals at risk for PF infection. The composition is provided as a single lipidated polypeptide that encompasses multiple epitopes. The vaccine is administered in an aqueous carrier comprised of Freunds Incomplete Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against PF infection.

Alternatively, the polyepitopic peptide composition can be administered as a nucleic acid in accordance with methodologies known in the art and disclosed herein.

Example 14 Polyepitopic Vaccine Compositions Derived from Native PF Sequences

A native PF polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes and is preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct, even overlapping, epitopes is selected and used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with frame shifted overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

The vaccine composition will preferably include, for example, three CTL epitopes and at least one HTL epitope from PF. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent analogs) directs the immune response to multiple peptide sequences that are actually present in native PF antigens thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions.

Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

Example 15 Polyepitopic Vaccine Compositions Directed to Multiple Diseases

The PF peptide epitopes of the present invention are used in conjunction with peptide epitopes from target antigens related to one or more other diseases, to create a vaccine composition that is useful for the prevention or treatment of PF as well as the one or more other disease(s). Examples of the other diseases include, but are not limited to, HIV, HCV, and HBV.

For example, a polyepitopic peptide composition comprising multiple CTL and HTL epitopes that target greater than 98% of the population may be created for administration to individuals at risk for both PF and HIV infection. The composition can be provided as a single polypeptide that incorporates the multiple epitopes from the various disease-associated sources, or can be administered as a composition comprising one or more discrete epitopes.

Example 16 Use of Peptides to Evaluate an Immune Response

Peptides of the invention may be used to analyze an immune response for the presence of specific CTL or HTL populations directed to PF. Such an analysis may be performed in a manner as that described by Ogg et al., Science 279:2103-2106, 1998. In the following example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, PF HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of infection or following immunization using an PF peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive uninfected donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the PF epitope, and thus the stage of infection with PF, the status of exposure to PF, or exposure to a vaccine that elicits a protective or therapeutic response.

Example 17 Use of Peptide Epitopes to Evaluate Recall Responses

The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from infection, who are chronically infected with PF, or who have been vaccinated with a PF vaccine.

For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any PF vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that are preferably highly conserved and, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

In the microculture format, 4×105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 ml of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with uninfected control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).

Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of 51Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

Cytolytic activity is determined in a standard 4-h, split well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release−spontaneous release)/maximum release−spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to PF or a PF vaccine.

The class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×105 cells/well and are stimulated with 10 μg/ml synthetic peptide, whole antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 3H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for 3H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the 3H-thymidine incorporation in the absence of antigen.

Example 18 Induction of CTL Responses Using a Prime Boost Protocol

A prime boost protocol similar in its underlying principle to that used to evaluated the efficacy of a DNA vaccine in transgenic mice, which was described in Example 12, may also be used for the administration of the vaccine to humans. Such a vaccine regimen is includes an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptides mixture administered in an adjuvant.

For example, the initial immunization may be performed using an expression vector, such as that constructed in Example 11, in the form of naked DNA administered IM (or SC or ID) in the amounts of 0.5-5, typically 100 g, at multiple sites. The DNA (0.1 to 1000 mg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5×109 pfu. Alternative recombinant virus, such as MVA, canarypox, adenovirus, and adeno-associated viruses can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples will be obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

Analysis of the results will indicate that a magnitude of sufficient response to achieve protective immunity against Pf is generated.

Example 19 Induction of Specific CTL Response in Humans

A human clinical trial to evaluate an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial in patients are not infected with Pf. Such a trial is designed, for example, as follows:

A total of about 27 subjects are enrolled and divided into 3 groups:

Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.

The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

The vaccine is found to be both safe and efficacious.

A prophylactic field trial can also be conducted to evaluate a vaccine composition of the invention. In such a trial, issues of patient compliance are also considered in the determination of vaccine efficacy.

Example 20 Administration of Vaccine Compositions Using Dendritic Cells

Vaccines comprising peptide epitopes of the invention may be administered using dendritic cells. In this example, the immunogenic peptide epitopes are used to elicit a CTL and/or HTL response ex vivo.

Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptides. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., PF-infected cells.

Example 21 Alternative Method of Identifying Motif-Bearing Peptides

Another way of identifying motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing, have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can then be infected with a pathogenic organism, e.g., PF, HIV, etc. or transfected with nucleic acids that express the antigen of interest. Thereafter, peptides produced by endogenous antigen processing of peptides produced consequent to infection (or as a result of transfection) will bind to HLA molecules within the cell and be transported and displayed on the cell surface.

The peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because, as disclosed herein, the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

Alternatively, cell lines that do not express any endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells may then be used as described, i.e., they may be infected with a pathogenic organism or transfected with nucleic acid encoding an antigen of interest to isolate peptides corresponding to the pathogen or antigen of interest that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than infection or transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

The above examples are provided to illustrate the invention but not to limit its scope. For example, the human terminology for the Major Histocompatibility Complex, namely HLA, is used throughout this document. It is to be appreciated that these principles can be extended to other species as well. Thus, other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent application cited herein are hereby incorporated by reference for all purposes.

TABLE I SUPERMOTIFS POSITION POSITION POSITION 2  3  C Terminus  (Primary Anchor) (Primary Anchor) (Primary Anchor) A1 TILVMS FWY A2 LIVMATQ IVMATL A3 VSMATLI RK A24 YFWIVLMT FIYWLM B7 P VILFMWYA B27 RHK FYLWMIVA B44 ED FWYLIMVA B58 ATS FWYLIVMA B62 QLIVMP FWYMIVLA MOTIFS A1 TSM Y A1 DEAS Y A2.1 LMVQIAT VLIMAT A3 LMVISATFCGD KYRHFA A11 VTMLISAGNCDF KRYH A24 YFWM FLIW A*3101 MVTALIS RK A*3301 MVALFIST RK A*6801 AVTMSLI RK B*0702 P LMFWYAIV B*3501 P LMFWYIVA B51 P LIVFWYAM B*5301 P IMFWYALV B*5401 P ATIVLMFWY Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearingif it has primary anchors at each primary anchor position for a motif or superrnotifas specified in the above table.

TABLE Ia SUPERMOTIFS POSITION POSITION POSITION 2  3  C Terminus  (Primary Anchor) (Primary Anchor) (Primary Anchor) A1 TILVMS FWY A2 VQAT VLIMAT A3 VSMATLI RK A24 YFWIVLMT FIYWLM B7 P VILFMWYA B27 RHK FYLWMIVA B58 ATS FWYLIVMA B62 QLIVMP FWYMIVLA MOTIFS A1 TSM Y A1 DEAS Y A2.1 VQAT* VLIMAT A3.2 LMVISATFCGD KYRHFA A11 VTMLISAGNCDF KRHY A24 YFW FLIW *If 2 is V, or Q, the C-term is not L Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearingif it has primary anchors at each primary anchor position for a motif or supermotifas specified in the above table.

TABLE 11 Position SUPERMOTIFS 1 2 3 4 5 A1 1° Anchor TILVMS A2 1° Anchor LIVMATQ A3 preferred 1° Anchor  YFW (4/5) VSMATLI RK deleterious DE (3/5);  DE (4/5) P (5/5) A24 1° Anchor YFWIVLMT B7 preferred FWY (5/5) 1° Anchor FWY (4/5) LIVM (3/5) P deleterious DE (3/5);  P(5/5); G(4/5);  A(3/5); QN (3/5) B27 1° Anchor RHK B44 1° Anchor ED B58 1° Anchor ATS B62 1° Anchor QLIVMP Position SUPERMOTIFS 6 7 8 C-terminus A1 1° Anchor FWY A2 1° Anchor LIVMAT A3 YFW (3/5)  YFW (4/5) P (4/5) 1° Anchor RK A24 1° Anchor FIYWLM B7 FWY (3/5)  1° Anchor VILFMWYA /5) QN (4/5) DE (4/5) B27 1° Anchor FYLWMIVA B44 1° Anchor FWYLIMVA B58 1° Anchor FWYLIVMA B62 1° Anchor FWYMIVLA Position MOTIFS 1 2 3 4 5 A1 preferred GFYW 1° Anchor DEA YFW 9-mer STM deleterious DE RHKLIVM A G P A1 preferred GRHK ASTCLIV 1° Anchor GSTC 9-mer M DEAS deleterious A RHKDEPY DE PQN FW Position MOTIFS 6 7 8 C-terminus A1 P DEQN YFW 1° Anchor 9-mer Y A A1 ASTC LIVM DE 1° Anchor 9-mer Y RHK PG GP Position 1 2 3 4 A1 peferred YFW 1° Anchor DEAQN A 10- STM mer deleterious GP RHKGLIV DE M A1 preferred YFW STCLIVM 1° Anchor A l0- DEAS mer deleterious RHK RHKDEPY FW A2.1 preferred YFW 1° Anchor YFW STC 9-mer LMIVQAT deleterious DEP DERKH A2.1 preferred AYFW 1° Anchor LVIM G l0- LMIVQAT mer deleterious DEP DE RKHA A3 preferred RHK 1° Anchor YFW PRHKYFW LMVISAT FCGD deleterious DEP DE A11 preferred A 1° Anchor YFW YFW VTLMISA GNCDF deleterious DEP A24 preferred YFWRHK 1° Anchor STC 9-mer YFWM deleterious DEG DE G A24 preferred 1° Anchor P 10- YFWM mer deleterious GDE QN A3101 preferred RHK 1° Anchor YFW P MVTALIS deleterious DEP DE A3301 preferred 1° Anchor YFW MVALFIS T deleterious GP DE A6801 preferred YFWSTC 1° Anchor AVTMSLI deleterious GP DEG B0702 preferred RHKFWY 1° Anchor RHK P deleterious DEQNP DEP DE B3501 preferred FWYLIVM 1° Anchor FWY P deleterious AGP B51 preferred LIVMFWY 1° Anchor FWY STC P deleterious  AGPDERHKSTC B5301 preferred LIVMFWY 1° Anchor FWY STC P deleterious  AGPQN B5401 preferred FWY 1° Anchor FWYLIVM P deleterious  GPQNDE GDESTC Position 9 or C- 6 7 8 terminus A1 peferred PASTC GDE P 10- mer deleterious QNA RHKYFW RHK A A1 preferred PG G YFW l0- mer deleterious G PRHK QN A2.1 preferred A P 1° Anchor 9-mer VLIMAT deleterious RKH DERKH A2.1 preferred G FYWL l0- VIM mer deleterious RKH DERK RKH A3 preferred A YFW P 1° Anchor KYRHFA deleterious A11 preferred YFW YFW P 1° Anchor KRYH deleterious A G A24 preferred YFW YFW 1° Anchor 9-mer FLIW deleterious DERHK G AQN A24 preferred P 10- mer deleterious DE A QN DEA A3101 preferred YFW YFW AP 1° Anchor RK deleterious DE DE DE A3301 preferred AYFW 1° Anchor RK deleterious A6801 preferred YFW P 1° Anchor RK deleterious A B0702 preferred RHK RHK PA 1° Anchor LMFWYAIV deleterious GDE QN DE B3501 preferred FWY 1° Anchor LMFWYIVA deleterious G B51 preferred G FWY 1° Anchor LIVFWYAM deleterious  G DEQN GDE B5301 preferred LIVMFWY FWY 1° Anchor IMFWYALV deleterious  G RHKQN DE B5401 preferred ALIVM FWYAP 1° Anchor ATIVLMFW Y deleterious  DE QNDGE DE Italicized residues indicate less preferred or ″tolerated″ residues. The information in Table II is specific for 9-meRs unless otherwise specified.

TABLE III POSITION SEQ ID 1° 1° NO: MOTIFS anchor 1 2 3 4 5 anchor 6 7 8 9 DR4 preferred FMYLIYW M T I VSTCPALIM MH MEI deleterious W R WDE DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM deleterious C CH FD CWD GDE D 3841 DR7 preferred MFLIVWY M W A IVMSACTPL M IV 3842 deleterious C G GRD N G DR Supermotif MFLIVWY VMSTACPLI DR3 MOTIFS 1° anchor 1 2 3 1° anchor 4 5 1° anchor 6 motif a LIVMFY D preferred motif b LIVMFAY DNQEST KRH preferred Italicized residues indicate less preferred or ″tolerated″ residues.

TABLE IV HLA Class I Standard Peptide Binding Affinity. SEQ STANDARD STANDARD ID BINDING ALLELE PEPTIDE SEQUENCE NO: AFFINITY (nM) A*0101  944.02 YLEPAIAKY 3575 25 A*0201  941.01 FLPSDYFPSV 3576  5.0 A*0202  941.01 FLPSDYFPSV 3577  4.3 A*0203  941.01 FLPSDYFPSV 3578 10 A*0205  941.01 FLPSDYFPSV 3579  4.3 A*0206  941.01 FLPSDYFPSV 3580  3.7 A*0207  941.01 FLPSDYFPSV 3581 23 A*6802 1072.34 YVIKVSARV 3582  8.0 A*0301  941.12 KVFPYALINK 3583 11 A*1101  940.06 AVDLYHFLK 3584  6.0 A*3101  941.12 KVFPYALINK 3585 18 A*3301 1083.02 STLPETYVVRR 3586 29 A*6801  941.12 KVFPYALINK 3587  8.0 A*2402  979.02 AYIDNYNKF 3588 12 B*0702 1075.23 APRTLVYLL 3589  5.5 B*3501 1021.05 FPFKYAAAF 3590  7.2 B51 1021.05 FPFKYAAAF 3591  5.5 B*5301 1021.05 FPFKYAAAF 3592  9.3 B*5401 1021.05 FPFKYAAAF 3593 10

TABLE V HLA Class II Standard Peptide Binding Affinity. Binding Standard Affinity Allele Nomenclature Peptide SEQ ID Sequence (nM) DRB1*0101 DR1  515.01 3594 PKYVKQNTLKLAT    5.0 DRB1*0301 DR3  829.02 3595 YKTIAFDEEARR  300 DRB1*0401 DR4w4  515.01 3596 PKYVKQNTLKLAT   45 DRB1*0404 DR4w14  717.01 3597 YARFQSQTTLKQKT   50 DRB1*0405 DR4w15  717.01 3598 YARFQSQTTLKQKT   38 DRB1*0701 DR7  553.01 3599 QYIKANSKFIGITE   25 DRB1*0802 DR8w2  553.01 3600 QYIKANSKFIGITE   49 DRB1*0803 DR8w3  553.01 3601 QYIKANSKFIGITE 1600 DRB1*0901 DR9  553.01 3602 QYIKANSKFIGITE   75 DRB1*1101 DR5w11  553.01 3603 QYIKANSKFIGITE   20 DRB1*1201 DR5w12 1200.05 3604 EALIHQLKINPYVLS  298 DRB1*1302 DR6w19  650.22 3605 QYIKANAKFIGITE    3.5 DRB1*1501 DR2w2β1  507.02 3606 GRTQDENPVVHFFK    9.1 NIVTPRTPPP DRB3*0101 DR52a  511 3607 NGQIGNDPNRDIL  470 DRB4*0101 DRw53  717.01 3608 YARFQSQTTLKQKT   58 DRB5*0101 DR2w2β2  553.01 3609 QYIKANSKFIGITE   20

The “Nomenclature” column lists the allelic designations used in Tables XIX and XX.

Table VI HLA- Allelle-specific HLA-supertype members supertype Verifieda Predictedb A1 A*0101, A*2501, A*2601, A*2602, A*3201 A*0102, A*2604, A*3601, A*4301, A*8001 A2 A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*0208, A*0210, A*0211, A*0212, A*0213 A*0209, A*0214, A*6802, A*6901 A3 A*0301, A*1101, A*3101, A*3301, A*6801 A*0302, A*1102, A*2603, A*3302, A*3303, A*3401, A*3402, A*6601, A*6602, A*7401 A24 A*2301, A*2402, A*3001 A*2403, A*2404, A*3002, A*3003 B7 B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503, B*1511, B*4201, B*5901 B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601, B*5602, B*6701, B*7801 B27 B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2701, B*2707, B*2708, B*3802, B*3903, B*3904, B*2706, B*3801, B*3901, B*3902, B*7301 B*3905, B*4801, B*4802, B*1510, B*1518, B*1503 B44 B*1801, B*1802, B*3701, B*4402, B*4403, B*4404, B*4001, B*4101, B*4501, B*4701, B*4901, B*5001 B*4002, B*4006 B58 B*5701, B*5702, B*5801, B*5802, B*1516, B*1517 B62 B*1501, B*1502, B*1513, B*5201 B*1301, B*1302, B*1504, B*1505, B*1506, B*1507, B*1515, B*1520, B*1521, B*1512, B*1514, B*1510 aVerified alleles include alleles whose specificity has been determined by pool sequencing analysis, peptide binding assays, or by analysis of the sequences of CTL epitopes. bPredicted alleles are alleles whose specificity is predicted on the basis of B and F pocket structure to overlap with the supertype specificity.

TABLE VII Malaria A01 Super Motif Peptides With Binding Data No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*010I Seq. Id. CSP AILSVSSF 6 8 19 100 1 CSP AILSVSSFLF 6 10 19 100 2 CSP ALFQEYQCY 18 9 19 100 3 CSP EMNYYGKQENW 52 11 19 100 4 CSP FLFVEALF 13 8 19 100 5 CSP FLFVEALFQEY 13 11 19 100 6 CSP FVEALFQEY 15 9 19 100 3.4000 7 CSP GLIMVLSF 421 8 19 100 8 CSP GLIMVLSFLF 421 10 19 100 9 CSP ILSVSSFLF 7 9 19 100 10 CSP IMVLSFLF 423 8 19 100 11 CSP KIQNSLSTEW 357 10 19 79 12 CSP KLAILSVSSF 4 10 19 100 13 CSP KMEKCSSVF 405 9 19 100 14 CSP LIMVLSFLF 422 9 19 100 15 CSP LSVSSFLF 8 8 19 100 16 CSP NLYNELEMNY 46 10 19 100 17 CSP NLYNELEMNYY 46 11 19 100 18 CSP NTRVLNELNY 31 10 19 100 0.0096 19 CSP PSDKHIEQY 346 9 19 79 20 CSP RVLELNY 33 8 19 100 21 CSP SIGLIMVLSF 419 10 19 100 22 CSP SSFLFVEALF 11 10 19 100 23 CSP SSIGLIMVLSF 418 11 19 100 24 CSP VSSFLFVEALF 10 11 19 100 25 CSP EVNKRKSKY 66 9 1 100 26 EXP FLALFFIIF 8 9 1 100 27 EXP ILSVFFLALF 3 10 1 100 28 EXP ILSVFFLALFF 3 11 1 100 29 EXP KILSVFFLALF 2 11 1 100 30 EXP LLGGVGLVLY 92 10 1 100 31 EXP LSVFFLALF 4 9 1 100 32 EXP LSVFFLALFF 4 10 1 100 33 EXP LVEVNKRKSKY 64 11 1 100 34 EXP NTEKGRHPF 102 9 1 100 35 EXP SVFFLALF 5 8 1 100 36 EXP SVFFLALFF 5 9 1 100 37 EXP VLLGGVGLVLY 91 11 1 100 38 LSA DLDEFKPIVQY 1781 11 1 100 39 LSA DVLQEDLY 1646 8 1 100 40 LSA DVNDFQISKY 1751 10 1 100 41 LSA ELPSENERGY 1662 10 1 100 42 LSA ELPSENERGYY 1662 11 1 100 43 LSA ELSEDITTKY 1897 9 1 100 44 LSA ELSEDITKYF 1897 10 1 100 45 LSA ETVNISDVNDF 1745 11 1 100 46 LSA FIKSLFHIF 1877 9 1 100 47 LSA FILVNLLIF 11 9 1 100 48 LSA HILYISFY 3 8 1 100 49 LSA HILYISFYF 3 9 1 100 50 LSA HVLSHNSY 59 8 1 100 51 LSA IINDDDDKKKY 127 11 1 100 52 LSA ILVNLLIF 12 8 1 100 53 LSA ILYISFYF 4 8 1 100 54 LSA KIKKGKKY 1834 8 1 100 55 LSA KSLYDEHIKKY 1854 11 1 100 56 LSA KTKNNENNKF 68 10 1 100 57 ISA KTKNNENNKFF 68 11 1 100 58 LSA LSEDITKY 1898 8 1 100 59 LSA LSEDITKYF 1898 9 1 100 60 LSA NISDVNDF 1748 8 1 100 61 LSA NLGVSENIF 103 9 1 100 62 ISA NVKNVSQTNF 88 10 1 100 63 ISA PIVQYDNF 1787 8 1 100 64 LSA PSENERGY 1664 8 1 100 65 LSA PSENERGYY 1664 9 1 100 0.0790 66 LSA QVNKEKEKF 1869 9 1 100 67 LSA SLYDEHIKKY 1855 10 1 100 68 LSA TVNISDVNDF 1746 10 1 100 69 SSP2 ALLACAGLAY 509 10 10 100 70 SSP2 ASCGVWDEW 242 9 10 100 71 SSP2 ATPYAGEPAPF 526 11 8 80 72 SSP2 CSGSIRRHNW 55 10 10 100 73 SSP2 DLDEPEQF 546 8 10 100 74 SSP2 EVCNDEVDLY 41 10 8 80 75 SSP2 EVEKTASCGVW 237 11 10 100 76 SSP2 FLIFFDLF 14 8 10 100 77 SSP2 FVVPGAATPY 520 10 8 80 78 SSP2 GIGQGINVAF 189 10 10 100 79 SSP2 GINVAFNRF 193 9 10 100 80 SSP2 GSIRRHNW 57 8 10 100 81 SSP2 IVFLIFFDLF 12 10 10 100 82 SSP2 KTASCGVW 240 8 10 100 83 SSP2 KTASCGVWDEW 240 11 10 100 84 SSP2 LLACAGLAY 510 9 10 100 85 SSP2 LLACAGLAYKF 510 11 10 100 86 SSP2 LLSTNLPY 121 8 9 90 87 SSP2 LVIVFLIF 10 8 10 100 88 SSP2 LVIVFLIFF 10 9 10 100 89 SSP2 NIVDEIKY 31 8 10 100 90 SSP2 NLYADSAW 213 8 10 100 91 SSP2 NVKNVIGPF 222 9 10 100 92 SSP2 NVKYLVIVF 6 9 10 100 93 SSP2 PSDGKCNLY 207 9 10 100 0.5400 94 SSP2 RLPEENEW 554 8 10 100 95 SSP2 SLLSTNLPY 120 9 9 90 96 SSP2 VIVFLIFF 11 8 10 100 97 SSP2 VIVFLIFFDLF 11 11 10 100 98 SSP2 VVPGAATPY 521 9 8 80 99 SSP2 YLVIVFLIF 9 9 10 100 100 SSP2 YLVIVFLIFF 9 10 10 100 101

TABLE VIII  Malaria A02 Motif Peptides With Binding Information No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*0201 CSP HIEQYLKKI 350 9 15 79 CSP KIQNSLST 361 8 15 79 CSP YLKKIQNSL 358 9 15 79 CSP YLKKIQNSLST 358 11 15 79 CSP NANANNAV 335 8 16 84 CSP NVDENANANNA 331 11 16 84 CSP ELNYDNAGI 37 9 18 95 CSP ELNYDNAGINL 37 11 18 95 CSP GINLYNEL 44 8 18 95 CSP GINLYNELEM 44 10 18 95 CSP NAGINLYNEL 42 10 18 95 CSP SLSTEWSPCSV 365 11 18 95 CSP AILSVSSFL 6 9 19 100 0.0220 CSP AILSVSSFLFV 6 11 19 100 CSP DIEKKICKM 402 9 19 100 CSP GIQVRIKPGSA 380 11 19 100 CSP GLIMVLSFL 425 9 19 100 0.0630 CSP GLIMVLSFLFL 425 11 19 100 CSP ILSVSSFL 7 8 19 100 CSP ILSVSSFLFV 7 10 19 100 0.0300 CSP IMVLSFLFL 427 9 19 100 0.0007 CSP IQVRIKPGSA 381 10 19 100 CSP KICKMEKCSSV 406 11 19 100 CSP KLAILSVSSFL 4 11 19 100 CSP KLRICPICHKKL 104 10 19 100 0.0001 CSP KMEKCSSV 409 8 19 100 CSP KMEKCSSVFNV 409 11 19 100 CSP KQENWYSL 58 8 19 100 CSP LAILSVSSFL 5 10 19 100 CSP LIMVLSFL 426 8 19 100 CSP LIMVLSFLFL 426 10 19 100 0.0019 CSP MMRKLAIL 1 8 19 100 CSP MMRKLAILSV 1 10 19 100 0.0012 CSP MVLSFLFL 428 8 19 100 CSP NVDPNANPNA 300 10 19 100 CSP NANPNVDPNA 196 10 19 100 CSP NLYNELEM 46 8 19 100 CSP NMPNDPNRNV 323 10 19 100 0.0007 CSP NQGNGQGHNM 315 10 19 100 CSP NTRVLNEL 31 8 19 100 CSP NVDENANA 331 8 19 100 CSP NVDPNANPNA 200 10 19 100 CSP NVDPNANPNV 128 10 19 100 CSP NVVNSSIGL 418 9 19 100 CSP NVVNSSIGLI 418 10 19 100 CSP NVVNSSIGLIM 418 11 19 100 CSP QVRIKPGSA 382 9 19 100 CSP RVLNELNYDNA 33 11 19 100 CSP SIGLIMVL 423 8 19 100 CSP SIGLIMVLSFL 423 11 19 100 CSP SLKKNSRSL 64 9 19 100 0.0001 CSP STEWSPCSV 367 9 19 100 CSP STEWSPCSVT 367 10 19 100 CSP SVFNVVNSSI 415 10 19 100 0.0005 CSP SVSSFLFV 9 8 19 100 CSP SVSSFLFVEA 9 10 19 100 CSP SVSSFLFVEAL 9 11 19 100 CSP SVTCQNGI 374 8 19 100 CSP SVTCQNGIQV 374 10 19 100 CSP VLNELNYDNA 34 10 19 100 CSP VTCGNGIQV 375 9 19 100 0.0011 CSP VTCGNGIQVRI 375 11 19 100 CSP VVNSSIGL 419 8 19 100 CSP VVNSSIGLI 419 9 19 100 CSP VVNSSIGL1M 419 10 19 100 CSP VVNSSIGLIMV 419 11 19 100 CSP YQCYGSSSNT 23 10 19 100 EXP ATSVLAGL 77 8 1 100 Exp ATSVLAGLL 77 9 1 100 EXP DMIKKEEEL 56 9 1 100 EXP DNMUCEEELV 56 10 1 100 EXP DVHDLISDM 49 9 1 100 EXP DVHDLISDMI 49 10 1 100 EXP EQPQGDDNINIL 147 10 1 100 EXP EQPQGDDNNLV 147 11 1 100 EXP EVNKRKSKYKL 66 11 1 100 EXP FIIFNICESL 13 9 1 100 EXP FIIFNKESLA 13 10 1 100 EXP FLALFFII 8 8 1 100 EXP GLLGNVST 83 8 1 100 EXP GLLGNVSTV 83 9 1 100 0.0160 EXP GLLGNVSTVL 83 10 1 100 0.0380 EXP GLLGNVSTVLL 83 11 1 100 EXP GVGLVLYNT 95 9 1 100 EXP IIFNKESL 14 8 1 100 EXP IIFNKESLA 14 9 1 100 EXP ILSVFFLA 3 8 1 100 EXP ILSVFFLAL 3 9 1 100 0.0058 EXP KIGSSDPA 111 8 1 100 EXP KIGSSDPADNA 111 11 1 100 EXP KILSVFFL 2 8 1 100 EXP KILSVFFLA 2 9 1 100 0.8500 EXP KILSVFFLAL 2 10 1 100 EXP KLATSVLA 75 8 1 100 EXP KLATSVLAGL 75 10 1 100 0.0047 EXP KLATSVLAGLL 75 11 1 100 EXP KTNKGTGSGV 24 10 1 100 EXP LABCTNKGT 21 9 1 100 EXP LAGLLGNV 81 8 1 100 EXP LAGLLGNVST 81 10 1 100 EXP LAGLLGNVSTV 81 11 1 100 EXP LATSVLAGL 76 9 1 100 EXP LATSVLAGLL 76 10 1 100 EXP LIDVHDLI 47 8 1 100 EXP LIDVHDLISDM 47 11 1 100 EXP LLGGVCLV 92 8 1 100 EXP LLGGVCLVL 92 9 1 100 0.0038 EXP LLGNVSTV 84 8 1 100 EXP LLGNVSTVL 84 9 1 100 0.0350 EXP LLGNVSTVLL 84 10 1 100 0.0059 EXP MIKKEEEL 37 8 1 100 EXP MIKKEEELV 57 9 1 100 EXP MIKKEEELVEV 37 11 1 100 EXP NADPQVTA 134 8 1 100 EXP NADPQVTAQDV 134 11 1 100 EXP NTEKGRHPFKI 102 11 1 100 EXP NVSTVLLGGV 87 10 1 100 EXP PADNANPDA 117 9 1 100 EXP PLIDVHDL 46 8 1 100 EXP PLIDVHDLI 46 9 1 100 EXP PQGDDNNL 149 8 1 100 EXP PQGDDNNLV 149 9 1 100 EXP PQVTAQDV 137 8 1 100 EXP PQVTAQDVT 137 9 1 100 EXP QVTAQDVT 138 8 1 100 EXP SLAEKTNKGT 20 10 1 100 EXP STVLLGGV 89 8 1 100 EXP STVLLGQVGL 89 10 1 100 EXP STVLLGGVGLV 89 11 1 100 EXP SVFFLALFFI 5 10 1 100 0.0017 EXP SVPFLALFFH 5 11 1 100 EXP SVLACLLGNV 79 10 1 100 0.0022 EXP TVLLGGVGL 90 9 1 100 EXP TVLLGGVCLV 90 10 1 100 EXP TVLLGGVGLVL 90 11 1 100 EXP VLAGLLGNV 80 9 1 100 0.0210 EXP VLAGLLGNVST 80 11 1 100 EXP VLLGGVCL 91 8 1 100 EXP VLLGOVGLV 91 9 1 100 0.0290 EXP VLLGGVCLVL 91 10 1 100 0.0290 LSA DIQNHILET 1138 9 1 100 LSA DIQNHTLETV 1738 10 1 100 LSA DITKYFMKL 1901 9 1 100 LSA DUDEFKPI 1781 8 1 100 LSA DLDEFKPIV 1781 9 1 100 0.0001 LSA DLEEKAAKET 148 10 1 100 LSA DLEEKAAKETL 148 11 1 100 LSA DLEQDRLA 1388 8 1 100 LSA DLEQERLA 1609 8 1 100 LSA DLEQERRA 1575 8 1 100 LSA DLEMADT 1626 9 1 100 LSA DUERTXASKET 1184 11 1 100 LSA DLYGRLEI 1651 8 1 100 LSA DLYGRLEIPA 1651 10 1 100 LSA DLYGRLEIPAI 1651 11 1 100 LSA DVLAEDLYGRL 1646 11 1 100 LSA EILQIVDEL 1890 9 1 100 LSA EISAEYDDSL 1763 10 1 100 LSA EISAEYDDSLI 1763 11 1 100 LSA EISIIEKT 1692 8 1 100 LSA ELSEDITKYFM 1897 11 1 100 LSA ELTMSNVKNV 83 10 1 100 LSA EQDRLWEKL 1390 10 1 100 LSA EQERLAKEKL 1611 10 1 100 LSA EQERLANEKL 1526 10 1 100 LSA EQERRAKEKL 1577 10 1 100 LSA EQKEDKSA 1730 8 1 100 LSA EQKEDKSADI 1730 10 1 100 LSA EQQRDLEQERL 1605 11 1 100 LSA EQQRDLEQRKA 1622 11 1 100 LSA EQQSDLEQDRL 1384 11 1 100 LSA EQQSDLEQERL 1588 11 1 100 LSA EQQSDLERT 1180 9 1 100 LSA EQQSDLERTKA 1180 11 1 100 LSA EQQSDSEQERL 517 11 1 100 LSA EQRKADTKKNL 1628 11 1 100 LSA ETLQEQQSDL 1193 10 1 100 LSA ETLWQQSDL 156 10 1 100 LSA ETVNISDV 1745 8 1 100 LSA FIKSLFHI 1877 8 1 100 LSA FILVNLLI 11 8 1 100 LSA FILVNLLIFIT 11 11 1 100 LSA FQDEENIGI 1794 9 1 100 LSA FQISKYEDE1 1755 10 1 100 LSA GIOCSSEEL 1822 9 1 100 LSA GIYKELEDL 1801 9 1 100 LSA GIYKELEDLI 1801 10 1 100 LSA GQDENRQEDL 140 10 1 100 LSA GQQSDIEQISRL 1129 11 1 100 LSA GVSENTFL 105 8 1 100 LSA HIFDGDNEI 1883 9 1 100 LSA HIFDGDNEIL 1883 10 1 100 LSA HIKKYKNDKQV 1860 11 1 100 LSA HILYISFYFI 3 10 1 100 0.0033 LSA HILYISFYFIL 3 11 1 100 LSA HLEEKKDGSI 1718 10 1 100 LSA HTLETVNI 1742 8 1 100 LSA HTLETVNISDV 1742 11 1 100 LSA HVLSHNSYEKT 59 11 1 100 LSA IIDONRESI 1695 10 1 100 LSA IIEKTNRESIT 1695 11 1 100 LSA IIKNSEKDEI 25 10 1 100 LSA IIKNSEKDEII 25 11 1 100 LSA ILQIVDEL 1891 8 1 100 LSA ILVNLLIFHI 12 10 1 100 0.0076 LSA ILYISFYFI 4 9 1 100 0.0023 LSA ILYISFYFIL 4 10 1 100 0.0035 LSA ILYISFYFILV 4 11 1 100 LSA IQNHTLET 1739 8 1 100 LSA IQNHTLETV 1739 9 1 100 LSA IQNHTLETVN1 1739 11 1 100 LSA IKYFMKL 1902 8 1 100 LSA ITTNVEGRRDI 1704 11 1 100 LSA IVDELSEDI 1894 9 1 100 LSA IVDELSEDIT 1894 10 1 100 LSA KADTICKNI 1631 8 1 100 LSA KIIKNSEKDEI 24 11 1 100 LSA KIKKGKKYEICT 1834 11 1 100 LSA KLNKEGKL 116 8 1 100 LSA KLNKEGKLI 116 9 1 100 LSA KLQEQQRDL 1619 9 1 100 LSA KLQGQQSDL 1585 9 1 100 0.0019 LSA KLQGQQSDL 1126 9 1 100 LSA KQVNKEKEKFI 1868 11 1 100 LSA KTNRESIT 1698 8 1 100 LSA KTINIRESITT 1698 9 1 100 LSA KTNRESITNV 1698 11 1 100 LSA LAEDLYGRL 1648 9 1 100 LSA LAEDLYGRLEI 1648 11 1 100 LSA LIDEEEDDEDL 1772 11 1 100 LSA LIEICNENL 1809 8 1 100 LSA LIEKNENLDDL 1809 11 1 100 LSA LIFHJNGKI 17 9 1 100 LSA LIFHINGKII 17 10 1 100 0.0002 LSA LLIFHINGKI 16 10 1 100 LSA LLIFHINGKII 16 11 1 100 LSA LLRNLGVSENI 100 11 1 100 LSA LQEQQRDL 1620 8 1 100 LSA LQEQQSDL 1586 8 1 100 LSA LQEQQSDLERT 1178 11 1 100 LSA LQOQQSDL 1127 8 1 100 LSA LQIVDELSEDI 1892 11 1 100 LSA LTMSNVKNV 84 9 1 100 0.0010 LSA LVNLLIFHI 13 9 1 100 0.0006 LSA N1FLKENKL 109 9 1 100 LSA NIGIYKEL 1799 8 1 100 LSA NIGIYKELEDL 1799 11 1 100 LSA NISDVNDFQI 1748 10 1 100 LSA NLDDLDEGI 1815 9 1 100 LSA NLERKKEHGDY 1637 11 1 100 LSA NLGVSEN1 103 8 1 100 LSA NLOVSENIFL 103 10 1 100 LSA NLLIFHINGKI 15 11 1 100 LSA NVEGRRDI 1707 8 1 100 LSA NVKNVSQT 88 8 1 100 LSA NVSQTNFKSL 91 10 1 100 LSA NVSQTNFKSLL 91 11 1 100 LSA QISKYEDEI 1756 9 1 100 LSA QISKYEDEISA 1756 11 1 100 LSA QIVDELSEDI 1893 10 1 100 LSA QIVDELSEDIT 1893 11 1 100 LSA QQRDLEQERL 1606 10 1 100 LSA QQRDLEQERLA 1606 11 1 100 LSA QQRDLEQERRA 1538 11 1 100 LSA QQRDLEQRKA 1623 10 1 100 LSA QQSDLEQDRL 1385 10 1 100 LSA QQSDLEQDRLA 1385 11 1 100 LSA QQSDLEQERL 1589 10 1 100 LSA QQSDLEQDRLA 1589 11 1 100 LSA QQSDLEQERRA 1572 11 1 100 LSA QQSDLERT 1181 8 1 100 LSA QQ6DLERTKA 1181 10 1 100 LSA QQSDSEQERL 518 10 1 100 LSA QQSDSEQERLA 518 11 1 100 LSA QINFKSLL 94 8 1 100 LSA QTNFKSLLRNL 94 11 1 100 LSA QVNKEKEKFI 1869 10 1 100 LSA RLEIPA1EL 1655 9 1 100 LSA RQEDLEEKA 145 9 1 100 LSA RQEDLEEKAA 145 10 1 100 LSA RTKASKET 1187 8 1 100 LSA RTKASKETL 1187 9 1 100 LSA SADIQNHT 1736 8 1 100 LSA SADIQNHTL 1736 9 1 100 LSA SADIONITTLET 1736 11 1 100 LSA SAEYDDSL 1765 8 1 100 LSA SAEYDDSLI 1765 9 1 100 LSA SIIEKTNRESI I694 11 1 100 LSA SLLRNLGV 99 8 1 100 LSA SQTNFKSL 93 8 1 100 LSA SQTNFKSLL 93 9 1 100 LSA TLETVRISOV 1743 10 1 100 LSA TLQEQQSDL 1194 9 1 100 LSA TLQGQQSDL 157 9 1 100 LSA TMSNVKNV 85 8 1 100 LSA TMSNVICNVSQT 85 11 1 100 LSA TTNVEGRRDI 1705 10 1 100 LSA VLAEDLYGRL 1647 10 1 100 LSA VLSHNSYEKT 60 10 1 100 LSA YIPHQSSL 1672 8 1 100 LSA YISFYFIL 6 8 1 100 LSA YISFYFILV 6 9 1 100 0.0016 LSA YISFYFILVNL 6 11 1 100 SSP2 AATPYAGEPA 525 10 8 80 SSP2 ATPYAGEPA 526 9 8 80 SSP2 EILHEGCTSEL 267 11 8 80 SSP2 EVCNDEVDL 41 9 8 80 SSP2 EVCNDEVDLVL 41 11 8 80 SSP2 EVDLYLLM 46 8 8 80 SSP2 FVVPGAATPYA 520 11 8 80 SSP2 GAATPYAGEPA 524 11 8 80 SSP2 ILHEGCTSEL 268 10 8 80 SSP2 LLSTNLPYGRT 121 11 8 80 SSP2 NLPYGRTNL 125 9 8 80 SSP2 SIRRHNWVNHA 58 11 8 80 SSP2 STNLPYGRT 123 9 8 80 SSP2 STNLPYQRTNI 123 11 8 80 SSP2 VVPGAATPYA 521 10 8 80 SSP2 WVNHAVPL 64 8 8 80 SSP2 WVNHAVPLA 64 9 8 80 0.0008 SSP2 WVNHAVPLAM 64 10 8 80 SSP2 YAGEPAPFDET 529 11 8 80 SSP2 ALLQVRKHL 136 9 9 90 0.0010 SSP2 DALLQVRKHL 135 10 9 90 SSP2 DAWNKEKALI 106 11 9 90 SSP2 DQPRPRGDNFA 302 11 9 90 SSP2 EIKYREEV 35 8 9 90 SSP2 IQDSLKESRKL 168 11 9 90 SSP2 IVDEIKYREEV 32 11 9 90 SSP2 LLQVRKHL 137 8 9 90 SSP2 LQVRKHLNDRI 138 11 9 90 SSP2 QVRKHLNDRI 139 10 9 90 0.0001 SSP2 SLICESRKL 171 8 9 90 SSP2 ALLACAGL 509 8 10 100 SSP2 ALLACAGLA 509 9 10 100 0.0006 SSP2 AMICLIQQL 72 8 10 100 SSP2 AMICLIQQLNL 72 10 10 100 0.0006 SSP2 AVCVEVEKT 233 9 10 100 SSP2 AVCVEVEKTA 233 10 10 100 SSP2 AVFGIGQGI 186 9 10 100 0.0001 SSP2 AVFGIGQGINV 186 11 10 100 SSP2 AVPLAMKL 68 8 10 100 SSP2 AVPLAMKLI 68 9 10 100 0.0001 SSP2 CAGLAYKFV 513 9 10 100 SSP2 CAGLAYKFVV 513 10 10 100 0.0015 SSP2 CVEVEKTA 235 8 10 100 SSP2 DASKNKEKA 106 9 10 100 SSP2 DASKNKD(AL 106 10 10 100 SSP2 DLDEPEQFRL 546 10 10 100 0.0001 SSP2 DLFLVNGRDV 19 10 10 100 SSP2 DVQNNIVDEI 27 10 10 100 SSP2 EIIRLHSDA 99 9 10 100 SSP2 ELHEGCT 267 8 10 100 SSP2 ETLGEEDKDL 538 10 10 100 SSP2 EVEKTASCGV 237 10 10 100 SSP2 FLIFFDLFL 14 9 10 100 1.2000 SSP2 FLIFFDLFLV 14 10 10 100 0.8000 SSP2 FLVNGRDV 21 8 10 100 SSP2 FMKAVCVEV 230 9 10 100 0.0290 SSP2 FVVPQAAT 520 8 10 100 SSP2 GIAGGLAL 503 8 10 100 SSP2 GIAGGLALL 503 9 10 100 0.0022 SSP2 GIAGGLALLA 503 10 10 100 SSP2 GIGQGTNV 189 8 10 100 SSP2 GIGQGINVA 189 9 10 100 SSP2 GINVAFNRFL 193 10 10 100 SSP2 GINVAFNRFLV 193 11 10 100 SSP2 GIPDSIQDSL 163 10 10 100 SSP2 GLALLACA 507 8 10 100 SSP2 GLALLACAGL 507 10 10 100 0.0170 SSP2 GLALLACAGLA 507 11 10 100 SSP2 GLAYKFVV 515 8 10 100 SSP2 GLAYKFVVPGA 515 11 10 100 SSP2 GTRSRKREI 260 9 10 100 SSP2 GTRSRKREIL 260 10 10 100 SSP2 GVKIAVFGI 182 9 10 100 SSP2 GVWDEWSPCSV 245 11 10 100 SSP2 HAVPLAMKL 67 9 10 100 SSP2 HAVPLAMKLI 67 10 10 100 SSP2 HLGNVKYL 3 8 10 100 SSP2 HLGNVKYLV 3 9 10 100 0.0017 SSP2 HLGNVKYLVI 3 10 10 100 SSP2 HLGNVKYLVIV 3 11 10 100 SSP2 HLNDRINRENA 143 11 10 100 SSP2 HVPNSEDRET 445 10 10 100 SSP2 LAGGIAGGL 500 9 10 100 SSP2 IAGGIAGGLA 500 10 10 100 SSP2 IAGGIAGGLAL 500 11 10 100 SSP2 LAGGLALL 504 8 10 100 SSP2 LAGGLALLA 504 9 10 100 0.0001 SSP2 IACTGLALLACA 504 11 10 100 SSP2 IAVFGIGQGI 185 10 10 100 SSP2 IIRLHSDA 100 8 10 100 SSP2 ILTDGIPDSI 159 10 10 100 SSP2 IVFLIFFDL 12 9 10 100 0.0024 SSP2 IVFLIFFDLFL 12 11 10 100 SSP2 KAVCVEVEKT 232 10 10 100 SSP2 KAVCVEVEKTA 232 11 10 100 SSP2 KIAGGIAGGL 499 10 10 100 SSP2 KIAGGIAGGLA 499 11 10 100 SSP2 KIAVFGIGQI 184 11 10 100 SSP2 KLIQQLNL 74 8 10 100 SSP2 LACAGLAYKFV 511 11 10 100 SSP2 LALLACAGL 508 9 10 100 SSP2 LALLACAGLA 508 10 10 100 SSP2 LAMKLIQQL 71 9 10 100 SSP2 LAMKLIQQLNL 71 11 10 100 SSP2 LAYKFVVPGA 516 10 10 100 SSP2 LAYICFVVPGAA 516 11 10 100 SSP2 LIFFDLFL I5 8 10 100 SSP2 LIFFDLFLV 15 9 10 100 0.0890 SSP2 LLACAGLA 510 8 10 100 SSP2 LLMDCSGSI 51 9 10 100 0.0460 SSP2 LMDCSGSI 52 8 10 100 SSP2 LTDGIPDSI 160 9 10 100 SSP2 LVIVFLIFFDL 10 11 10 100 SSP2 LVNGRDVQNNI 22 11 10 100 SSP2 LVVILTDGI 156 9 10 100 SSP2 NANQLVVI 152 8 10 100 SSP2 NANQLVVIL 152 9 10 100 SSP2 NANQLVVILT 152 10 10 100 SSP2 NIPEDSEKEV 366 10 10 100 SSP2 NLYADSAWENV 213 11 10 100 SSP2 NQLVVILT 154 8 10 100 SSP2 NQLVVILTDGI 154 11 10 100 SSP2 NVAFNRFL 195 8 10 100 SSP2 NVAFNRFLV 195 9 10 100 0.0001 SSP2 NVIGPFMKA 225 9 I0 100 0.0002 SSP2 NVIGPFMKAV 225 10 10 100 0.0008 SSP2 NVKNVIGPFM 222 10 10 100 SSP2 NVKYLVIV 6 8 10 100 SSP2 NVKYLVIVFL 6 10 10 100 SSP2 NVKYLVIVFLI 6 11 10 100 SSP2 PAPFDETL 533 8 10 100 SSP2 PLANIKLIQQL 70 10 10 100 SSP2 QLVVILIDGI 155 10 10 100 0.0002 SSP2 RINRENANQL 147 10 10 100 SSP2 RINRENANQLV 147 11 10 100 SSP2 SAWENVKNV 218 9 10 100 0.0019 SSP2 SAWENVKNVI 218 10 10 100 SSP2 SIRRHNWV 58 8 10 100 SSP2 SQDNNGNRHV 437 10 10 100 SSP2 SVTCGKGT 254 8 10 100 SSP2 TLGEEDKDL 539 9 10 100 0.0001 SSP2 VAFNRFLV 196 8 10 100 SSP2 VIGPFMKA 226 8 10 100 SSP2 VIGPFMKAV 226 9 10 100 0.0004 SSP2 VIGPFMKAVCV 226 11 10 100 SSP2 VILTDGIPDSI 158 11 10 100 SSP2 VIVFLIFFDL 11 10 10 100 0.0038 SSP2 VQNNIVDEI 28 9 10 100 SSP2 VVILTDGI 157 8 10 100 SSP2 YADSAWENV 215 9 10 100 SSP2 YLLMDCSGSI 50 10 10 100 0.1700 SSP2 YLVIVFLI 9 8 10 100 Protein A*0202 A*0203 A*0206 A*6802 Seq. Id CSP 102 CSP 103 CSP 104 CSP 105 CSP 106 CSP 107 CSP 108 CSP 109 CSP 110 CSP 111 CSP 112 CSP 113 CSP 114 CSP 115 CSP 116 CSP 117 CSP 118 CSP 119 CSP 120 CSP 121 CSP 122 CSP 123 CSP 124 CSP 125 CSP 126 CSP 127 CSP 128 CSP 129 CSP 130 CSP 131 CSP 132 CSP 133 CSP 134 CSP 135 CSP 136 CSP 137 CSP 138 CSP 139 CSP 140 CSP 141 CSP 142 CSP 143 CSP 144 CSP 145 CSP 146 CSP 147 CSP 148 CSP 149 CSP 150 CSP 151 CSP 152 CSP 153 CSP 154 CSP 155 CSP 156 CSP 157 CSP 158 CSP 159 CSP 160 CSP 161 CSP 162 CSP 163 CSP 164 CSP 165 CSP 166 CSP 167 CSP 168 EXP 169 EXP 170 EXP 171 EXP 172 EXP 173 EXP 174 EXP 175 EXP 176 EXP 177 EXP 178 EXP 179 EXP 180 EXP 181 EXP 182 EXP 183 EXP 184 EXP 185 EXP 186 EXP 187 EXP 188 EXP 189 EXP 190 EXP 191 EXP 192 EXP 193 EXP 194 EXP 195 EXP 196 EXP 197 EXP 198 EXP 199 EXP 200 EXP 201 EXP 202 EXP 203 EXP 204 EXP 205 EXP 206 EXP 207 EXP 208 EXP 209 EXP 210 EXP 211 EXP 212 EXP 213 EXP 214 EXP 215 EXP 216 EXP 217 EXP 218 EXP 219 EXP 220 EXP 221 EXP 222 EXP 223 EXP 224 EXP 225 EXP 226 EXP 227 EXP 228 EXP 229 EXP 230 EXP 231 EXP 232 EXP 233 EXP 234 DT 235 EXP 236 EXP 237 EXP 238 EXP 239 EXP 240 EXP 241 LSA 242 LSA 243 LSA 244 LSA 245 LSA 246 LSA 247 LSA 248 LSA 249 LSA 250 LSA 251 LSA 252 LSA 253 LSA 255 LSA 256 LSA 257 LSA 258 LSA 259 LSA 260 LSA 261 LSA 262 LSA 263 LSA 264 LSA 265 LSA 266 LSA 267 LSA 268 LSA 269 LSA 270 LSA 271 LSA 272 LSA 273 LSA 274 LSA 275 LSA 276 LSA 277 LSA 278 LSA 279 LSA 280 LSA 281 LSA 282 LSA 283 LSA 284 LSA 285 LSA 286 LSA 287 LSA 288 LSA 289 LSA 290 LSA 291 LSA 292 LSA 293 LSA 294 LSA 295 LSA 296 LSA 297 LSA 298 LSA 299 LSA 300 LSA 301 LSA 302 LSA 303 LSA 304 LSA 305 LSA 306 LSA 307 LSA 308 LSA 309 LSA 310 LSA 311 LSA 312 LSA 313 LSA 314 LSA 315 LSA 316 LSA 317 LSA 318 LSA 319 LSA 320 LSA 321 LSA 322 LSA 323 LSA 324 LSA 325 LSA 326 LSA 327 LSA 328 LSA 329 LSA 330 LSA 331 LSA 332 LSA 333 LSA 334 LSA 335 LSA 336 LSA 337 LSA 338 LSA 339 LSA 340 LSA 341 LSA 342 LSA 343 LSA 344 LSA 345 LSA 346 LSA 347 LSA 348 LSA 349 LSA 350 LSA 351 LSA 352 LSA 353 LSA 354 LSA 355 LSA 356 LSA 357 LSA 258 LSA 359 LSA 360 LSA 361 LSA 362 LSA 363 LSA 364 LSA 365 LSA 366 LSA 367 LSA 368 LSA 369 LSA 370 LSA 371 LSA 372 LSA 373 LSA 374 LSA 375 LSA 376 LSA 377 LSA 378 LSA 379 LSA 380 LSA 381 LSA 382 LSA 383 LSA 384 LSA 385 LSA 386 LSA 387 LSA 388 LSA 389 LSA 390 LSA 391 LSA 392 LSA 393 LSA 394 LSA 395 LSA 396 LSA 397 LSA 398 LSA 399 LSA 400 LSA 401 LSA 402 LSA 403 LSA 404 LSA 405 SSP2 406 SSP2 407 SSP2 408 SSP2 409 SSP2 410 SSP2 411 SSP2 412 SSP2 413 SSP2 414 SSP2 415 SSP2 416 SSP2 417 SSP2 418 SSP2 419 SSP2 420 SSP2 421 SSP2 422 SSP2 423 SSP2 424 SSP2 425 SSP2 426 SSP2 427 SSP2 428 SSP2 429 SSP2 430 SSP2 431 SSP2 432 SSP2 433 SSP2 434 SSP2 435 SSP2 436 SSP2 437 SSP2 438 SSP2 439 SSP2 440 SSP2 441 SSP2 442 SSP2 443 SSP2 444 SSP2 445 SSP2 446 SSP2 447 SSP2 448 SSP2 449 SSP2 450 SSP2 451 SSP2 452 SSP2 453 SSP2 454 SSP2 455 SSP2 456 SSP2 457 SSP2 458 SSP2 459 SSP2 460 SSP2 461 SSP2 462 SSP2 463 SSP2 464 SSP2 465 SSP2 466 SSP2 467 SSP2 468 SSP2 469 SSP2 470 SSP2 471 SSP2 472 SSP2 473 SSP2 474 SSP2 475 SSP2 476 SSP2 477 SSP2 478 SSP2 479 SSP2 480 SSP2 481 SSP2 482 SSP2 483 SSP2 484 SSP2 485 SSP2 486 SSP2 487 SSP2 488 SSP2 489 SSP2 490 SSP2 491 SSP2 492 SSP2 493 SSP2 494 SSP2 495 SSP2 496 SSP2 497 SSP2 498 SSP2 499 SSP2 500 SSP2 501 SSP2 502 SSP2 503 SSP2 504 SSP2 505 SSP2 506 SSP2 507 SSP2 508 SSP2 509 SSP2 510 SSP2 511 SSP2 512 SSP2 513 SSP2 514 SSP2 515 SSP2 516 SSP2 517 SSP2 518 SSP2 519 SSP2 520 SSP2 521 SSP2 522 SSP2 523 SSP2 524 SSP2 525 SSP2 526 SSP2 327 SSP2 528 SSP2 529 SSP2 530 SSP2 531 SSP2 532 SSP2 533 SSP2 534 SSP2 535 SSP2 536 SSP2 337 SSP2 538 SSP2 339 SSP2 540 SSP2 541 SSP2 542 SSP2 543 SSP2 544 SSP2 545 SSP2 546 SSP2 547 SSP2 548 SSP2 549 SSP2 550 SSP2 551 SSP2 552 SSP2 553 SSP2 554 SSP2 555 SSP2 556 SSP2 557

TABLE IX Malaria A03 Super Motif Peptides With Binding Data No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*301 CSP DIEKKICK 402 8 19 100 CSP DIEKKICKMEK 402 11 19 100 CSP ELEMNYYGK 50 9 19 100 0.0001 CSP KLRKPKHK 104 8 19 100 CSP KLRKPKHKK 104 9 19 100 0.1300 CSP KLRKPKHKKLK 104 11 19 100 CSP NANANNAVK 335 9 16 84 0.0001 CSP NANPNANPNK 304 10 19 100 0.0005 CSP NMPNDPNR 323 8 19 100 CSP SVTCGNGIQVR 374 11 19 100 CSP VTCGNGIQVR 375 10 19 100 0.0005 CSP YSLKKNSR 63 8 19 100 EXP ALFFIIFNK 10 9 1 100 1.1000 EXP DLISDMIK 52 8 1 100 EXP DLISDMIKK 52 9 1 100 0.0001 EXP DVHDLISDMIK 49 11 1 100 EXP ELVEVNKR 63 8 1 100 EXP ELVEVNKRK 63 9 1 100 0.0001 EXP ELVEVNKRKSK 63 11 1 100 EXP ESLAEKTNK 19 9 1 100 0.0001 EXP EVNKRKSK 66 8 1 100 EXP EVNKRKSKYK 66 10 1 100 0.0005 EXP FLALFFIIFNK 8 11 1 100 EXP GLVLYNTEK 97 9 1 100 0.0069 EXP GLVLYNTEKGR 97 11 1 100 EXP GSGVSSKK 30 8 1 100 EXP GSGVSSKKK 30 9 1 100 0.0003 EXP GSGVSSKKKNK 30 11 1 100 EXP GTGSGVSSK 28 9 1 100 0.0039 EXP GTGSGVSSKK 28 10 1 100 0.0071 EXP GTGSGVSSKKK 28 11 1 100 EXP GVGLVLYNTEK 95 11 1 100 EXP GVSSKKKNK 32 9 1 100 0.0001 EXP GVSSKKKNKK 32 10 1 100 0.0011 EXP IIFNKESLAEK 14 11 1 100 EXP LALFFTIIFNK 9 10 1 100 0.014 EXP LISDMIKK 53 8 1 100 EXP LVEVNKRK 64 8 1 100 EXP LVEVNKRKSK 64 10 1 100 0.0005 EXP LVLYNTEK 98 8 1 100 EXP LVLYNTEKGR 98 10 1 100 0.0005 EXP NTEKGRHPFK 102 10 1 100 0.0047 EXP SLAEKTNK 20 8 1 100 EXP SSKKKNKK 34 8 1 100 EXP VLYNTEKGRS 99 9 1 100 0.0110 EXP VSSKKKNK 33 8 1 100 EXP VSSKKKNKK 33 9 1 100 0.0001 LSA AIELPSENER 1660 10 1 100 0.0001 LSA DIHKGHLEEK 1713 10 1 100 0.0004 LSA DIHKGHLEEKK 1713 11 1 100 LSA DITKYFMK 1901 8 1 100 LSA DLDEGIEK 1818 8 1 100 LSA DLEEKAAK 148 8 1 100 LSA DLEQDRLAK 1388 9 1 100 0.0001 LSA DLEQDRLAKEK 1388 11 1 100 LSA DLEQERLAK 1609 9 1 100 0.0001 LSA DLEQERLAKEK 1609 11 1 100 LSA DLEQERLANEK 1524 11 1 100 LSA DLEQERRAK 1575 9 1 100 0.0001 LSA DLEQERRAIUEK 1575 11 1 100 LSA DLEQRKADTK 1626 10 1 100 0.0001 LSA DLEQRKADTKK 1626 11 1 100 LSA DLERTICASK 1184 9 1 100 0.0001 LSA DSEQERLAK 521 9 1 100 0.0001 LSA CGEQERLAKEK 521 11 1 100 LSA DSKEISIIEK 1689 10 1 100 0.0001 LSA DTKKNLER 1633 8 1 100 LSA DTKKNLERK 1633 9 1 100 0.0001 LSA DTKKKNLERKK 1633 10 1 100 0.0001 LSA DVLAEDLYGR 1646 10 1 100 0.0001 LSA DVNDFQISK 1751 9 1 100 0.0001 LSA EIIKSNLR 33 8 1 100 LSA EISIIEKTNR 1692 10 1 100 0.0001 LSA ELEDLIEK 1805 8 1 100 LSA ELPSENER 1662 8 1 100 LSA ELSEDITK 1897 8 1 100 LSA ELSEEKIK 1829 8 1 100 LSA ELSEEKIKK 1829 9 1 100 0.0002 LSA ELSEEKIKKGK 1829 11 1 100 LSA ELTMSNVK 83 8 1 100 LSA ESITTNVEGR 1702 10 1 100 0.0001 LSA ESITTNVEGRR 1702 11 1 100 LSA FLKENKLNK 111 9 1 100 0.0260 LSA GSIKPEQK 1725 8 1 100 LSA GSIKPEQKEDK 1725 11 1 100 LSA GSSNSRNR 42 8 1 100 LSA GVSENIFLK 105 9 1 100 0.2700 LSA HIINDDDDK 126 9 1 100 0.0002 LSA HIINDDDDKK 126 10 1 100 0.0001 LSA HIINDDDDKKK 126 11 1 100 LSA HIKKYKNDK 1860 9 1 100 0.0002 LSA HINGKIIK 20 8 1 100 LSA HLEEKICDGSIK 1718 11 1 100 LSA HVLSHNSYEK 59 10 1 100 0.0170 LSA QNDDDDK 127 8 1 100 LSA IINDDDDKK 127 9 1 100 0.0002 LSA IINDDDDIUCK 127 10 1 100 0.0001 LSA ISDVNDFQISK 1749 11 1 100 LSA ISIIEKTNR 1693 9 1 100 0.0001 LSA ITTNVEGR 1704 8 1 100 LSA ITINVEGRR 1704 9 1 100 0.0002 LSA IVDELSEDMC 1894 11 1 100 LSA ICADIKKNLER 1631 10 1 100 0.0001 LSA KADTKKNLERK 1631 11 1 100 LSA KIIKNSEK 24 8 1 100 LSA ICQUCGKKYEK 1834 10 1 100 0.0081 LSA KLQEQQSDLER 1177 11 1 100 LSA KSLYDEHIK 1854 9 1 100 0.0005 LSA KSLYDEHIKIC 1854 10 1 100 0.0094 LSA KSSEELSEEK 1825 10 1 100 0.0001 LSA KTKDNNFK 1843 8 1 100 LSA KTKNNENNK 68 9 1 100 0.0028 LSA LAEDLYGR 1648 8 1 100 LSA LAKEKLQEQQR 1615 11 1 100 LSA LANEKLQEQQR 1530 11 1 100 LSA LIFHINGK 17 8 1 100 LSA LIGHINKKIIK 17 11 1 100 LSA LLIFHINKGK 16 9 1 100 0.0260 LSA LSEDITKYFMK 1898 11 1 100 LSA LSEEKIKK 1830 8 1 100 LSA LSEEKIKKGK 1830 10 1 100 0.0004 LSA LSEEKIKKGKK 1830 11 1 100 LSA LSHNSYEK 61 8 1 100 LSA LSHNSYEKTK 61 10 1 100 0.0004 LSA NIFLKENK 109 8 1 100 LSA NKFLKENKLNK 109 11 1 100 LSA LNDDLDEGIEK 1815 11 1 100 LSA NLGVSENTFLK 103 11 1 100 LSA NLLIGHINGK 15 10 1 100 0.0049 LSA NLRSGSSNSR 38 10 1 100 0.0004 LSA NSEKDETIK 28 9 1 100 0.0002 LSA NSRNRINEEK 45 10 1 100 0.0004 LSA NVEGRRDIHK 1707 10 1 100 0.0004 LSA NVKNVSQTNFK 88 11 1 100 LSA NVSQTNFK 91 8 1 100 LSA PAIELPSENER 1659 11 1 100 LSA QSDLEQDR 1386 8 1 100 LSA QSDLEQDRLAK 1386 11 1 100 LSA QSKLEQER 1590 8 1 100 LSA QSDLEQERLAK 1590 11 1 100 LSA QSKLEQERR 1573 9 1 100 0.0002 LSA QSDLEQERRAK 1573 11 1 100 LSA QSDLERTK 1182 8 1 100 LSA QSDLERTKASK 1182 11 1 100 LSA QSDSEQER 519 8 1 100 LSA QSDSEQERLAK 519 11 1 100 LSA QSSLPQDNR 1676 9 1 100 0.0002 LSA QTNFKSLLR 94 9 1 100 0.0320 LSA QVNKEKEK 1869 8 1 100 LSA QVNKEKEKFIK 1869 11 1 100 LSA RINEEKHEK 49 9 1 100 0.0033 LSA RINEEKHEKK 49 10 1 100 0.0024 LSA RSGSSNSR 40 8 1 100 LSA RSGSSNSRNR 40 10 1 100 0.0011 LSA SIIEKTNR 1694 8 1 100 LSA SIKPEQKEDK 1726 10 1 100 0.0002 LSA SITTNVEGR 1703 9 1 100 0.0002 LSA SITTNVEGRR 1703 10 1 100 0.0002 LSA SLPQDNRDNSR 1678 11 1 100 LSA SLYDEHIK 1855 8 1 100 LSA SLYDEHIKK 1855 9 1 100 0.0460 LSA SLYDEHIKKYK 1855 11 1 100 LSA SSEELSEEK 1826 9 1 100 0.0002 LSA SSEELSEEKIK 1826 11 1 100 LSA SSLPQDNR 1677 8 1 100 LSA TTNVEGRR 1705 8 1 100 LSA VLAEDLYGR 1647 9 1 100 0.0013 LSA VLSHNSYEK 60 9 1 100 0.0280 LSA VLSHNSYEKTK 60 11 1 100 LSA VSENTIFLK 106 8 1 100 LSA VSENIFLKENK 106 11 1 100 LSA VSQTNFKSLLR 92 11 1 100 LSA YIKGQDENR 137 9 1 100 0.0025 SSP2 ALLACAGLAYK 509 11 10 100 SSP2 AVCVEVEK 233 8 10 100 SSP2 CSVTCGKGTR 253 10 10 100 0.0002 SSP2 DALLQVRK 135 8 9 90 SSP2 DASKNKEK 106 8 10 100 SSP2 DIPKKPENK 392 9 10 100 0.0004 SSP2 DLDEPEQFR 546 9 10 100 0.0002 SSP2 DLFLVNGR 19 8 10 100 SSP2 DSAWENVK 217 8 10 100 SSP2 DSIQDSLK 166 8 10 100 SSP2 DSIQDSLKESR 166 11 10 100 SSP2 DSLKESRK 170 8 9 90 SSP2 DVPKNPEDDR 378 10 10 100 0.0002 SSP2 DVQNNIVDEIK 27 11 10 100 SSP2 EIIRLHSDASK 99 11 10 100 SSP2 ELQEQCEEER 276 10 8 80 0.0002 SSP2 ETLGEEDK 538 8 10 100 SSP2 EVPSDVPK 374 8 10 100 SSP2 FLVGCHPSDCK 201 11 10 100 SSP2 FMKAVCVEVEK 230 11 10 100 SSP2 GINVAFNR 193 8 10 100 SSP2 GIPDSIQDSLK 163 11 10 100 SSP2 HAVPLAMK 67 8 10 100 SSP2 HLNDRINR 143 8 10 100 SSP2 HSDASKNK 104 8 10 100 SSP2 HSDASKNKEK 104 10 10 100 0.0004 SSP2 HVPNSEDR 445 8 10 100 SSP2 HVPNSEDRETR 445 11 9 90 SSP2 IIRLHSDASK 100 10 10 100 0.0230 SSP2 1VDEIKYR 32 8 9 90 SSP2 KAVCVEVEK 232 9 10 100 0.0004 SSP2 KVLDNERK 421 8 8 80 SSP2 LACAGLAYK 511 9 10 100 0.0240 SSP2 LLACAGLAYK 510 10 10 100 0.9500 SSP2 LLMDCSGSIR 51 10 10 100 0.0004 SSP2 LLMDCSGSIRR 51 11 10 100 SSP2 LLQVRKHLNDR 137 11 9 90 SSP2 LLSTNLPYGR 121 10 8 80 0.0017 SSP2 LMDCSGSIR 52 9 10 100 0.0004 SSP2 LMDCSGSIRR 52 10 10 100 0.0015 SSP2 LSTNLPYGR 122 9 8 80 0.0004 SSP2 LVGCHPSDGK 202 10 10 100 0.0004 SSP2 NIPEDSEK 366 8 10 100 SSP2 NIVDEIKYR 31 9 9 90 0.0005 SSP2 NLPNDKSDR 406 9 10 100 0.0005 SSP2 NSEDRETFT 448 8 9 90 SSP2 NVIGPFMK 225 8 10 100 SSP2 NVICNVIGPFMK 222 11 10 100 SSP2 PSPNPEEGK 328 9 10 100 0.0005 SSP2 QSQDNNGNR 436 9 10 100 0.0005 SSP2 QVRKHLNDR 139 9 9 90 0.0005 SSP2 RLHSDASK 102 8 10 100 SSP2 RLHSDASKNK 102 10 10 100 0.0240 SSP2 SIQDSLKESR 167 10 10 100 0.0004 SSP2 SIQDSLKESRK 167 11 9 90 SSP2 SLLSTNLPYGR 120 11 8 80 SSP2 STNLPYGR 123 8 8 80 SSP2 SVTCGKGTR 254 9 10 100 0.0005 SSP2 SVTCGKGTRSR 254 11 10 100 SSP2 VTCGKGTR 255 8 10 100 SSP2 VPCGKGTISR 255 10 10 100 0.0004 SSP2 VTCGKGTRSRK 255 11 10 100 SSP2 WSPCSVTCGK 250 10 10 100 0.0004 SSP2 WVNHAVPLAMK 64 11 8 80 SSP2 YADSAWENVK 215 10 10 100 0.0004 SSP2 YLLMDCSGSIR 50 11 10 100 Protein A*1101 A*3101 A*3301 A*6801 Seq id. CSP 558 CSP 559 CSP 0.0003 560 CSP 561 CSP 0.0037 562 CSP 563 CSP 0.0002 0.0006 0.0096 0.0210 564 CSP 0.0021 0.0009 0.0009 0.0054 565 CSP 566 CSP 567 CSP 0.0340 568 CSP 569 EXP 1.2000 570 EXP 571 EXP 0.0003 572 EXP 573 EXP 574 EXP 0.0002 575 EXP 576 EXP 0.0002 0.0004 0.0110 0.0260 577 EXP 578 EXP 0.0002 579 EXP 580 EXP 0.0055 581 EXP 582 EXP 583 EXP 0.0065 0.0004 0.0010 0.0002 584 EXP 585 EXP 0.0180 586 EXP 0.0340 587 EXP 588 EXP 589 EXP 0.0002 590 EXP 0.0002 591 EXP 592 EXP 0.0530 0.0072 0.0076 0.0039 593 EXP 594 EXP 595 EXP 0.0002 596 EXP 597 EXP 0.0002 598 EXP 0.0080 599 EXP 600 EXP 601 EXP 0.0007 0.0039 0.0055 0.0022 602 EXP 603 EXP 0.0002 0.0004 0.0010 0.0002 604 LSA 0.0002 0.0009 0.0008 0.0029 605 LSA 0.0002 0.0009 0.0055 0.0046 606 LSA 607 LSA 608 LSA 609 LSA 610 LSA 0.0002 611 LSA 612 LSA 0.0002 613 LSA 614 LSA 615 LSA 0.0002 616 LSA 617 LSA 0.0002 618 LSA 619 LSA 0.0002 620 LSA 0.0002 0.0004 0.0010 0.0002 621 LSA 622 LSA 0.0002 623 LSA 624 LSA 0.0002 625 LSA 0.0002 626 LSA 0.0002 627 LSA 0.0018 628 LSA 629 LSA 0.0002 630 LSA 631 LSA 632 LSA 633 LSA 634 LSA 0.0002 635 LSA 636 LSA 637 LSA 0.0002 638 LSA 639 LSA 0.0005 640 LSA 641 LSA 642 LSA 643 LSA 0.6600 644 LSA 0.0002 645 LSA 0.0002 0.0009 0.0009 0.0003 646 LSA 647 LSA 0.0002 648 LSA 649 LSA 650 LSA 0.0140 651 LSA 652 LSA 0.0002 653 LSA 0.0002 654 LSA 655 LSA 0.0008 0.0320 0.0150 0.0054 656 LSA 657 LSA 0.0007 0.0025 0.0043 0.3200 658 LSA 659 LSA 0.0002 0.0086 0.0011 0.0003 660 LSA 661 LSA 662 LSA 0.0007 0.0042 0.0009 0.0003 663 LSA 664 LSA 0.0340 0.0004 0.0010 0.0002 665 LSA 0.0490 666 LSA 0.0009 667 LSA 668 LSA 0.0038 669 LSA 670 LSA 671 LSA 672 LSA 673 LSA 674 LSA 0.0100 675 LSA 676 LSA 677 LSA 0.0002 678 LSA 679 LSA 680 LSA 0.0002 681 LSA 682 LSA 683 LSA 684 LSA 685 LSA 0.0008 686 LSA 0.0002 687 LSA 0.0002 0.0004 0.0010 0.0002 688 LSA 0.0002 689 LSA 0.0002 690 LSA 691 LSA 692 LSA 692 LSA 694 LSA 695 LSA 696 LSA 697 LSA 0.0002 0.0006 0.0005 0.0005 698 LSA 699 LSA 700 LSA 701 LSA 702 LSA 703 LSA 0.0013 0.0150 0.014 0.0480 704 LSA 0.0440 0.0820 0.0180 0.1300 705 LSA 706 LSA 707 LSA 0.0370 708 LSA 0.0018 0.0009 0.0009 0.0003 709 LSA 710 LSA 0.0002 711 LSA 712 LSA 0.0002 0.0009 0.0009 0.0003 713 LSA 0.0027 714 LSA 0.0002 715 LSA 716 LSA 717 LSA 0.4100 718 LSA 719 LSA 0.0017 0.0004 0.0010 0.0002 720 LSA 721 LSA 722 LSA 723 LSA 0.0004 0.0083 0.0220 0.0032 724 LSA 0.0280 725 LSA 726 LSA 727 LSA 728 LSA 729 LSA 0.0002 730 SSP2 731 SSP2 732 SSP2 0.0002 733 SSP2 734 SSP2 735 SSP2 0.0002 736 SSP2 0.0002 0.0004 0.0170 0.0002 737 SSP2 738 SSP2 739 SSP2 740 SSP2 741 SSP2 742 SSP2 0.0002 743 SSP2 744 SSP2 745 SSP2 0.0002 746 SSP2 747 SSP2 748 SSP2 749 SSP2 750 SSP2 751 SSP2 752 SSP2 753 SSP2 754 SSP2 755 SSP2 0.0002 756 SSP2 757 SSP2 758 SSP2 0.0002 0.0009 0.0009 0.0013 759 SSP2 760 SSP2 0.0076 0.0009 0.0005 0.0029 761 SSP2 762 SSP2 0.0290 0.0150 0.3200 0.1100 763 SSP2 0.0870 764 SSP2 0.0005 765 SSP2 766 SSP2 767 SSP2 0.0025 768 SSP2 0.0002 0.0370 0.0430 0.0010 769 SSP2 0.0002 770 SSP2 0.0100 0.2900 0.0760 0.2700 771 SSP2 0.0002 772 SSP2 773 SSP2 0.0002 774 SSP2 0.0002 775 SSP2 776 SSP2 777 SSP2 778 SSP2 0.0002 0.0004 0.0010 0.0002 779 SSP2 0.0002 0.0020 0.0093 0.0018 780 SSP2 0.0002 0.0041 0.0570 0.0002 781 SSP2 782 SSP2 0.0002 783 SSP2 0.0009 784 SSP2 785 SSP2 786 SSP2 787 SSP2 0.0009 0.0031 0.0039 0.0310 788 SSP2 789 SSP2 790 SSP2 0.0017 791 SSP2 792 SSP2 0.0002 793 SSP2 794 SSP2 0.0002 0.0009 0.0009 0.0077 795 SSP2 796

TABLE X Malaria A24 Super Motif Peptides With Binding Information No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*201 Seq Id. CSP AILSVSSF 6 8 18 95 797 CSP AILSVSSFL 6 9 19 100 798 CSP AILSVSSFLF 6 10 19 100 799 CSP ALFQEYQCY 18 9 19 100 800 CSP CYGSSSNTRVL 25 11 19 100 801 CSP DIEKKICKM 402 9 19 100 802 CSP DYENDIEKKI 398 10 18 95 803 CSP ELNYDNAGI 37 9 18 95 804 CSP ELNYDNAGINL 37 11 18 95 805 CSP EMNYYGKQENW 52 11 19 100 806 CSP FLFVEALF 13 8 19 100 807 CSP FLFVEALFQEY 13 11 19 100 808 CSP FVEALFQEY 15 9 19 100 809 CSP GINLYNEL 44 8 18 95 810 CSP GINLYNELEM 44 10 18 95 811 CSP GLIMVLSF 425 8 19 100 812 CSP GLIMVLSFL 425 9 19 100 813 CSP GLIMVLSFLF 425 10 19 100 814 CSP GLIMVLSFLFL 425 11 19 100 815 CSP HIEQYLKKI 350 9 15 79 816 CSP ILSVSSFL 7 8 19 100 817 CSP ILSVSSFLF 7 9 19 100 818 CSP IMVLSFLF 427 8 19 100 819 CSP IMVLSFLFL 427 9 19 100 0.0008 820 CSP KIQNSLSTEW 361 10 15 79 821 CSP KLAILSVSSF 4 10 19 100 822 CSP KLAILSVSSFL 4 11 19 100 823 CSP KLRKPICHICKL 104 10 19 100 824 CSP KMEKCSSVF 409 9 19 100 825 CSP LFQEYQCY 19 8 19 100 826 CSP LFVEALFQEY 14 10 19 100 827 CSP LIMVLSFL 426 8 19 100 828 CSP LIMVLSFLF 426 9 19 100 829 CSP LIMVLSFLFL 426 10 19 100 830 CSP LYNELEMNY 47 9 19 100 831 CSP LYNELEMNYY 47 10 19 100 832 CSP MMRKLAIL 1 8 19 100 833 CSP MVLSFLFL 428 8 19 100 834 CSP NLYNELEM 46 8 19 100 835 CSP NLYNELEIINY 46 10 19 100 836 CSP NLYNELINNYY 46 11 19 100 837 CSP NTRVLNEL 31 8 19 100 838 CSP NTRYLNELNY 31 10 19 100 839 CSP NVVNSSIGL 418 9 19 100 840 CSP NVVNSSIGLI 418 10 19 100 841 CSP NVVNSSIGLIM 418 11 19 100 842 CSP NYDNAGINL 39 9 18 95 0.0004 843 CSP NYDNAGINLY 39 10 18 95 844 CSP NYYGKQENW 54 9 19 100 845 CSP NYYGKQENWY 54 10 19 100 846 CSP RVLNELNY 33 8 19 100 847 CSP SFLFVEAL 12 8 19 100 848 CSP SFLFVEALF 12 9 19 100 849 CSP SIGLIMVL 423 8 19 100 850 CSP SIGLIMVLSF 423 10 19 100 851 CSP SIGLIMVLSFL 423 11 19 100 852 CSP SLKKNSRSL 64 9 19 100 853 CSP SVFNVVNSSI 415 10 19 100 854 CSP SVSSFLFVEAL 9 11 19 100 855 CSP SVTCGNGI 374 8 19 100 856 CSP VFNVVNSSI 416 9 19 100 857 CSP VFNVVNSSIGL 416 11 19 100 858 CSP VTCGNGIQVRI 375 11 19 100 859 CSP VVNSSIGL 419 8 19 100 860 CSP VVNSSIGLI 419 9 19 100 861 CSP VVNSSIGL1M 419 10 19 100 862 CSP WYSLKKNSRSL 62 11 19 100 863 CSP YLKKIQNSL 358 9 15 79 864 CSP YYGKQENW 55 8 19 100 865 CSP YYGKQENWY 55 9 19 100 866 CSP YYGKQENWYSL 55 11 19 100 867 EXP ATSVLAGL 77 8 1 100 868 EXP ATSVLAGLL 77 9 1 100 869 EXP DMIKKEEEL 56 9 1 100 870 EXP DVHDLISDM 49 9 1 100 871 EXP DVHDLISDMI 49 10 1 100 872 EXP EVNKRKSKY 66 9 1 100 873 EXP EVNKRICSKYKL 66 11 1 100 874 EXP FFIIFNKESL 12 10 1 100 875 EXP FFLALFFI 7 8 1 100 876 EXP FFLALFFII 7 9 1 100 877 EXP FFLALFFIIF 7 10 1 100 878 EXP FITFNKESL 13 9 1 100 879 EXP FLALFFII 8 8 1 100 880 EXP FLALFFIIF 8 9 1 100 881 EXP GLLGNVSTVL 83 10 1 100 882 EXP GLLGNVSTVLL 83 11 1 100 883 EXP IIFNKESL 14 8 1 100 884 EXP ILSVFFLAL 3 9 1 100 885 EXP ILSVFFLALF 3 10 1 100 886 EXP ILSVFFLALFF 3 11 1 100 887 EXP KILSVFFL 2 8 1 100 888 EXP KILSVFFLAL 2 10 1 100 889 EXP KILSVFFLALF 2 11 1 100 890 EXP KLATSVLAGL 75 10 1 100 891 EXP KLATSVLAGLL 75 11 1 100 892 EXP KYKLATSVL 73 9 1 100 0.0960 893 EXP LFFIIFNICESL 11 11 1 100 894 EXP LIDVHDLI 47 8 1 100 895 EXP LIDVHDLISDM 47 11 1 100 896 EXP LLGGVGLVL 92 9 1 100 897 EXP LLGGVGLVLY 92 10 1 100 898 EXP LLGNVSTVL 84 9 1 100 899 EXP LLGNVSTVLL 84 10 1 100 900 EXP LVEVNICRICSKY 64 11 1 100 901 EXP LYNTEKGRHPF 100 11 1 100 902 EXP MIKKEEEL 57 8 1 100 903 EXP NTEKGRHPF 102 9 1 100 904 EXP NTEKGRHPFKI 102 11 1 100 905 EXP PLIDVHDL 46 8 1 100 906 EXP PLIDVHDLI 46 9 1 100 907 EXP STVLLGGVGL 89 10 1 100 908 EXP SVFFLALF 5 8 1 100 909 EXP SVFFLALFF 5 9 1 100 910 EXP SVFFLALFFI 5 10 1 100 911 EXP SVFFLALFFII 5 11 1 100 912 EXP TVLLGGVGL 90 9 1 100 913 EXP TVLLGGVQLVL 90 11 1 100 914 EXP VFFLALFF 6 8 1 100 915 EXP VFFLALFFI 6 9 1 100 916 EXP VFFLALFFII 6 10 1 100 917 EXP VFFLALFFIIF 6 11 1 100 918 EXP VLLCrGVGL 91 8 1 100 919 EXP VLLGGVGLVL 91 10 1 100 920 EXP VLLGGVGLVLY 91 11 1 100 921 LSA DFQISKYEDEI 1754 11 1 100 922 LSA DITKYFMKI 1901 9 1 100 923 LSA DLDEFKPI 1781 8 1 100 924 LSA DLDEFKFIVQY 1781 11 1 100 925 LSA DLEEXAAKETL 148 11 1 100 926 LSA DLIEXNENL 1808 9 1 100 927 LSA DLYGRLEI 1651 8 1 100 928 LSA DLYGRLEIPAI 1651 11 1 100 929 LSA DVLAEDLY 1646 8 1 100 930 LSA DVLAEDLYGRL 1646 11 1 100 931 LSA DVNDFQISKY 1751 10 1 100 932 LSA EFXPIVQY 1784 8 1 100 933 LSA EFKPIVQYDNF 1784 11 1 100 934 LSA ERQIVDEL 1890 9 1 100 935 LSA EISAEYDDSL 1763 10 1 100 936 LSA EISAEYDDSLI 1763 11 1 100 937 LSA ELPSENERGY 1662 10 1 100 938 LSA ELPSENERGYY 1662 11 1 100 939 LSA ELSEDTIKY 1897 9 1 100 940 LSA ELSEDTIKYF 1897 10 1 100 941 LSA ELSEDIDCYFM 1897 11 1 100 942 LSA ETLQBQQSDL 1193 10 1 100 943 LSA ETLQGQQSDL 156 10 1 100 944 LSA ETVNISDVNDF 1745 11 1 100 945 LSA FFDKDKEL 77 8 1 100 946 LSA FFDKDKELTM 77 10 1 100 947 LSA FIKSLFHI 1877 8 1 100 948 LSA FIKSLFH1F 1877 9 1 100 949 LSA FILVNLLI 11 8 1 100 950 LSA FILVNLLIF 11 9 1 100 951 LSA FILVNLLIFHI 11 11 1 100 952 LSA FYF1LVNL 9 8 1 100 953 LSA FYFILVNLL 9 9 1 100 7.5000 954 LSA FYFILVNLLI 9 10 1 100 955 LSA FYFILVNLLIF 9 11 1 100 956 LSA GIEKSSEEL 1822 9 1 100 957 LSA GIYKELEDL 1801 9 1 100 958 LSA GIYKELEDL1 1801 10 1 100 959 LSA GVSEN1FL 105 8 1 100 960 LSA GYYIPHQSSL 1670 10 1 100 0.0074 961 LSA HIFDGDNEI 1883 9 1 100 962 LSA HIFDGDNEIL 1883 10 1 100 963 LSA HILYISFY 3 8 1 100 964 LSA HILYISFYF 3 9 1 100 965 LSA NILYISFYFI 3 10 1 100 966 LSA LIILYISFYFIL 3 11 1 100 967 LSA HLEEKKDOS1 1718 10 1 100 968 LSA FITLETVNI 1742 8 1 100 969 LSA HVLSHNSY 59 8 1 100 970 LSA IFDGDNEI 1884 8 1 100 971 LSA IFDGDNEIL 1884 9 1 100 972 LSA IFDODNEILQI 1884 11 1 100 973 LSA IFHINGKI 18 8 1 100 974 LSA IFHINGKII 18 9 1 100 975 LSA IFLKENKL 110 8 1 100 976 LSA IIEKTNRESI 1695 10 1 100 977 LSA IIKNSEKDEI 25 10 1 100 978 LSA IIKNSEKDEII 25 11 1 100 979 LSA IINDDDDYKKY 127 11 1 100 980 LSA ILQIVDEL 1891 8 1 100 981 LSA ILVNLLIF 12 8 1 100 982 LSA ILVNLLIFHI 12 10 1 100 983 LSA ILYISFYF 4 8 1 100 984 LSA ILYISFYFI 4 9 1 100 985 LSA ILYISFYFIL 4 10 1 100 986 LSA IIKYFMKL 1902 8 1 100 987 LSA ITINVEGRRDI 1704 11 1 100 988 LSA IVDELSEDI 1894 9 1 100 989 LSA IYKELEDL 1802 8 1 100 990 LSA IYKELEDLI 1802 9 1 100 991 LSA KFFDKDKEL 76 9 1 100 992 LSA KFFDKDKELTM 76 11 1 100 993 LSA KFIKSLFHI 1876 9 1 100 994 LSA KFIKSLFHIF 1876 10 1 100 995 LSA KIIKNSEKDEI 24 11 1 100 996 LSA KIKKGKKY 1834 8 1 100 997 LSA KLNKEGKL 116 8 1 100 998 LSA KLNKEGKLI 116 9 1 100 999 LSA KLQEQQRDL 1619 9 1 100 1000 LSA KLQEQQSDL 1585 9 1 100 1001 LSA KLQGQQSDL 1126 9 1 100 1002 LSA KTKNNENNKF 68 10 1 100 1003 LSA KTKNNENNKFF 68 11 1 100 1004 LSA KYEDEISAEY 1759 10 1 100 1005 LSA KYEKTKDNNF 1140 10 1 100 0.0004 1006 LSA LFHTFDODNEI 1881 11 1 100 1007 LSA LIDEEEDDEDL 1772 11 1 100 1008 LSA LISCNENL 1809 8 1 100 1009 LSA LIEKNENLDDL 1809 11 1 100 1010 LSA LIFHINGKI 17 9 1 100 1011 LSA LIFHINGKII 17 10 1 100 1012 LSA LLIFHINGKI 16 10 1 100 1013 LSA LLIFHINGKII 16 11 1 100 1014 LSA LLRNLGVSENI 100 11 1 100 1015 LSA LVNLLIFHI 13 9 1 100 1016 LSA LYDEHIKKY 1856 9 1 100 1017 LSA LYGRLEIPAI 1652 10 1 100 1018 LSA LYISFYFI 5 8 1 100 1019 LSA LYISFYFIL 5 9 1 100 0.0088 1020 LSA NFIONDKSL 1848 9 1 100 1021 LSA NFKPNDKSLY 1848 10 1 100 1022 LSA NFKSLLRNL 96 9 1 100 1023 LSA NFQDEENI 1793 8 1 100 1024 LSA NFQDEENIGI 1793 10 1 100 1025 LSA NFQDEENIG1Y 1793 11 1 100 1026 LSA NIFLKENKL 109 9 1 100 1027 LSA MGIYKEL 1799 8 1 100 1028 LSA MGIYKELEDL 1799 11 1 100 1029 LSA MSDVNDF 1748 8 1 loo 1030 LSA NISDVNDFQI 1748 10 1 100 1031 LSA NLDDLDEGI 1815 9 1 100 1032 LSA NLGVSENI 103 8 1 100 1033 LSA NLGVSENIF 103 9 1 100 1034 LSA NLGVSEN1FL 103 10 1 100 1035 LSA NLLIFHINGKI 15 11 1 100 1036 LSA NVEGRRDI 1707 8 1 100 1037 LSA NVKNVSQTNF 88 10 1 100 1038 LSA NVSQTNFKSL 91 10 1 100 1039 LSA NVSQTNFKSLL 91 11 1 100 1040 LSA PIVQYDNF 1787 8 1 100 1041 LSA QISKYEDEI 1756 9 1 100 1042 LSA QtVDELSEDI 1893 10 1 100 1043 LSA QTNFKSLL 94 8 1 100 1044 LSA QTNFKSLLFINL 94 11 1 100 1045 LSA QVNKEKEKF 1869 9 1 100 1046 LSA QVNKEKEKF1 1869 10 1 100 1047 LSA QYDNFQDEENI 1790 11 1 100 1048 LSA RLEIPAIEL 1655 9 1 100 1049 LSA RIKASKETL 1187 9 1 100 1050 LSA SFYFILVNL 8 9 1 100 1051 LSA SFYFILVNLL 8 10 1 100 1052 LSA SFYFILVNLLI 8 11 1 100 1053 LSA SIIEKTNRESI 1694 11 1 100 1054 LSA SLYDEHIKKY 1855 10 1 100 1055 LSA TLQEQQSDL 1194 9 1 100 1056 LSA TLQGQQSDL 157 9 1 100 1057 LSA TTNVEGRRDI 1705 10 1 100 1058 LSA TVNISDVNDF 1746 10 1 100 1059 LSA VLAEDLYGRL 1647 10 1 100 1060 LSA YFILVNLL 10 8 1 100 1061 LSA YFILVNLLI 10 9 1 100 1062 LSA YFILVNLLIF 10 10 1 100 1063 LSA YIPHQSSL 1672 8 1 100 1064 LSA YISFYFIL 6 8 1 100 1065 LSA YISFYFILVNL 6 11 1 100 1066 LSA YYIPHQSSL 1671 9 1 100 4.3000 1067 SSP2 ALLACAGL 509 8 10 100 1068 SSP2 ALLACAGLAY 509 10 10 100 1069 SSP2 ALLQVRKHL 136 9 9 90 1070 SSP2 AMKLIQQL 72 8 10 100 1071 SSP2 AMKLIQQLNL 72 10 10 100 0.0006 1072 SSP2 ATPYAGEPAPF 526 11 8 80 1073 SSP2 AVFGIGQI 186 9 10 100 1074 SSP2 AVPLAMKL 68 8 10 100 1075 SSP2 AVPLAMKLI 68 9 10 100 1076 SSP2 AWENVKNVI 219 9 10 100 1077 SSP2 DLDEPEQF 546 8 10 100 1078 SSP2 DLDEPEQFRL 546 10 10 100 1079 SSP2 DVQNNIVDEI 27 10 10 100 1080 SSP2 EILHEGCTSEL 267 11 8 80 1081 SSP2 ETLGEEDKDL 538 10 10 100 1082 SSP2 EVCNDEVDL 41 9 8 80 1083 SSP2 EVCNDEVDLY 41 10 8 80 1084 SSP2 EVCNDEVDLYL 41 11 8 80 1085 SSP2 EVDLYLLM 46 8 8 80 1086 SSP2 EVEKTASCGVW 237 11 10 100 1087 SSP2 FLIFFDLF 14 8 10 100 1088 SSP2 FLIFFDLFL 14 9 10 100 1089 SSP2 FVVPGAATPY 520 10 8 80 1090 SSP2 GIAGGLAL 503 8 10 100 1091 SSP2 GIAGGLALL 503 9 10 100 1092 SSP2 GIGQGINVAF 189 10 10 100 1093 SSP2 GINVAFNRF 193 9 10 100 1094 SSP2 GNVAFNRFL 193 10 10 100 1095 SSP2 GIPDSIQDSL 163 10 10 100 1096 SSP2 GLALLACAGL 507 10 10 100 1097 SSP2 GTRSRXREI 260 9 10 100 1098 SSP2 GTRSRKREIL 260 10 10 100 1099 SSP2 GVKIAVFGI 182 9 10 100 1100 SSP2 HLGNVKYL 3 8 10 100 1101 SSP2 HLGNVKYLVI 3 10 10 100 1102 SSP2 ILHEOCTSEL 268 10 8 80 1103 SSP2 ILTDGIPDSI 159 10 10 100 1104 SSP2 IVFLWFDL 12 9 10 100 1105 SSP2 IVFLIFFDLF 12 10 10 100 1106 SSP2 IVFLIFFDLFL 12 11 10 100 1107 SSP2 KFVVPGAATPY 519 11 8 80 1108 SSP2 KIAGGIAGOL 499 10 10 100 1109 SSP2 KIAVFGIGQGI 184 11 10 100 1110 SSP2 KLIQQLNL 74 8 10 100 1111 SSP2 KTASCGVW 240 8 10 100 1112 SSP2 KTASCGVWDEW 240 11 10 100 1113 SSP2 KYKIAGGI 497 8 9 90 1114 SSP2 KYLVIVFL 8 8 10 100 1115 SSP2 KYLVIVFLI 8 9 10 100 4.6000 1116 SSP2 KYLVIVFLIF 8 10 10 100 0.0003 1117 SSP2 KYLVIVFLIFF 8 11 10 100 1118 SSP2 LIFFDLFL 15 8 10 100 1119 SSP2 LLACAGLAY 510 9 10 100 1120 SSP2 LLACAGLAYKF 510 11 10 100 1121 SSP2 LLMDCSGSI 51 9 10 100 1122 SSP2 LLQVRKHL 137 8 9 90 1123 SSP2 LLSTNLPY 121 8 9 90 1124 SSP2 LMDCSGSI 52 8 10 100 1125 SSP2 LIDGIPDSI 160 9 10 100 1126 SSP2 LVTVFLIF 10 8 10 100 1127 SSP2 LVIVFLIFF 10 9 10 100 1128 SSP2 LVIVFLIFFDL 10 11 10 100 1129 SSP2 LVNGRDVQNNI 22 11 10 100 1130 SSP2 LVVILTDQI 156 9 10 100 1131 SSP2 LYLLMDCSGSI 49 11 9 90 1132 SSP2 NIVDEIKY 31 8 10 100 1133 SSP2 NLPYGRTNL 125 9 8 80 1134 SSP2 NLYADSAW 213 8 10 100 1135 SSP2 NVAFNRFL 195 8 10 100 1136 SSP2 NVKNVIGPF 222 9 10 100 1137 SSP2 NVKNVIGPFM 222 10 10 100 1138 SSP2 NVKYLVIVF 6 9 10 100 1139 SSP2 NVKYLVIIVFL 6 10 10 100 1140 SSP2 NVKYLVIVFLI 6 11 10 100 1141 SSP2 NWVNHAVPL 63 9 8 80 1142 SSP2 NWVNHAVPLAM 63 11 8 80 1143 SSP2 PLAMKLIQQL 70 10 10 100 1144 SSP2 PYAQEPAPF 528 9 8 80 0.0370 1145 SSP2 QFRLPEENEW 552 10 10 100 1146 SSP2 QLVVILIDGI 155 10 10 100 1147 SSP2 QVRKHLNDFTI 139 10 9 90 1148 SSP2 RINRENANQL 147 10 10 100 1149 SSP2 RLPEENEW 554 8 10 100 1150 SSP2 SLKESRKL 171 8 9 90 1151 SSP2 SLLSTNLPY 120 9 9 90 1152 SSP2 STNLPYGRTNL 123 11 8 80 1153 SSP2 TLGEEDKDL 539 9 10 100 1154 SSP2 VFGIGQGI 187 8 10 100 1155 SSP2 VFLIFFDL 13 8 10 100 1156 SSP2 VFLIFFDLF 13 9 10 100 1157 SSP2 VFLIFFDLFL 13 10 10 100 1158 SSP2 VILTDGIPDSI 158 11 10 100 1159 SSP2 VIVFLIFF 11 8 10 100 1160 SSP2 VIVFLIFFDL 11 10 10 100 1161 SSP2 VIVFLIFFDLF 11 11 10 100 1162 SSP2 VVILTDGI 157 8 10 100 1163 SSP2 VVPGAATPY 521 9 8 80 1164 SSP2 WVNHAVPL 64 8 8 80 1165 SSP2 WVNHAVPLAM 64 10 8 80 1166 SSP2 YLLMDCSGSI 50 10 10 100 1167 SSP2 YLVIVFLI 9 8 10 100 1168 SSP2 YLVIVFLIF 9 9 10 100 1169 SSP2 YLVIVFLIFF 9 10 10 100 1170

TABLE XI Malaria B07 Super Motif Peptides With Binding Information No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) B*0702 Seq. Id. CSP EPSDKHIEQY 345 10 15 79 171 CSP EPSDKHIEQYL 345 11 15 79 172 CSP DPNANPNA 202 8 19 100 173 CSP DPNANPNV 130 8 19 100 174 CSP DPNRNVDBIA 327 10 19 100 0.0002 175 CSP MPNDPNRNV 324 9 19 100 0.0001 176 CSP NPDPNANPNV 120 10 19 100 0.0001 177 CSP NPNANPNA 302 8 19 100 0.0001 178 CSP NPNVDPNA 198 8 19 100 0.0001 179 CSP QPGDGNPDPNA 115 11 19 100 180 CSP SPCSVTCGNGI 371 11 19 100 181 EXP DPADNANPDA 116 10 1 100 0.0002 182 EXP DPQVTAQDV 136 9 1 100 0.0001 183 EXP EPLIDVHDL 45 9 1 100 0.0001 184 EXP EPLIDVHDLI 45 10 1 100 0.0002 185 EXP EPNADPQV 132 8 1 100 0.0001 186 EXP EPNADPQVTA 132 10 1 100 0.0002 187 EXP HPFKIGSSDPA 108 11 1 100 188 EXP QPQGDDNNL 148 9 1 100 0.0001 189 EXP QPQGDDNNLV 148 10 1 100 0.0002 190 LSA KPEQKEDKSA 1728 10 1 100 0.0002 191 LSA KPIVQYDNF 1786 9 1 100 0.0001 192 LSA KPNDKSLY 1850 8 1 100 0.0004 193 LSA LPSENERGY 1663 9 1 100 0,0001 194 LSA LPSENERGYY 1663 10 1 100 0.0001 195 LSA LPSENERGYYI 1663 11 1 100 196 SSP2 EPAPFDETL 532. 9 10 100 0.0001 197 SSP2 GPFMKAVCV 228 9 10 100 0.0023 198 SSP2 GFFMKAVCVEV 228 11 10 100 199 SSP2 HPSDGKCNL 206 9 10 100 0.0220 200 SSP2 HPSDGKCNLY 206 10 10 100 0.0001 201 SSP2 HPSDGKCNLYA 206 11 10 100 202 SSP2 IPDSIQDSL 164 9 10 100 0.0022 203 SSP2 IPEDSEKEV 367 9 10 100 0.0001 204 SSP2 LPYGRTNL 126 8 8 80 0.1100 205 SSP2 NPEDDREENF 382 10 10 100 0.0001 206 SSP2 QPRPRGDNF 303 9 9 90 0.0160 207 SSP2 QPRPRGDNFA 303 10 9 90 0.0009 208 SSP2 QPRPRGDNFAV 303 11 9 90 209 SSP2 RPRGDNFA 305 8 9 90 0.0110 210 SSP2 RPRGDNFAV 305 9 9 90 0.4800 211 SSP2 TPYAGEPA 527 8 8 80 212 SSP2 TPYAGEPAPF 527 10 8 80 0.0990 213 SSP2 VPGAATPY 522 8 8 80 214 SSP2 VPGAAIPYA 522 9 8 80 0.0001 215 SSP2 VPLAMKLI 69 8 10 100 0.0001 216 SSP2 VPLAMKLIQQL 69 11 10 100 217

TABLE XII Malaria B27 Super Motif Peptides No. of Sequence Conservancy Seq. Protein Sequence Position Amino Acids Frequency (%) Id CSP CKMEKCSSVF 408 10 19 100 1218 CSP DKHIEQYL 348 8 15 79 1219 CSP DKHIEQYLKKI 348 11 15 79 1220 CSP EKLRKPKHKKL 103 11 19 100 1221 CSP GKQENWYSL 57 9 19 100 1222 CSP KHIEQYLKKI 349 10 15 79 1223 CSP KKIQNSLSTEW 360 11 15 79 1224 CSP LKKIQNSL 359 8 15 79 1225 CSP LKICNSRSL 65 8 19 100 1226 CSP LRKPKHKKL 105 9 19 100 1227 CSP RKLAILSVSSF 3 11 19 100 1228 CSP RKPKHKKL 106 8 19 100 1229 CSP TRVLNELNY 32 9 19 100 1230 EXP EKGRHPFKI 104 9 1 100 1231 EXP KKGSGEPL 40 8 1 100 1232 EXP KKGSGEPLI 40 9 1 100 1233 EXP KKNKKGSGEPL 37 11 1 100 1234 EXP KRKSKYKL 69 8 1 100 1235 EXP MKILSVFF 1 8 1 100 1236 EXP MKILSVFFL 1 9 1 100 1237 EXP MK1LSVFFLAL 1 11 1 100 1238 EXP NKKGSGEPL 39 9 1 100 1239 EXP NKKGSGEPLI 39 10 1 100 1240 EXP NKRKSKYKL 68 9 1 100 1241 EXP SKYKLATSVL 72 10 1 100 1242 EXP VHDLISDM 50 8 1 100 1243 EXP VHDLISDMI 50 9 1 100 1244 EXP YKLATSVL 74 8 1 100 1245 EXP YKLATSVLAGL 74 11 1 100 1246 LSA DKDKELIM 79 8 1 100 1247 LSA DKQVNKEKEICF 1867 11 1 100 1248 LSA DKSADIQNHIL 1734 11 1 100 1249 LSA DKSLYDEHI 1853 9 1 100 1250 LSA DRLAKEKL 1392 8 1 100 1251 LSA EHGDVLAEDL 1643 10 1 100 1252 LSA EHODVIAEDLY 1643 11 1 100 1253 LSA EKAAKEIL 151 8 1 100 1254 LSA EKDEIIKSNL 30 10 1 100 1255 LSA EKEKFIKSL 873 9 1 100 1256 LSA EKEXFIKSLF 873 10 1 100 1257 LSA EKFIKSLF 875 8 1 100 1258 LSA EKFIKSLFHI 875 10 1 100 1259 LSA EKFIKSLFHIF 875 11 1 100 1260 LSA EXHECKHVL 53 9 1 100 1261 LSA EKIKKGKKY 833 9 1 100 1262 LSA DUCHVLSHNSY 56 11 1 100 1263 LSA EKLQEQQRDL 618 10 1 100 1264 LSA EKLQEQQSDL 584 10 1 100 1265 LSA SCLQGQQSDL 125 10 1 100 1266 LSA EISNENLDDL 811 9 1 100 1267 LSA EKTICDNNF 842 8 1 100 1268 LSA EKTKNNENNKF 67 11 1 100 1269 LSA EXINRESI 697 8 1 100 1270 LSA ERKKEHGDVL 639 10 1 100 1271 LSA ERLAICEKL 613 8 1 100 1272 LSA ERLANEKL 528 8 1 100 1273 LSA ERRAKEKL 1579 8 1 100 1274 LSA ERTKASKETL 1186 10 1 100 1275 LSA FHIFDGDNEI 1882 10 1 100 1276 LSA FHTFDGDNEIL 1882 11 1 100 1277 LSA FHINGKII 19 8 1 100 1278 LSA FKPIVQYDNF 1785 10 1 100 1279 LSA FKPNDKSL 1849 8 1 100 1280 LSA FIQNDKSLY 1849 9 1 100 1281 LSA FKSLLRNL 97 8 1 100 1282 LSA GHLEEKKDGSI 1717 11 1 100 1283 LSA GKLIEHII 121 8 1 100 1284 LSA GRLEIPAI 1654 8 1 100 1285 LSA GRLEIPAIEL 1654 10 1 100 1286 LSA GRRDIHKGHL 1710 10 1 100 1287 LSA IKNSEKDEI 26 9 1 100 1288 LSA IKNSEKDEII 26 10 1 100 1289 LSA IKSLFHIF 1878 8 1 100 1290 LSA KHEKKHVL 54 8 1 100 1291 LSA KHILYISF 2 8 1 100 1292 LSA KHILYISFY 2 9 1 100 1293 LSA KHILYISFYF 2 10 1 100 1294 LSA KHILYISFYFI 2 11 1 100 1295 LSA KHVLSHNSY 58 9 1 100 1296 LSA KKEHGDVL 1641 8 1 100 1297 LSA KKHVLSHNSY 57 10 1 100 1298 LSA KKYEKIKDNNF 1839 11 1 100 1299 LSA LRNLGVSENI 101 10 1 100 1300 LSA LRNLGVSENIF 101 11 1 100 1301 LSA MKHILYISF 1 9 1 100 1302 LSA MKHILYISFY 1 10 1 100 1303 LSA MKHILYISFYF 1 11 1 100 1304 LSA NHTLETVNi 1741 9 1 100 1305 LSA NKEGKLIEH1 118 10 1 100 1306 LSA NKEGKLIEHII 118 11 1 100 1307 LSA NICEKEKSI 1871 8 1 100 1308 LSA NKEKEKFRSL 1871 11 1 100 1309 LSA NKFFDKDKEL 75 10 1 100 1310 LSA NKLNKEGKL 115 9 1 100 1311 LSA NKLNKEGKU 115 10 1 100 1312 LSA NRGNSRDSKEI 1683 11 1 100 1313 LSA QKEDILSADI 1731 9 1 100 1314 LSA QRDLEQERL 1607 9 1 100 1315 LSA QRKADTKKNL 1629 10 1 100 1316 LSA RKADTKKNL 1630 9 1 100 1317 LSA RKKEHGDVL 1640 9 1 100 1318 LSA RRDIHKGHL 1711 9 1 100 1319 LSA SKYEDEISAEY 1758 11 1 100 1320 LSA SRDSKEISI 1687 9 1 100 1321 LSA SRDSKEISII 1687 10 1 100 1322 LSA TKASKEIL 1188 8 1 100 1323 LSA TICNNENNKF 69 9 1 100 1324 LSA TKNNENNKFF 69 10 1 100 1325 LSA VKNVSQTNF 89 9 1 100 1326 LSA YKELEDLI 1803 8 1 100 1327 SSP2 CHPSDGKCNL 205 10 10 100 1328 SSP2 CHPSDGKCNLY 205 11 10 100 1329 SSP2 DKDLDEPEQF 544 10 10 100 1330 SSP2 DREENFDI 386 8 10 100 1331 SSP2 DRGVKIAVF 180 9 9 90 1332 SSP2 DRGVKIAVEGI 180 11 9 90 1333 SSP2 DRINRENANQL 146 11 10 100 1334 SSP2 EKTASCGVW 239 9 10 100 1335 SSP2 FRLPEENEW 333 9 10 100 1336 SSP2 GKCNLYADSAW 210 11 10 100 1337 SSP2 GKGTRSRKREI 258 11 10 100 1338 SSP2 GRDVQNNI 25 8 10 100 1339 SSP2 GRNNENRSY 458 9 10 100 1340 SSP2 KHDNQNNL 400 8 10 100 1341 SSP2 LHEGCTSEL 269 9 8 80 1342 SSP2 MKLIQQLNL 73 9 10 100 1343 SSP2 NHAVPLAM 66 8 8 80 1344 SSP2 NHAVPLAMKL 66 10 8 80 1345 SSP2 NHAVPLAMKLI 66 11 8 80 1346 SSP2 NHLGNVKY 2 8 10 100 1347 SSP2 NHLGNVKYL 2 9 10 100 1348 SSP2 NHLGNVKYLVI 2 11 10 100 1349 SSP2 NKEKALII 110 8 9 90 1350 SSP2 NKEKALIII 110 9 9 90 1351 SSP2 NKHDNQNNL 399 9 10 100 1352 SSP2 NKYKIAGGI 496 9 9 90 1353 SSP2 NRENANQL 149 8 10 100 1354 SSP2 NRENANQLVVI 149 11 10 100 1355 SSP2 PHGRNNENRSY 456 11 10 100 1356 SSP2 PRPRGDNF 304 8 9 90 1357 SSP2 RHNWVNHAVPL 61 11 8 80 1358 SSP2 RKHLNDRI 141 8 10 100 1359 SSP2 SKNKEKAL 108 8 10 100 1360 SSP2 SKNKSCALI 108 9 9 90 1361 SSP2 SKNKEKALII 108 10 9 90 1362 SSP2 SKNKEKALIII 108 11 9 90 1363 SSP2 TRSRKREI 261 8 10 100 1364 SSP2 TRSRKREIL 261 9 10 100 1365 SSP2 VKIAVFGI 183 8 10 100 1366 SSP2 VKNVIGPF 223 8 10 100 1367 SSP2 VKNVIGPFM 223 9 10 100 1368 SSP2 VKYLVIVF 7 8 10 100 1369 SSP2 VKYLVIVFL 7 9 10 100 1370 SSP2 VKYLVIVFLI 7 10 10 100 1371 SSP2 VKYLVIVFLIF 7 11 10 100 1372 SSP2 VRKHLNDRI 140 9 10 100 1373 SSP2 YKIAGGIAGGL 498 11 10 100 1374

TABLE XIII Malaria B58 Super Motif Peptides No. of Sequence Conservancy Seq. Protein Sequence Position Amino Acids Frequency (%) Id CSP CSSVFNVV 413 8 19 100 1375 CSP CSVTCGNGI 373 9 19 100 1376 CSP CSVTCGNGIQV 373 11 19 100 1377 CSP EALFQEYQCY 17 10 19 100 1378 CSP GSSSNTRV 27 8 19 100 1379 CSP GSSSNTRVL 27 9 19 100 1380 CSP LAILSVSSF 5 9 19 100 1381 CSP LAILSVSSFL 5 10 19 100 1382 CSP LAILSVSSFLF 5 11 19 100 1383 CSP LSTEWSPCSV 366 10 18 95 1384 CSP LSVSSFLF 8 8 19 100 1385 CSP LSVSSFLFV 8 9 19 100 1386 CSP NAGINLYNEL 42 10 18 95 1387 CSP NANANNAV 335 8 16 84 1388 CSP NSSIGLIM 421 8 19 100 1389 CSP NSSIGLIMV 421 9 19 100 1390 CSP NSSIGLIMVL 421 10 19 100 1391 CSP NTRVLNEL 31 8 19 100 1392 CSP NTRVLNELNY 31 10 19 100 1393 CSP PSDKHIEQY 346 9 15 79 1394 CSP PSDKHIEQYL 346 10 15 100 1395 CSP SSFLFVEAL 11 9 19 100 1396 CSP SSFLFVEALF 11 10 19 100 1397 CSP SSIGLIMV 422 8 19 100 1398 CSP SSIGLIMVL 422 9 19 100 1399 CSP SSIGLIMVLSF 422 11 19 100 1400 CSP SSNTRVLNEL 29 10 19 100 1401 CSP SSSNTRVL 28 8 19 100 1402 CSP SSSNTRVLNEL 28 11 19 100 1403 CSP SSVFNVVNSSI 414 11 19 100 1404 CSP STEWSPCSV 367 9 19 100 1405 CSP VSSFLFVEAL 10 10 19 100 1406 CSP VSSFLFVEALF 10 11 19 100 1407 CSP VTCGNGIQV 375 9 19 100 1408 CSP VTCGNGIQVRI 375 11 19 100 1409 CSP YSLKKNSRSL 63 10 19 100 1410 EXP ATSVLAGL 77 8 1 100 1411 EXP ATSVLAGLL 77 9 1 100 1412 EXP GSGEPLIDV 42 9 1 100 1413 EXP ISDMIKKEEEL 54 11 1 100 1414 EXP KSKYKLATSV 71 10 1 100 1415 EXP KSKYKLATSVL 71 11 1 100 1416 EXP KTNKGTGSGV 24 10 1 100 1417 EXP LAGLLGNV 81 8 1 100 1418 EXP LAGLLGNVSTV 81 11 1 100 1419 EXP LALFFIIF 9 8 1 100 1420 EXP LATSVLAGL 76 9 1 100 1421 EXP LATSVLAGLL 76 10 1 100 1422 EXP LSVFFLAL 4 8 1 100 1423 EXP LSVFFLALF 4 9 1 100 1424 EXP LSVFFLALFF 4 10 1 100 1425 EXP LSVFFLALFFI 4 11 1 100 1426 EXP NADPQVTAQDV 134 11 1 100 1427 EXP NTEKGRHPF 102 9 1 100 1428 EXP NTEKGRHPFKI 102 11 1 100 1429 EXP STVLLGGV 89 8 1 100 1430 EXP STVLIGGVGL 89 10 1 100 1431 EXP STVLLGGVGLV 89 11 1 100 1432 EXP TSVLAGLL 78 8 1 100 1433 EXP TSVLAGLLGNV 78 11 1 100 1434 EXP VSTVLLGGV 88 9 1 100 1435 EXP VSTVLLGGVGL 88 11 1 100 1436 LSA DSKEISII 1689 8 1 100 1437 LSA ETLQEQQSDL 1193 10 1 100 1438 LSA ETLQGQQSDL 156 10 1 100 1439 LSA ETVNISDV 1745 8 1 100 1440 LSA EIVNISDVNDF 1745 11 1 100 1441 LSA GSSNSRNRI 42 9 1 100 1442 LSA HTLETVNI 1742 8 1 100 1443 LSA HTLETVNISDV 1742 11 1 100 1444 LSA ISAEYDDSL 1764 9 1 100 1445 LSA ISAEYDDSLI 1764 10 1 100 1446 LSA ISDVNDFQI 1749 9 1 100 1447 LSA ISFYFILV 7 8 1 100 1448 LSA ISFYFILVNL 7 10 1 100 1449 LSA ISFYFILVNLL 7 11 1 100 1450 LSA ISKYEDEI 1757 8 1 100 1451 LSA ITKYFMKL 1902 8 1 100 1452 LSA ITTNVEGRRDI 1704 11 1 100 1453 LSA KADTKKNL 1631 8 1 100 1454 LSA KSADIQNHTL 1735 10 1 100 1455 LSA KSLLRNLGV 98 9 1 100 1456 LSA KSLYDEHI 1854 8 1 100 1457 LSA KSLYDEHIKKY 1854 11 1 100 1458 LSA KSSEELSEEKI 1825 11 1 100 1459 LSA KTKNNENNKF 68 10 1 100 1460 LSA KTKNNENNKFF 68 11 1 100 1461 LSA KTNRESITTNV 1698 11 1 100 1462 LSA LAEDLYGRL 1648 9 1 100 1463 LSA LAEDLYGRLEI 1648 11 1 100 1464 LSA LSEDITKY 1898 8 1 100 1465 LSA LSEDITKYF 1898 9 1 100 1466 LSA LSEDITKYFM 1898 10 1 100 1467 LSA LTMSNVKNV 84 9 1 100 1468 LSA NSEKDEII 28 8 1 100 1469 LSA NSRDSKEI 1686 8 1 100 1470 LSA NSRDSKEISI 1686 10 1 100 1471 LSA NSRDSKEISII 1686 11 1 100 1472 LSA PSENERGY 1664 8 1 100 1473 LSA PSENERGYY 1664 9 1 100 1474 LSA PSENERGYYI 1664 10 1 100 1475 LSA QSDLEQDRL 1386 9 1 100 1476 LSA QSDLEQERL 1590 9 1 100 1477 LSA QSDSEQERL 519 9 1 100 1478 LSA QTNFKSLL 94 8 1 100 1479 LSA QTNFKSLLRNL 94 11 1 100 1480 LSA RSGSSNSRNRI 40 11 1 100 1481 LSA RTKASKETL 1187 9 1 100 1482 LSA SADIQNHTL 1736 9 1 100 1483 LSA SAEYDDSL 1765 8 1 100 1484 LSA SAEYDDSLI 1765 9 1 100 1485 LSA SSEELSEEKI 1826 10 1 100 1486 LSA SSNSRNRI 43 8 1 100 487 LSA TTNVEGRRDI 1705 10 1 100 488 LSA VSQTNFKSL 92 9 1 100 489 LSA VSQTNFKSLL 92 10 1 100 490 SSP2 ASCGVWDEW 242 9 10 100 491 SSP2 ASKNKEKAL 107 9 10 100 492 SSP2 ASKNKEKALI 107 10 9 90 493 SSP2 ASKNKEKALII 107 11 9 90 494 SSP2 AIPYAGEPAPF 526 11 8 80 495 SSP2 CAGLAYKF 513 8 10 100 496 SSP2 CAGLAYKFV 513 9 10 100 497 SSP2 CAGLAYKFVV 513 10 10 100 498 SSP2 CSGSIRRHNW 55 10 10 100 499 SSP2 CSGSIRRHNWV 55 11 10 100 500 SSP2 DALLQVRKHL 135 10 9 90 501 SSP2 DASKNKEKAL 106 10 10 100 502 SSP2 DASKNKEKALI 106 11 9 90 503 SSP2 DSAWENVKNV 217 10 10 100 504 SSP2 DSAWENVKNVI 217 11 10 100 505 SSP2 DSEKEVPSDV 370 10 10 100 506 SSP2 DSLKESRKL 170 9 9 90 507 SSP2 ETLGEEDKDL 538 10 10 100 508 SSP2 GSIRRHNW 57 8 10 100 509 SSP2 GSIRRHNWV 57 9 10 100 510 SSP2 GTRSRKREI 260 9 10 100 511 SSP2 GTRSRKREIL 260 10 10 100 512 SSP2 HAVPLAMKL 67 9 10 100 513 SSP2 HAVPLAMKLI 67 10 10 100 514 SSP2 IAGGIAGGL 500 9 10 100 515 SSP2 IAGGIAGGLAL 500 11 10 100 516 SSP2 IAGGLALL 504 8 10 100 517 SSP2 IAVFGIGQGI 185 10 10 100 518 SSP2 KTASCGVW 240 8 10 100 519 SSP2 KTASCGVWDEW 240 11 10 100 520 SSP2 LACAGLAY 511 8 10 100 521 SSP2 LACAGLAYKF 511 10 10 100 522 SSP2 LACAGLAYKFV 511 11 10 100 523 SSP2 LALLACAGL 508 9 10 100 524 SSP2 LALLACAGLAY 508 11 10 100 525 SSP2 LAMKLIQQL 71 9 10 100 526 SSP2 LAMKLIQQLNL 71 11 10 100 527 SSP2 LTDGIPDSI 160 9 10 100 528 SSP2 NANQLVVI 152 8 10 100 529 SSP2 NANQLVVIL 152 9 10 100 530 SSP2 PAPFDETL 533 8 10 100 531 SSP2 PSCGKCNL 207 8 10 100 532 SSP2 PSDGKCNLY 207 9 10 100 533 SSP2 QSQDNNGNRHV 436 11 10 100 534 SSP2 RSRKREIL 262 8 10 100 535 SSP2 SAWENVKNV 218 9 10 100 536 SSP2 SAWENVKNVI 218 10 10 100 537 SSP2 STNLPYGRTNL 123 11 8 80 538 SSP2 TASCGVWDEW 241 10 10 100 539 SSP2 VAFNRFLV 196 8 10 100 540 SSP2 YADSAWENV 215 9 10 100 541 SSP2 YAGEPAPF 529 8 8 80 1542

TABLE XIV Malaria B62 Super Motif Peptides No. of Sequence Conservancy Seq. Protein Sequence Position Amino Acids Frequency (%) Id. CSP AILSVSSF 6 8 9 100 1543 CSP AILSVSSFLF 6 10 9 100 1544 CSP AILSVSSFLFV 6 11 9 100 1545 CSP ALFQEYQCY 18 9 9 100 1546 CSP DIEKKICKM 402 9 9 100 1547 CSP DPNANPNV 130 8 9 100 1548 CSP ELNYDNAGI 37 9 8 95 1549 CSP EMNYYGKQENW 52 11 9 100 1550 CSP EPSDKHIEQY 345 10 5 79 1551 CSP FLFVEALF 13 8 9 100 1552 CSP FLFVEALFQEY 13 11 9 100 1553 CSP FVEALFQEY 1S 9 9 100 1554 CSP GINLYNELEM 44 10 8 95 1555 CSP GLIMVLSF 425 8 9 100 1556 CSP GLIMVLSFLF 425 10 9 100 1557 CSP HIEQYLKKI 350 9 5 79 1558 CSP ILSVSSFLF 7 9 9 100 1559 CSP ILSVSSFLFV 7 10 9 100 1560 CSP IMVLSFLF 427 8 9 100 1561 CSP IQNSLSTEW 362 9 5 79 1562 CSP KICKMEKCSSV 406 11 9 100 1563 CSP KIQNSLSTEW 361 10 5 79 1564 CSP KLAILSVSSF 4 10 9 100 1565 CSP KMEKCSSV 409 8 9 100 1566 CSP KMEKCSSVF 409 9 9 100 1567 CSP KMEKCSSVFNV 409 11 9 100 1568 CSP LIMVLSFLF 426 9 9 100 1569 CSP MMRKLAILSV 1 10 9 100 1570 CSP MPNDPNRNV 324 9 9 100 1571 CSP NLYNELEM 46 8 9 100 1572 CSP NLYNELEMNY 46 10 9 100 1573 CSP NLYNELEMNYY 46 11 9 100 1574 CSP NMPNDPNRNV 323 10 9 100 1575 CSP NPDPNANPNV 120 10 9 100 1576 CSP NQGNGQGHNM 315 10 9 100 1577 CSP NVDPNANPNV 128 10 9 100 1578 CSP NVVNSSIGLI 418 10 9 100 1579 CSP NVVNSSIGLIM 418 11 9 100 1580 CSP RVLNELNY 33 8 9 100 1581 CSP SIGLIMVLSF 423 10 9 100 1582 CSP SLSTEWSPCSV 365 11 8 95 1583 CSP SPCSVTCGNGI 371 11 9 100 1584 CSP SVFNVVNSSI 415 10 9 100 1585 CSP SVSSFLFV 9 8 9 100 1586 CSP SVTCGNGI 374 8 9 100 1587 CSP SVTCGNGIQV 374 10 9 100 1588 CSP VVNSSIGLI 419 9 9 100 1589 CSP VVNSSIGLIM 419 10 9 100 1590 CSP VVNSSIGLIMV 419 11 9 100 1591 EXP DMIKKEEELV 56 10 1 100 1592 EXP DPQVTAQDV 136 9 1 100 1593 EXP DVHDLISDM 49 9 1 100 1594 EXP DVHDLISDMI 49 10 1 100 1595 EXP EPLIDVHDLI 45 10 1 100 1596 EXP EPNADPQV 132 8 1 100 1597 EXP EQPQGDDNNLV 147 11 1 100 1598 EXP EVNKRKSKY 66 9 1 100 1599 EXP FLALFFII 8 8 1 100 1600 EXP FLALFFIIF 8 9 1 100 1601 EXP GLLGNVSTV 83 9 1 100 1602 EXP ILSVFFLALF 3 10 1 100 1603 EXP ILSVFFLALFF 3 11 1 100 1604 EXP KILSVFFLALF 2 11 1 100 1605 EXP LIDVHDLI 47 8 1 100 1606 EXP LIDVHDLISDM 47 11 1 100 1607 EXP LLGGVGLV 92 8 1 100 1608 EXP LLGGVGLVLY 92 10 1 100 1609 EXP LLGNVSTV 84 8 1 100 1610 EXP LVEVNKRKSKY 64 11 1 100 1611 EXP MIKKEEELV 57 9 1 100 1612 EXP MIKKEEELVEV 57 11 1 100 1613 EXP NVSTVLLGGV 87 10 1 100 1614 EXP PLIDVHDLI 46 9 1 100 1615 EXP PQGDDNNLV 149 9 1 100 1616 EXP PQVTAQDV 137 8 1 100 1617 EXP QPQGDDNNLV 148 10 1 100 1618 EXP SVFFLALF 5 8 1 100 1619 EXP SVFFLALFF 5 9 1 100 1620 EXP SVFFLALFFI 5 10 1 100 1621 EXP SVFFLALFFII 5 11 1 100 1622 EXP SVLAGLLGNV 79 10 1 100 1623 EXP TVLLGGVGLV 90 10 1 100 1624 EXP VLAGLLGNV 80 9 1 100 1625 EXP VLLGGVGLV 91 9 1 100 1626 EXP VLLGGVGLVLY 91 11 1 100 1627 LSA DIQNHTLETV 1738 10 1 100 1628 LSA DLDEFKPI 1781 8 1 100 1629 LSA DLDEFKPIV 1781 9 1 100 1630 LSA DLDEFKPIVQY 1781 11 1 100 1631 LSA DLYGRLEI 1651 8 1 100 1632 LSA DLYGRLEIPAI 1651 11 1 100 1633 LSA DVLAEDLY 1646 8 1 100 1634 LSA DVNDFQISKY 1751 10 1 100 1635 LSA EISAEYDDSLI 1763 11 1 100 1636 LSA ELPSENERGY 1662 10 1 100 1637 LSA ELPSENERGYY 1662 11 1 100 1638 LSA ELSEDITKY 1897 9 1 100 1639 LSA ELSEDITKYF 1897 10 1 100 1640 LSA ELSEDRKYFM 1897 11 1 100 1641 LSA ELTMSNVKNV 83 10 1 100 1642 LSA EQKEDKSADI 1730 10 1 100 1643 LSA FIKSLFHI 1877 8 1 100 1644 LSA FIKSLFHIF 1877 9 1 100 1645 LSA FILVNLLI 11 8 1 100 1646 LSA FILVNLLIF 11 9 1 100 1647 LSA FILVNLLIFFII 11 11 1 100 1648 LSA FQDEENIGI 1794 9 1 100 1649 LSA FQDEENIGIY 1794 10 1 100 1650 LSA FQISKYEDE1 1755 10 1 100 1651 LSA GIYKELEDLI 1801 10 1 100 1652 LSA HIFDGDNEI 1883 9 1 100 1653 LSA HIKKYKNDKQV 1860 11 1 100 1654 LSA HILYISFY 3 8 1 100 1655 LSA HILYISFYF 3 9 1 100 1656 LSA HILYISFYFI 3 10 1 100 1657 LSA HLEEKKDGSI 1718 10 1 100 1658 LSA HVLSHNSY 59 8 1 100 1659 LSA IIEKTNRESI 1695 10 1 100 1660 LSA IIKNSEKDEI 25 10 1 100 1661 LSA IIKNSEKDEII 25 11 1 100 1662 LSA IINDDDDKKKY 127 11 1 100 1663 LSA RILVNLLIF 12 8 1 100 1664 LSA ILVNLLIFHI 12 10 1 100 1665 LSA ILYYISFYF 4 8 1 100 1666 LSA ILYISFYFI 4 9 1 100 1667 LSA ILYISFYFILV 4 11 1 100 1668 LSA IQNHTLETV 1739 9 1 100 1669 LSA IQNHTLETVNI 1739 11 1 100 1670 LSA IVDELSEDI 1894 9 1 100 1671 LSA KIIKNSEKDEI 24 11 1 100 1672 LSA KIKKGKKY 1834 8 1 100 1673 LSA KLNKEGKLI 116 9 1 100 1674 LSA KPIVQYDNF 1786 9 1 100 1675 LSA KPNDKSLY 1850 8 1 100 1676 LSA KQVNKEKEKF 1868 10 1 100 1677 LSA KQVNKEKEKFI 1868 11 1 100 1678 LSA LIFHINGKI 17 9 1 100 1679 LSA LIFHINGKII 17 10 1 100 1680 LSA LLIFHINGKI 16 10 1 100 1681 LSA LLIFHINGKII 16 11 1 300 1682 LSA LLRNLGVSENI 100 11 1 100 1683 LSA LPSENERGY 1663 9 1 100 1684 LSA LPSENERGYY 1663 10 1 100 1685 LSA LPSENERGYYI 1663 11 1 100 1686 LSA LQIVDELSEDI 1892 11 1 100 1687 LSA LVNLLIFHI 13 9 1 100 1688 LSA NISDVNDF 1748 8 1 100 1689 LSA NISDVNDFQI 1748 10 1 100 1690 LSA NLDDLDEGI 1815 9 1 100 1691 LSA NLERKKEHGDV 1637 11 1 100 1692 LSA NLGVSENI 103 8 1 100 1693 LSA NLGVSENIF 103 9 1 100 1694 LSA NLLIFHTNGKI 15 11 1 100 1695 LSA NVEGRRDI 707 8 1 100 1696 LSA NVKNVSQTNF 88 10 1 100 1697 LSA PIVQYDNF 787 8 1 100 1698 LSA QISKYEDEI 756 9 1 100 1699 LSA QIVDELSEDI 893 10 1 100 1700 LSA QVNKEKEKF 869 9 1 100 1701 LSA QVINIKEKEKFI 869 10 1 100 1702 LSA SIIEKTNRESI 694 11 1 100 1703 LSA SLLRNLGV 99 8 1 100 1704 LSA SLYDEHIKKY 855 10 1 100 1705 LSA TLETVNISDV 743 10 1 100 1706 LSA TMSNVKNV 85 8 1 100 1707 LSA TVNISDVNDF 746 10 1 100 1708 LSA YISFYFILV 6 9 1 100 1709 SSP2 ALLACAGLAY 509 10 10 100 1710 SSP2 AVFGIGQGI 186 9 10 100 1711 SSP2 AVFGIGQGINV 186 11 10 100 1712 SSP2 AVPLAMKLI 68 9 10 100 1713 SSP2 DLDEPDQF 546 8 10 100 1714 SSP2 DLFLVNGRDV 19 10 10 100 1715 SSP2 DQPRPRGDNF 302 10 9 90 1716 SSP2 DVQNNIVDEI 27 10 10 100 1717 SSP2 EIKYREEV 35 8 9 90 1718 SSP2 EQFRLPEENEW 551 11 10 100 1719 SSP2 EVCNDEVDLY 41 10 8 80 1720 SSP2 EVDLYLLM 46 8 8 80 1721 SSP2 EVEKTASCGV 237 10 10 100 1722 SSP2 EVEXTASCGVW 237 11 10 100 1723 SSP2 FLIFFDLF 14 8 10 100 1724 SSP2 FLIFFDLFLV 14 10 10 100 1725 SSP2 FLVNGRDV 21 8 10 100 1726 SSP2 FMKAVCVEV 230 9 10 100 1727 SSP2 FVVPGAATPY 520 10 8 80 1728 SSP2 GIGQGINV 189 8 10 100 1729 SSP2 GIGQGINVAF 189 10 10 100 1730 SSP2 GINVAFNRF 193 9 10 100 1731 SSP2 GINVAFNRFLV 193 11 10 100 1732 SSP2 GLAYKFVV 515 8 10 100 1733 SSP2 GPFMKAVCV 228 9 10 100 1734 SSP2 GPFMKAVCVEV 228 11 10 100 1735 SSP2 GQGINVAF 191 8 10 100 1736 SSP2 GQGINVAFNRF 191 11 10 100 1737 SSP2 GVKIAVFGI 182 9 10 100 1738 SSP2 GVWDEWSPCSV 245 11 10 100 1739 SSP2 HLGNVKYLV 3 9 10 100 1740 SSP2 HLGNVKYLVI 3 10 10 100 1741 SSP2 HLGNVKYLVIV 3 11 10 100 1742 SSP2 HPSDGKCNLY 206 10 10 100 1743 SSP2 ILTDGIPDSI 159 10 10 100 1744 SSP2 IPEDSEKEV 367 9 10 100 1745 SSP2 IVDEIKYREEV 32 11 9 90 1746 SSP2 IVFLIFFDLF 12 10 10 100 1747 SSP2 KIAVFGIGQGI 184 11 10 100 1748 SSP2 LIFFDLFLV 15 9 10 100 1749 SSP2 LLACAGLAY 510 9 10 100 1750 SSP2 LLACAGLAYKF 510 11 10 100 1751 SSP2 LLMDCSGSI 51 9 10 100 1752 SSP2 LLSTNLPY 121 8 9 90 1753 SSP2 LMDCSGSI 52 8 10 100 1754 SSP2 LQVRKHLNDRI 138 11 9 90 1755 SSP2 LVIVFLIF 10 8 10 100 1756 SSP2 LVIVFLIFF 10 9 10 100 1757 SSP2 LVNGRDVQNNI 22 11 10 100 1758 SSP2 LVVILTDGI 156 9 10 100 1759 SSP2 NIPEDSEKEV 366 10 10 100 1760 SSP2 NIVDEIKY 31 8 10 100 1761 SSP2 NLYADSAW 213 8 10 100 1762 SSP2 NLYADSAWENV 213 11 10 100 1763 SSP2 NPEDDREENF 382 10 10 100 1764 SSP2 NQLVVILTDGI 154 11 10 100 1765 SSP2 NVARAFIN 195 9 10 100 1766 SSP2 NVIGPFMKAV 225 10 10 100 1767 SSP2 NVKNVIGPF 222 9 10 100 1768 SSP2 NVKNVIGPFM 222 10 10 100 1769 SSP2 NVKYLVIV 6 8 10 100 1770 SSP2 NVKYLVIVF 6 9 10 100 1771 SSP2 NVKYLVIVFLI 6 11 10 100 1772 SSP2 QLVVILTDGI 155 10 10 100 1773 SSP2 QPRPRGDNF 303 9 9 90 1774 SSP2 QPRPRGDNFAV 303 11 9 90 1775 SSP2 QVRKHLNDR1 139 10 9 90 1776 SSP2 RINRENANQLV 147 11 10 100 1777 SSP2 RLPEENEW 554 8 10 100 1778 SSP2 RPRGDNFAV 305 9 9 90 1779 SSP2 SIRRHNWV 58 8 10 100 1780 SSP2 SLLSTNLPY 120 9 9 90 1781 SSP2 SQDNNGNRHV 437 10 10 100 1782 SSP2 TPYAGEPAPF 527 10 8 80 1783 SSP2 VIGPFMKAV 226 9 10 100 1784 SSP2 VIGPFMKAVCV 226 11 10 100 1785 SSP2 VILIDGIPDSI 158 11 10 100 1786 SSP2 VIVFLIFF 11 8 10 100 1787 SSP2 VIVFLIFFDLF 11 11 10 100 1788 SSP2 VPGAATPY 522 8 8 80 1789 SSP2 VPLAMKLI 69 8 10 100 1790 SSP2 VQNNIVDEI 28 9 10 100 1791 SSP2 VQNNIVDE1KY 28 11 10 100 1792 SSP2 VVILTDM 157 8 10 100 1793 SSP2 VVPGAATPY 521 9 8 80 1794 SSP2 WVNHAVPLAM 64 10 8 80 1795 SSP2 YLLMDCSGS1 50 10 10 100 1796 SSP2 YLVIVFLI 9 8 10 100 1797 SSP2 YLV1VFLIF 9 9 10 100 1798 SSP2 YLVIVFLIFF 9 10 10 100 1799

TABLE XV Malaria A01 Motif Peptides With Binding Information No. of Sequence Conservancy Seq. Protein Sequence Pos Amino Acids Freq. (%) A*0101 Id. CSP DNAGINLY 41 8 19 100 1800 CSP EPSDKHIEQY 345 10 15 79 1801 CSP FVEALFQEY 15 9 19 100 3.4000 1802 CSP NTRVLNELNY 31 10 19 100 0.0096 1803 CSP NYDNAGINLY 39 10 18 95 0.0012 1804 CSP PSDKHIEQY 346 9 15 79 1805 CSP VEALFQEY 16 8 19 100 1806 CSP VEALFQEYQCY 16 11 19 100 1807 CSP YNELEMNY 48 8 19 100 1808 CSP YNELEMNYY 48 9 19 100 1809 EXP LVEVNKRKSKY 64 11 1 100 1810 LSA DDDDKKKY 130 8 1 100 1811 LSA DEENIGIY 1796 8 1 100 1812 LSA DLDEFKPIVQY 1781 11 1 100 1813 LSA EDEISAEY 1761 8 1 100 1814 LSA ELSEDIAY 1897 9 1 100 1815 LSA FQDEENIGIY 1794 10 1 100 1.1000 1816 LSA HGDVLAEDLY 1644 10 1 100 0.0012 1817 LSA INDDDDKKKY 128 10 1 100 1818 LSA KSLYDEHIKKY 1854 11 1 100 1819 LSA KYEDEISAEY 1759 10 1 100 0.0011 1820 LSA LDEFKPIVQY 1782 10 1 100 1821 LSA LPSENERGY 1663 9 1 100 0.6700 1822 LSA LPSENERGYY 1663 10 1 100 0.0011 1823 LSA LSEDIMY 1898 8 1 100 1824 LSA LYDEHIKKY 1856 9 1 100 0.0011 1825 LSA NDDDDKKKY 129 9 1 100 1826 LSA PSENERGY 1664 8 1 100 1827 LSA PSENERGYY 1664 9 1 100 0.0790 1828 LSA QDEENIGIY 1795 9 1 100 1829 LSA SEEKIKKGKKY 1831 11 1 100 1830 LSA VDELSEDITKY 1895 11 1 100 1831 LSA VNDFQISKY 1752 9 1 100 1832 LSA YDEHGCY 1857 8 1 100 1833 LSA YEDEISAEY 1760 9 1 100 0.0012 1834 SSP2 CNDEVDLY 43 8 8 80 1835 SSP2 HPSDGKCNLY 206 10 10 100 0.0260 1836 SSP2 LLACAGLAY 510 9 10 100 1837 SSP2 LLSTNLPY 121 8 9 90 1838 SSP2 PSDGKCNLY 207 9 10 100 0.5400 1839

TABLE XVI Malaria A3 Motif Peptides With Binding Information No. of Sequence Conservancy SEQ. Protein Sequence Position Amino Acids Frequency (%) A*0301 Id. CSP NMPNDPNR 323 8 19 100 1897 CSP NIRVLNELNY 31 10 19 100 0.0005 1898 CSP NVDENANA 331 8 19 100 1899 CSP NVDENANANNA 331 11 16 84 1900 CSP NVDPNANPNA 200 10 19 100 1901 CSP PGDGNPDPNA 116 10 19 100 1902 CSP PSDKHIEQY 346 9 15 79 1903 CSP PSDICHIEQYLK 346 11 15 79 1904 CSP QCYGSSSNTR 24 10 19 100 1905 CSP QGHNMPNDPNR 320 11 19 100 1906 CSP QVRIKPGSA 382 9 19 100 1907 CSP RDGNNEDNEK 95 10 19 100 0.0005 1908 CSP RVLNEHNY 33 8 19 100 1909 CSP RVLNELNYDNA 33 11 19 100 1910 CSP SDKHIEQY 347 8 15 79 1911 CSP SDKHIEQYLK 347 10 15 79 1912 CSP SDKHIEQYLKK 347 11 15 79 1913 CSP SFLFVEALF 12 9 19 100 1914 CSP StGLIMVLSF 423 10 19 100 1915 CSP SSFLFVEA 11 8 19 100 1916 CSP SSFLFVEALF 11 10 19 100 1917 CSP SSIGLIMVLSF 422 11 19 100 1918 CSP SVSSFLFVEA 9 10 19 100 1919 CSP SVTCGNGIQVR 374 11 19 100 1920 CSP TCGNGIQVR 376 9 19 100 1921 CSP TCGNGIQVRIK 376 11 19 100 1922 CSP VDENANANNA 332 10 16 84 1923 CSP VDPNANPNA 201 9 19 100 1914 CSP VLNEINYDNA 34 10 19 100 1925 CSP VSSFLFVEA 10 9 19 100 1926 CSP VSSFLFVEALF 10 11 19 100 1927 CSP VTCGNGIQVR 375 10 19 100 0.0005 1928 CSP YDNAGINLY 40 9 18 95 1929 CSP YGKQENWY 56 8 19 100 1930 CSP YGKQENWYSLK 56 11 19 100 1931 CSP YGSSSNTR 26 8 19 100 1932 CSP YSLKKNSR 63 8 19 100 1933 EXP ADNANPDA 118 8 1 100 1934 EXP ADSESNGEPNA 125 11 1 100 1935 EXP ALFFITFNIC 10 9 1 100 1.1000 1936 EXP DDNNLVSGPEH 152 11 1 100 1937 EXP DLISDMIK 52 8 1 100 1938 EXP DLISDMIKK 52 9 1 100 0.0001 1939 EXP DSESNGEPNA 126 10 1 100 1940 EXP DVHDLISDMIK 49 11 1 100 1941 EXP ELYEVNKR 63 8 1 100 1942 EXP ELVEVNKRK 63 9 1 100 0.0001 1943 EXP ELVEVNKRKSK 63 11 1 100 1944 EXP ESLAEKTNIC 19 9 1 100 0.0001 1945 EXP ESNGEPNA 128 8 1 100 1946 EXP EVNKRKSK 66 8 1 100 1947 EXP EVNKRKSKY 66 9 1 100 0.0001 1948 EXP EVNKRKSKYK 66 10 1 100 0.0005 1949 EXP FFIIFNKESLA 12 11 1 100 1950 EXP FFLALFFIIF 7 10 1 100 1951 EXP FFIFNKESLA 13 10 1 100 1952 EXP FLALFFIIF 8 9 1 100 1953 EXP FLALFFIIFNK 8 11 1 100 1954 EXP GGVGLVLY 94 8 1 100 1955 EXP GLVLYNTEK 97 9 1 100 0.0069 1956 EXP GLVLYNTEKGR 97 11 1 100 1957 EXP GSGEPLIDVH 42 10 1 100 0.0005 1958 EXP GSGVSSKK 30 8 1 100 1959 EXP GSGVSSKKK 30 9 1 100 0.0003 1960 EXP GSGVSSKKKNK 30 11 1 100 1961 EXP GSSDPADNA 113 9 1 100 1962 EXP GTGSGVSSK 28 9 1 100 0.0039 1963 EXP GTGSGVSSKX 28 10 1 100 0.0071 1964 EXP GTGSGVSSKKK 28 11 1 100 1965 EXP GVGLVLYNTEK 95 11 1 100 1966 EXP GVSSKKKNK 32 9 1 100 0.0001 1967 EXP GVSSKKKNKK 32 10 1 100 0.0011 1968 EXP HDLISDMIK 51 9 1 100 0.0001 1969 EXP HDLISDMIKK 51 10 1 100 0.0009 1970 EXP IFNKESLA 15 8 1 100 1971 EXP IFNKESLAEK 15 10 1 100 0.0005 1972 EXP IGSSDPADNA 112 10 1 100 1973 EXP IIFNKESLA 14 9 1 100 1974 EXP IIFNKESLAEK 14 11 1 100 1975 EXP ILSVFFLA 3 8 1 100 1976 EXP ILSVFFLALF 3 10 1 100 1977 EXP ILSVFFLALFF 3 11 1 100 1978 EXP KGSGEPLIDVH 41 11 1 100 1979 EXP KGTGSGVSSK 27 10 1 100 0.0005 1980 EXP KGTGSOVSSKK 27 11 1 100 1981 EXP KIGSSDPA 111 8 1 100 1982 EXP KIGSSDPADNA 111 11 1 100 1983 EXP KILSVFFLA 2 9 1 100 0.1400 1984 EXP KILSVFFLALF 2 11 1 100 1985 EXP KLATSVLA 75 8 1 100 1986 EXP LALFFIIF 9 8 1 100 1987 EXP LALFFIIFNK 9 10 1 100 0.0140 1988 EXP LFFIIFNK 11 8 1 100 1989 EXP LGGVGLVLY 93 9 1 100 0.0001 1990 EXP LISDMIKK 53 8 1 100 1991 EXP LLGGVGLVLY 92 10 1 100 0.0034 1992 EXP LSVFFLALF 4 9 1 100 1993 EXP LSVFFLALFF 4 10 1 100 1994 EXP LVEVNKRK 64 8 1 100 1995 EXP LVEVNKRKSK 64 10 1 100 0.0005 1996 EXP LVEVNKRKSKY 64 11 1 100 1997 EXP LVLYNIEK 98 8 1 100 1998 EXP LVLYNTEKGR 98 10 1 100 0.0005 1999 EXP LVLYNTEKGRH 98 11 1 100 2000 EXP NADPQVTA 134 8 1 100 2001 EXP NLVSGPEH 155 8 1 100 2002 EXP NTEKGRHPF 102 9 1 100 2003 EXP NTEKGFHPFK 102 10 1 100 0.0047 2004 EXP PADNANPDA 117 9 1 100 2005 EXP PFKIGSSDPA 109 10 1 100 2006 EXP SDPADNANPDA 115 11 1. 100 2007 EXP SGEPLIDVH 43 9 1 100 0.0001 2008 EXP SGVSSKKK 31 8 1 100 2009 EXP SGVSSKKKNK 31 10 1 100 0.0005 2010 EXP SGVSSKKKNKK 31 11 1 100 2011 EXP SLAEKTINIK 20 8 1 100 2012 EXP SSDPADNA 114 8 1 100 2013 EXP SSKKKNKK 34 8 1 100 2014 EXP SVFFLALF S 8 1 100 2015 EXP SVFFLALFF 5 9 1 100 2016 EXP TGSGVSSK 29 8 1 100 2017 EXP TGSGVSSKK 29 9 1 100 0.0001 2018 EXP TGSGVSSKKK 29 10 1 100 0.0005 2019 EXP VFFLALFF 6 8 1 100 2020 EXP VFFLALFFIIF 6 11 1 100 2021 EXP VGLVLYNIEK 96 10 1 100 0.0005 2022 EXP VLLGGVGLVLY 91 11 1 100 2023 EXP VLYNTEKGR 99 9 1 100 0.0110 2024 EXP VLYNIEKGRH 99 10 1 100 0.0029 2025 EXP VSSKKKNK 33 8 1 100 2026 EXP VSSKKKNKK 33 9 1 100 0.0001 2027 LSA ADTKKNLER 1632 9 1 100 2028 LSA ADTKKNLERK 1632 10 1 100 0.0001 2029 LSA ADTKKNLERKK 1632 11 1 100 2030 LSA AIELPSENER 1660 10 1 100 0.0001 2031 LSA DDDDKKKY 130 8 1 100 2032 LSA DDDDKKKYIK 130 10 1 100 0.0001 2033 LSA DDDKKKYIK 131 9 1 100 0.0001 2034 LSA DDEDLDEF 1778 8 1 100 2035 LSA DDEDLDEFK 1778 9 1 100 0.0001 2036 LSA DDKKKYIK 132 8 1 100 2037 LSA DDIDEGIEK 1817 9 1 100 0.0001 2038 LSA DGSIKPEQK 1724 9 1 100 0.0001 2039 LSA DIHKGHLEEK 1713 10 1 100 0.0004 2040 LSA DIHKGHLEEKK 1713 11 1 100 2041 LSA DITKYFMK 1901 8 1 100 2042 LSA DLDEFKPIVQY 1781 11 1 100 2043 LSA DLDEGIEK 1818 8 1 100 2044 LSA DLEEKAAK 148 8 1 100 2045 LSA DLEQDRLA 1388 8 1 100 2046 LSA DLEQDRLAK 1388 9 1 100 0.0001 2047 LSA DLEQDRLAKEK 1388 11 1 100 2048 LSA DLEQERLA 1609 8 1 100 2049 LSA DLEQERLAK 1609 9 1 100 0.0001 2050 LSA DLEQERLAKEK 1609 11 1 100 2051 LSA DLEQERLANEK 1524 11 1 100 2052 LSA DLEpERRA 1575 8 1 100 2053 LSA DLEQERRAK 1575 9 1 100 0.0001 2054 LSA DLEQERRAKEK 1575 11 1 100 2055 LSA DLEQRKADTK 1626 10 1 100 0.0001 2056 LSA DLEQRKADIKK 1626 11 1 100 2057 LSA DLERTKASK 1184 9 1 100 0.0001 2058 LSA DLYGRLEIPA 1651 10 1 100 2059 LSA DSEQERLA 521 8 1 100 2060 LSA DSEQERLAK 521 9 1 100 0.0001 2061 LSA DSEQERLAKEK 521 11 1 100 2062 LSA DSKEISIIEK 1689 10 1 100 0.0001 2063 LSA DTKKNLER 1633 8 1 100 2064 LSA DTKIMERK 1633 9 1 100 0.0001 2065 LSA DTKKNLERKK 1633 10 1 100 0.0001 2066 LSA DVLAEDLY 1646 8 1 100 2067 LSA DVLAEDLYGR 1646 10 1 100 0.0001 2068 LSA DVNDFQISK 1751 9 1 100 0.0001 2069 LSA DVNDFQISKY 1751 10 1 100 0.0003 2070 LSA EDDEDLDEF 1777 9 1 100 2071 LSA EDDEDLDEFK 1777 10 1 100 0.0001 2072 LSA EDEISAEY 1761 8 1 100 2073 LSA EDITKYFMK 1900 9 1 100 0.0001 2074 LSA EDKSADIQNH 1733 10 1 100 2075 LSA EDLEEKAA 147 8 1 100 2076 LSA EDLEEKAAK 147 9 1 100 0.0002 2077 LSA EDLYGRLEIPA 1650 11 1 100 2078 LSA EFKPIVQY 1784 8 1 100 2079 LSA EFPIVQYDNF 1784 11 1 100 2080 LSA EGRRDIHK 709 8 1 100 2081 LSA EGRRDIHKGH 1709 10 1 100 0.0001 2082 LSA EIIKSNLR 33 8 1 100 2083 LSA EISIIEKTNR 1692 10 1 100 0.0001 2084 LSA ELEDLIEK 1805 8 1 100 2085 LSA ELPSENER 1662 8 1 100 2086 LSA ELPSENERGY 1662 10 1 100 0.0001 2087 LSA ELPSENERGYY 1662 11 1 100 2088 LSA ELSEDITK 1897 8 1 100 2089 LSA ESLSEDITKY 1897 9 1 100 0.0002 2090 LSA ELSEDITKYF 1897 10 1 100 2091 LSA ELSEEKIK 1829 8 1 100 2092 LSA ELSEEKIKK 1829 9 1 100 0.0002 2093 LSA ELSEEKIKKGK 1829 11 1 100 2094 LSA ELTMSNVK 83 8 1 100 2095 LSA ESITTNVEGR 1702 10 1 100 0.0001 2096 LSA ESITTNVEGRR 1702 11 1 100 2097 LSA ETVNISDVNDF 1745 11 1 100 2098 LSA FIKSLFHIF 1877 9 1 100 2099 LSA FILVNLLIF 11 9 1 100 2100 LSA FILVNLLIFH 11 10 1 100 0.0310 2101 LSA FLKENKLNK 111 9 1 100 0.0260 2102 LSA GDVLAEDLY 1645 9 1 100 2103 LSA GDVLAEDLYGR 1645 11 1 100 2104 LSA GSIKPEQK 1725 8 1 100 2105 LSA GSIKPEQKEDK 1725 11 1 100 2106 LSA GSSNSRNR 42 8 1 100 2107 LSA GVSENIFLK 105 9 1 100 0.2700 2108 LSA HGDVLAEDLY 1644 10 1 100 0.0001 2109 LSA HIINDDDDK 126 9 1 100 0.0002 2110 LSA HIINDDDDKK 126 10 1 100 0.0001 2111 LSA HIINDDDDKKK 126 11 1 100 2112 LSA HIKKYKNDK 1860 9 1 100 0.0002 2113 LSA HILYISFY 3 8 1 100 2114 LSA HILYISFYF 3 9 1 100 2115 LSA HINGKIIK 20 8 1 100 2116 LSA HLEEKKDGSIK 1718 11 1 100 2117 LSA HVLSHNSY 59 8 1 100 2118 LSA HVLSHNSYEK 59 10 1 100 0.0170 2119 LSA IFHINGKIIK 18 10 1 100 0.0001 2120 LSA IFLKENKLNK 110 10 1 100 0.0001 2121 LSA IINDDDDK 127 8 1 100 2122 LSA IINDDDDKK 127 9 1 100 0.0002 2123 LSA IINDDDDKKK 127 10 1 100 0.0001 2124 LSA IINDDDDKKKY 127 11 1 100 2125 LSA ILVNLLIF 12 12 8 100 2126 LSA ILVNLLIFH 12 9 1 100 0.0150 2127 LSA ILYISFYF 4 8 1 100 2128 LSA ISDVNDMISK 749 11 1 100 2129 LSA ISHEKTNR 693 9 1 100 0.0001 2130 LSA ISKYEDEISA 757 10 1 100 2131 LSA ITTNVEGR 704 8 1 100 2132 LSA ITTNVEGRR 704 9 1 100 0.0002 2133 LSA DAMESEDITK 894 11 1 100 2134 LSA KADTKKNLER 631 10 1 100 0.0001 2135 LSA KADTKKNLERK 631 11 1 100 2136 LSA KDEGIKSNIR 31 10 1 100 2137 LSA KDGSIKPEQK 723 10 1 100 0.0004 2138 LSA KDKELTMSNVK 80 11 1 100 2139 LSA KDNNFKPNDK 845 10 1 100 0.0001 2140 LSA KFIKSLFH 876 8 1 100 2141 LSA KFIKSLFHIF 876 10 1 100 2142 LSA KGHLEEKK 716 8 1 100 2143 LSA KGKKYEKIK 837 9 1 100 0.0002 2144 LSA KIIKNSEK 24 8 1 100 2145 LSA KKKKGKKY 834 8 1 100 2146 LSA KIKKGKKYEK 834 10 1 100 0.0081 2147 LSA KLNKEGKLIEN 116 1t 1 100 2148 LSA KLQEQQSDLER 177 11 1 100 2149 LSA KSADIQNH 735 8 1 100 2150 LSA KSLYDEIHK 854 9 1 100 0.0005 2151 LSA KSLYDMIKK 854 10 1 100 0.0094 2152 LSA KSLYDEHIKKY 854 11 1 100 2153 LSA KSSEELSEEK 825 10 1 100 0.0001 2154 LSA KTKDNNFK 843 8 1 100 2155 LSA KTKNNENNK 68 9 1 100 0.0028 2156 LSA KTKNNENNKF 68 10 1 100 2157 LSA KTKNNENNKFF 68 11 1 100 2158 ISA LAEDLYGR 1648 8 1 100 2159 LSA LAKEKLQEQQR 1615 11 1 100 2160 LSA LANEKLQEQQR 1530 11 1 100 2161 LSA LDDLDEGIEK 1816 10 1 100 0.0001 2162 LSA LDEFKPIVQY 1782 10 1 100 2163 LSA LGVSENIF 104 8 1 100 2164 LSA LGVSENIFLK 104 10 1 100 0.0001 2165 LSA LIFHINGK 17 8 1 100 2166 LSA LIFHINGKIIK 17 11 1 100 2167 LSA LLIFNINGK 16 9 1 100 0.0260 2168 LSA LSEDITKY 1898 8 1 100 2169 LSA LSEDITKYF 1898 9 1 100 2170 LSA LSEDITKYDAK 1898 11 1 100 2171 LSA LSEEKIKK 1830 8 1 100 2172 ISA LSEEKIKKGK 1830 10 1 100 0.0004 2173 LSA LSEEKIKKGKK 1830 11 1 100 2174 LSA LSHNSYEK 61 8 1 100 2175 LSA LSFINSYEKTK 61 10 1 100 0.0004 2176 LSA LVNLLIFH 13 8 1 100 2177 LSA NDDDDKKK 129 8 1 100 2178 LSA NDDDDKKKY 129 9 1 100 2179 LSA NDDDDKKKYIK 129 11 1 100 2180 LSA NDFQISKY 1753 8 1 100 2181 LSA NDKQVNKEK 1866 9 1 100 0.0002 2182 LSA NDKQVNKEKEK 1866 11 1 100 2183 LSA NDKSLYDEH 1852 9 1 100 2184 LSA NDKSLYDEHIK 1852 11 1 100 2185 LSA NFKPNDKSLY 1848 10 1 100 2186 LSA NFQDEENIGIY 1793 11 1 100 2187 ISA NGKIIKNSEK 22 10 1 100 0.0004 2188 LSA NIFLKENK 109 8 1 100 2189 LSA NIFLKENKLNK 109 11 1 100 2190 LSA NISDVNDF 1748 8 1 100 2191 LSA NLDDLDEGIEK 1815 11 1 100 2192 LSA NLERKKEH 1637 8 1 100 2193 LSA NLGVSENIF 103 9 1 100 2194 LSA NLGVSENIFLK 103 11 1 100 2195 LSA NLLIFHINGK 15 10 1 100 0.0049 2196 LSA NLRSGSSNSR 38 10 1 100 0.0004 2197 LSA NSEKDFIKK 28 9 1 100 0.0002 2198 LSA NSRNRKNEEK 45 10 1 100 0.0004 2199 LSA NSRNRINEEKH 45 11 1 100 2200 LSA NVEGRRDIH 1707 9 1 100 0.0002 2201 LSA NVEGRRDIHK 1707 10 1 100 0.0004 2202 LSA NVKNVSQINF 88 10 1 100 2203 LSA NVKNVSQINFK 88 11 1 100 2204 LSA NVSQTNFK 91 8 1 100 2205 LSA PAIELPSENER 659 11 1 100 2206 LSA PIVQYDNF 787 8 1 100 2207 LSA PSENERGY 664 8 1 100 2208 LSA PSENERGYY 664 9 1 100 0.0001 2209 LSA QDEENIGIY 795 9 1 100 2210 LSA QDEENIGIYK 795 10 1 100 0.0004 2211 LSA QDNRGNSR 681 8 1 100 2212 LSA QDNRGNSRDSK 681 11 1 100 2213 LSA QDRLAKEK 391 8 1 100 2214 LSA QGWISCLEM 128 11 1 100 2215 LSA QISKYEDEISA 756 11 1 100 2216 LSA QSDLEQDR 386 8 1 100 2217 LSA QSDLEQDRLA 386 10 1 100 2218 LSA QSDLEQDRLAK 386 11 1 100 2219 LSA QSDLEQER 590 8 1 100 2220 LSA QSDLEQERLA 590 10 1 100 2221 LSA QSDLEQERLAK 590 11 1 100 2222 LSA QSDLEQERR 573 9 1 100 0.0002 2223 LSA QSDLEQERRA 573 10 1 100 2224 LSA QSDLEQDRLAK 573 11 1 100 2225 LSA QSDLERTK 182 8 1 100 2226 LSA QSDLERTKA 182 9 1 100 2227 LSA QSDLERTKASK 182 11 1 100 2228 LSA QSDSEQER 519 8 1 100 2229 LSA QSDSEQERLA 519 10 1 100 2230 LSA QSDLEQDRLAK 519 11 1 100 2231 LSA QSSLPQDNR 1676 9 1 100 0.0002 2232 LSA QTNFKSLLR 94 9 1 100 0.0320 2233 ISA QVNKEKEK 1869 8 1 100 2234 ISA QVNKEIEKF 1869 9 1 100 2235 LSA QVNKEKEKFIK 1869 11 1 100 2236 LSA RDIHKGHLEIEK 1712 11 1 100 2237 ISA RDLEQERLA 1608 9 1 100 2238 LSA RDLEQERLAK 608 10 1 100 0.0004 2239 LSA RDLEQERR 540 8 1 100 2240 LSA RDLEQERRA 540 9 1 100 2241 LSA RDLEQERRAK 540 10 1 100 0.0004 2242 LSA RDLEQRKA 625 8 1 100 2243 ISA RDLEQRKADTK 625 11 1 100 2244 ISA RDSKEISIIEK 688 11 1 100 2245 ISA RGNSRDSK 684 8 1 100 2246 LSA RINEEKHEK 49 9 1 100 0.0033 2247 LSA RINEEKNEKK 49 10 1 100 0.0024 2248 ISA RINEEKHEKKH 49 11 1 100 2249 LSA RSGSSNSR 40 8 1 100 2250 ISA RSGSSNSRNR 40 10 1 100 0.0011 2251 LSA SDLEQDRLA 1387 9 1 100 2252 ISA SDLBQDRLAK 1387 10 1 100 0.0002 2253 LSA SDLEQERLA 1591 9 1 100 2254 ISA SDLEQERLAK 1591 10 1 100 0.0002 2255 ISA SDLEQERR 1574 8 1 100 2256 LSA SDLEQERRA 1574 9 1 100 2257 LSA SDLEQERRAK 1574 10 1 100 0.0002 2258 LSA SDLERTKA 1183 8 1 100 2259 ISA SDLERTKASK 1183 10 1 100 0.0002 2260 LSA SDSEQERLA 520 9 1 100 2261 ISA SDSEQERLAK 520 10 1 100 0.0002 2262 ISA SDVNDFQISK 1750 10 1 100 0.0002 2263 LSA SDVNDFQISKY 1750 11 1 100 2264 LSA SGSSNSRNR 41 9 1 100 0.0002 2265 LSA SIIEKTNR 1694 8 1 100 2266 LSA SIKPEQKEDK 1726 10 1 100 0.0002 2267 LSA MTTNVEGR 1703 9 1 100 0.0002 2268 LSA MTTNVEGRR 1703 10 1 100 0.0002 2269 LSA SLPQDNRGNSR 1678 11 1 100 2270 LSA SLYDEHKK 1855 8 1 100 2271 LSA SLYDEHIKK 1855 9 1 100 0.0460 2272 LSA SLYDEHIKKY 1855 10 1 100 0.0015 2273 ISA SLYDEHIKKYK 1855 11 1 100 2274 LSA SSEELSEEK 1826 9 1 100 0.0002 2275 LSA SSEEBEDUK 1826 11 1 100 2276 LSA SSLPQDNR 1677 8 1 100 2277 LSA TTNVEGRR 1705 8 1 100 2278 LSA TTNVEGRRIMH 1705 11 1 100 2279 ISA TVNISDVNDF 1746 10 1 100 2280 ISA VDESEDITK 1895 10 1 100 0.0002 2281 LSA VDELSEDITKY 1895 11 1 100 2282 ISA VLAEDLYGR 1647 9 1 100 0.0013 2283 LSA VLSHNSYEK 60 9 1 100 0.0280 2284 LSA VLSHNSYEKTK 60 11 1 100 2285 LSA VSENIFLK 106 8 1 100 2286 LSA VSENIFLKENK 106 11 1 100 2287 ISA VSQTNFKSLLR 92 11 1 100 2288 LSA YEEHDUCY 1857 8 1 100 2289 LSA YDEHIKKYK 1857 9 1 100 0.0005 2290 LSA YFILVNLLIF 10 10 1 100 2291 LSA YFILVNLLWH 10 11 1 100 2292 LSA YGRLEIPA 1653 8 1 100 2293 LSA YIKGQDENR 137 9 1 100 0.0025 2294 SSP2 AATPYAGEPA 525 10 8 80 2295 SSP2 ACAGLAYK 512 8 10 100 2296 SSP2 ACAGLAYKF 512 9 10 100 2297 SSP2 ADSAWENVK 216 9 10 100 0.0002 2298 SSP2 AFNRFLVGCH 197 10 10 100 2299 SSP2 AGGIAGGLA 501 9 10 100 2300 SSP2 AGGLALLA 505 8 10 100 2301 SSP2 AGGLALLACA 505 10 10 100 2302 SSP2 ALLACAGLA 509 9 10 100 0.0002 2303 SSP2 ALLACAGLAY 509 10 10 100 0.0630 2304 SSP2 ALLACAGLAYK 509 11 10 100 2305 SSP2 ALLQVRKH 136 8 9 90 2306 SSP2 ASKNKEKA 107 8 10 100 2307 SSP2 ATPYAGEPA 526 9 8 80 2308 SSP2 ATPYAGEPAPF 526 11 8 80 2309 SSP2 AVCVEVEK 233 8 10 100 2310 SSP2 AVCVEVEKTA 233 10 10 100 2311 SSP2 CAGLAYKF 513 8 10 100 2312 SSP2 CGKGTRSR 257 8 10 100 2313 SSP2 CGKGTRSRK 257 9 10 100 0.0002 2314 SSP2 CGKGIRSRKR 257 10 10 100 0.0002 2315 SSP2 CSGSIRRH 55 8 10 100 2316 SSP2 CSVTCGKGTR 253 10 10 100 0.0002 2317 SSP2 CVEVEKTA 235 8 10 100 2318 SSP2 DALLQVRK 135 8 9 90 2319 SSP2 DALLQVRKH 135 9 9 90 0.0004 2320 SSP2 DASKNKEK 106 8 10 100 2321 SSP2 DASKNKEKA 106 9 10 100 2322 SSP2 DCSGSIRR 54 8 10 100 2323 SSP2 DCSGSIRRH 54. 9 10 100 2324 SSP2 DDQPRPRGDNF 301 11 9 90 2325 SSP2 DDREENFDIPK 385 11 10 100 2326 SSP2 CCKCNLYA 209 8 10 100 2327 SSP2 DGKCNLYADSA 209 11 10 100 2328 SSP2 DIPKKPENK 392 9 10 100 0.0004 2329 SSP2 DIPICKPENKH 392 10 10 100 0.0002 2330 SSP2 DLDEPEQF 546 8 10 100 2331 SSP2 DLDEPEQFR 546 9 10 100 0.0002 2332 SSP2 DLFLVNGR 19 8 10 100 2333 SSP2 DSAWENVK 217 8 10 100 2334 SSP2 DSIQDSLK 166 8 10 100 2335 SSP2 DSIQDSLKESR 166 11 10 100 2336 SSP2 DSLKESRK 170 8 9 90 2337 SSP2 DVPKNPEDDR 378 10 10 100 0.0002 2338 SSP2 DVQNNIVDBK 27 11 10 100 2339 SSP2 EDDQPRPR 300 8 10 100 2340 SSP2 EDDREENF 384 8 10 100 2341 SSP2 EDKDLDEPEQF 543 11 10 100 2342 SSP2 EDRETRPH 450 8 9 90 2343 SSP2 EDRETRPHGR 450 10 9 90 2344 SSP2 EIIRLHSDA 99 9 10 100 2345 SSP2 EIIRLHSDASK 99 11 10 100 2346 SSP2 ELQEQCEEER 276 10 8 80 0.0002 2347 SSP2 ETLGEEDK 538 8 10 100 2348 SSP2 EVCNDEVDLY 41 10 8 80 0.0002 2349 SSP2 EVPSDVPK 374 8 10 100 2350 SSP2 FDETLGEEDK 536 10 10 100 0.0002 2351 SSP2 FDIPKKPENK 391 10 10 100 0.0002 2352 SSP2 FDIPKKPENKH 391 11 10 100 2353 SSP2 FDLFLVNGR 18 9 10 100 2354 SSP2 FFDLFLVNGR 17 10 10 100 2335 SSP2 FGIGQGINVA 188 10 10 100 2356 SSP2 FGIGQGINVAF 188 11 10 100 2357 SSP2 FLIFFDLF 14 8 10 100 2358 SSP2 FLVGCHPSDGK 201 11 10 100 2359 SSP2 FMKAVCVEVEK 230 11 10 100 2360 SSP2 FVVPGAATPY 520 10 8 80 0.0002 2361 SSP2 FVVPGAATPYA 520 11 8 80 2362 SSP2 GAATPYAGEPA 524 11 8 80 2363 SSP2 GCHPSDGK 204 8 10 100 2364 SSP2 GDNFAVEK 308 8 9 90 2365 SSP2 GGIAGGLA 502 8 10 100 2366 SSP2 GGIAGGLALLA 502 11 10 100 2367 SSP2 GGLALLACA 506 9 10 100 2368 SSP2 GIAGGLALLA 503 10 10 100 2369 SSP2 GIGQGINVA 189 9 10 100 2370 SSP2 GIGQGINVAF 189 10 10 100 2371 SSP2 GINVAFNR 193 8 10 100 2372 SSP2 GINVAFNRF 193 9 10 100 2373 SSP2 GIPDSIQDSLK 163 11 10 100 2374 SSP2 GLALLACA 507 8 10' 100 2375 SSP2 GLALLACAGLA 507 11 10 100 2376 SSP2 GLAYKFVVPGA 515 11 10 100 2377 SSP2 GSIRRHNWVNH 37 11 8 80 2378 SSP2 GTRSRKRELH 260 11 10 100 2379 SSP2 HAVPLAMK 67 8 10 100 2380 SSP2 HDNQNNLPNDK 401 11 10 100 2381 SSP2 HGRNNENR 457 8 10 100 2382 SSP2 HGRNNENRSY 457 10 10 100 0.0004 2383 SSP2 HLNDRINR 143 8 10 100 2384 SSP2 HLNDRINRENA 143 11 10 100 2385 SSP2 HSDASKNK 104 8 10 100 2386 SSP2 HSDASKNKEK 104 10 10 100 0.0004 2387 SSP2 HSDASKNKEKA 104 11 10 100 2388 SSP2 HVPNSEDR 445 8 10 100 2389 SSP2 HVPNSEDRE1R 445 11 9 90 2390 SSP2 IAGGIAGGLA 500 10 10 100 2391 SSP2 IAGGLALLA 504 9 10 100 0.0002 2392 SSP2 IAGGLALLACA 504 11 10 100 2393 SSP2 IFFDLFLVNGR 16 11 10 100 2394 SSP2 IGQGINVA 190 8 10 100 2395 SSP2 IGQGINVAF 190 9 10 100 2396 SSP2 IGQGINVAFNR 190 11 10 100 2397 SSP2 RRLHSDA 100 8 10 100 2398 SSP2 IIRLHSDASK 100 10 10 100 0.0230 2399 SSP2 IVDEIKYR 32 8 9 90 2400 SSP2 IVFLIFFDLF 12 10 10 100 2401 SSP2 KAVCVEVEK 232 9 10 100 0.0004 2402 SSP2 KAVCVEVEKTA 232 11 10 100 2403 SSP2 KCNLYADSA 211 9 10 100 2404 SSP2 KDLDEPEQF 545 9 10 100 2405 SSP2 KDLDEPEQFR 545 10 10 100 2406 SSP2 KFVVPGAA 519 8 10 100 2407 SSP2 KFVVPGAAIPY 519 11 8 80 2408 SSP2 KGIRSRICR 259 8 10 100 2409 SSP2 KIAGGIAGGLA 499 11 10 100 2410 SSP2 KVLDNERK 421 8 8 80 2411 SSP2 LACACLAY 511 8 10 100 2412 SSP2 LACAGLAYK 511 9 10 100 0.0240 2413 SSP2 LACAGLAYKF 511 10 10 100 2414 SSP2 LALLACAGLA 508 10 10 100 2415 SSP2 LALLACAGIAY 508 11 10 100 2416 SSP2 LAYKFVVPGA 516 10 10 100 2417 SSP2 LAYKFVVPGAA 516 11 10 100 2418 SSP2 LDEPEQFR 547 8 10 100 2419 SSP2 LGNVKYLVIVF 4 11 10 100 2420 SSP2 LLACAGLA 510 8 10 100 2421 SSP2 LLACAGLAY 510 9 10 100 0.0120 2422 SSP2 LLACAGLAYK 510 10 10 100 0.9500 2423 SSP2 LLACAGLAYKF 510 11 10 100 2424 SSP2 LLMDCSGSIR 51 10 10 100 0.0004 2425 SSP2 LLMDCSGSIRR 51 11 10 100 2426 SSP2 LLQVRKHLNDR 137 11 9 90 2427 SSP2 LLSINLPY 121 8 9 90 2428 SSP2 LLSTNLPYGR 121 10 8 80 0.0017 2429 SSP2 LMDCSGSIR 52 9 10 100 0.0004 2430 SSP2 LMDCSGSIRR 52 10 10 100 0.0015 2431 SSP2 LMDCSGSIRRH 52 11 10 100 2432 SSP2 LSTNLPYGR 122 9 8 80 0.0004 2433 SSP2 LVGCHPSDOK 202 10 10 100 0.0004 2434 SSP2 LVIVFLIF 10 8 10 100 2435 SSP2 LVIVFLIFF 10 9 10 100 2436 SSP2 MDCSGSIR 53 8 10 100 2437 SSP2 MDCSGSIRR 53 9 10 100 2438 SSP2 MDCSGSIRRH 53 10 10 100 2439 SSP2 NDRINRENA 145 9 10 100 2440 SSP2 NFDIPKKPENK 390 11 10 100 2441 SSP2 NIPEDSEK 366 8 10 100 2442 SSP2 NIVDSKY 31 8 10 100 2443 SSP2 NIVDEIKYR 31 9 9 90 0.0005 2444 SSP2 NLPNDKSDR 406 9 10 100 0.0005 2445 SSP2 NSEDRETR 448 8 9 90 2446 SSP2 NSEDRETRPH 448 10 9 90 0.0004 2447 SSP2 NVIGPFMK 225 8 10 100 2448 SSP2 NVIGPFMKA 225 9 10 100 0.0002 2449 SSP2 NVKNVIGPF 222 9 10 100 2450 SSP2 NVKNVIGPFMK 222 11 10 100 2451 SSP2 NVKYLVIVF 6 9 10 100 2452 SSP2 PCSVTCGK 252 8 10 100 2453 SSP2 PCSVTCGKGTR 252 11 10 100 2454 SSP2 PDSIQDSLK 165 9 10 100 0.0005 2455 SSP2 PFDETLGEEDK 535 11 10 100 2456 SSP2 PGAATPYA 523 8 8 80 2457 SSP2 PSDGKCNLY 207 9 10 100 0.0002 2458 SSP2 PSDOKCNLYA 207 10 10 1013 2459 SSP2 PSPNPEEGK 328 9 10 100 0.0005 2460 SSP2 QCEEERCPPK 280 10 8 80 0.0004 2461 SSP2 QDNNGNRH 438 8 10 100 2462 SSP2 QDSLKESR 169 8 10 100 2463 SSP2 QDSLKESRK 169 9 9 90 0.0005 2464 SSP2 QGINVAFNR 192 9 10 100 0.0009 2465 SSP2 QGINVAFNRF 192 10 10 100 2466 SSP2 QSQDNNGNR 436 9 10 100 0.0005 2467 SSP2 QSQDNNONRH 436 10 10 100 0.0004 2468 SSP2 QVRICHLNDR 139 9 9 90 0.0005 2469 SSP2 RGDNFAVEK 307 9 9 90 0.0005 2470 SSP2 RGVKIAVF 181 8 9 90 2471 SSP2 RLHSDASK 102 8 10 100 2472 SSP2 RLHSDASKNK 102 10 10 100 0.0240 2473 SSP2 RSRKREILH 262 9 10 100 0.0110 2474 SSP2 SDASICNKEK 105 9 10 100 0.0005 2475 SSP2 SDASICNICEKA 105 10 10 100 2476 SSP2 SDGKCNLY 208 8 10 100 2477 SSP2 SDGKCNLYA 208 9 10 100 2478 SSP2 SDNKYKIA 494 8 9 90 2479 SSP2 SDVPKNPEDDR 377 11 10 100 2480 SSP2 SIQDSLKESR 167 10 10 100 0.0004 2481 SSP2 SIQDSLKESRK 167 11 9 90 2482 SSP2 SIRRHNWVNH 58 10 8 80 0.0011 2483 SSP2 SIRRHNWVNHA 58 11 8 80 2484 SSP2 SLLSTNLPY 120 9 9 90 0.0280 2485 SSP2 SLLSTNLPYGR 120 11 8 80 2486 SSP2 STNLPYGR 123 8 8 80 2487 SSP2 SVTCGKGTR 254 9 10 100 0.0005 2488 SSP2 SVICGKGTRSR 254 11 10 100 2489 SSP2 TCGKGTRSR 256 9 10 100 2490 SSP2 TCGKGTRSRK 256 10 10 100 0.0004 2491 SSP2 TCGKGIRSRKR 256 11 10 100 2492 SSP2 VAFNRFLVGCH 196 11 10 100 2493 SSP2 VCNDEVDLY 42 9 8 80 2494 SSP2 VCVEVEKTA 234 9 10 100 2495 SSP2 VFGIGQGINVA 187 11 10 100 2496 SSP2 VFLIFFDLF 13 9 10 100 2497 SSP2 VGCHPSDGK 203 9 10 100 0.0005 2498 SSP2 VIGPFMKA 226 8 10 100 2499 SSP2 VIVFLIFF 11 8 10 100 2500 SSP2 VIVFLIFFDLF 11 11 10 100 2501 SSP2 VTCGKGTR 255 8 10 100 2502 SSP2 VTCGKGTRSR 255 10 10 100 0.0004 2503 SSP2 VTCGKGTRSRK 255 11 10 100 2504 SSP2 VVPGAATPY 521 9 8 80 0.0005 2505 SSP2 VVPGAATPYA 521 10 8 80 2506 SSP2 WSPCSVTCGK 250 10 10 100 0.0004 2507 SSP2 WVNHAVPLA 64 9 8 80 0.0002 2508 SSP2 WVNHAVPLAMK 64 11 8 80 2509 SSP2 YADSAWENVIC 215 10 10 100 0.0004 2510 SSP2 YAGEPAPF 529 8 8 80 2511 SSP2 YLLMDCSGSIR 50 11 10 100 2512 SSP2 YLVIVFLIF 9 9 10 100 2513 SSP2 YLVIVFLIFF 9 10 10 100 2514

TABLE XVII Malaria All Motif Peptides With Binding Information No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*1101 Seq. Id. CSP ALFQEYQCY 18 9 19 100 0.0021 2515 CSP ANANNAVK 336 8 16 84 2516 CSP ANPNANKNK 305 9 19 100 2517 CSP CGNGIQVR 377 8 19 100 2518 CSP CGNGIQVRIK 377 10 19 100 0.0002 2519 CSP DGNNEDNEX 96 9 19 100 0.0002 2520 CSP DGNNEDNEKLR 96 11 19 100 2521 CSP DGNNNNGDNGR 77 11 17 89 2522 CSP DIEKKICK 402 8 19 100 2523 CSP DIEKKICKMEK 402 11 19 100 2524 CSP DNAGINLY 41 8 18 95 2525 CSP DNEKLRKPK 101 9 19 100 2526 CSP DNEKLRKPKH 101 10 19 100 2527 CSP DNEKLRKPKHK 101 11 19 100 2528 CSP DNGREGKDEDK 84 11 19 100 2529 CSP EALFQEYQCY 17 10 19 100 0.0002 2530 CSP EDNEKLRK 100 8 19 100 2531 CSP EDNEKLRKPK 100 10 19 100 0.0002 2532 CSP EDNEKLRKPKH 100 11 19 100 2533 CSP EGKDEDKR 88 8 19 100 2534 CSP ELEMNYYGK 50 9 19 100 0.0003 2535 CSP ENANANNAVK 334 10 16 84 2536 CSP ENKIEKKICK 400 10 19 100 2537 CSP ENWYSLKK 60 8 19 100 2538 CSP ENWYSLKKNSR 60 11 19 100 2539 CSP FLFVEALFQEY 13 11 19 100 2540 CSP FVEALFQEY 15 9 19 100 0.0003 2541 CSP GDNGREGK 83 8 19 100 2542 CSP GNGIQVRIK 378 9 19 100 2543 CSP GNNEDNEK 97 8 19 100 2544 CSP GNNEDNEKLR 97 10 19 100 2545 CSP GNNEDNEKLRK 97 11 19 100 2546 CSP GNNNNGDNGR 78 10 19 100 2547 CSP HIEQYLKK 350 8 15 79 2548 CSP HNMPNDPNR 322 9 19 100 2549 CSP INLYNELEMNY 45 11 18 95 2550 CSP KLRKPKHK 104 8 19 100 2551 CSP KLRKPKHKK 104 9 19 100 0.0037 2552 CSP KLRKPKHKKLK 104 11 19 100 2553 CSP KNNNNEEPSDK 343 11 19 100 2554 CSP KNNQGNGQGH 313 10 19 100 2555 CSP LDYENDIEK 397 9 18 95 0.0002 2556 CSP LDYENDIEKK 397 10 18 95 0.0002 2557 CSP LFQEYQCY 19 8 19 100 2558 CSP LFVEALFQEY 14 10 19 100 2559 CSP LNYDNAGINLY 38 11 18 95 2560 CSP MNYYGKQENWY 53 11 19 100 2561 CSP NANANNAVK 335 9 16 1984 0.0002 2562 CSP NANPNANPNK 304 10 19 100 0.0021 2563 CSP NDIEKKICK 401 9 19 100 0.0002 2564 CSP NGDNGREGK 82 9 19 100 0.0002 2565 CSP NGIQVRIK 379 8 19 100 2566 CSP NGREGKDEDK 85 10 19 100 0.0002 2567 CSP NGEGKDEDKR 85 11 19 100 2568 CSP NLYNELEMNY 46 10 19 100 0.0002 2569 CSP NLYNELEMNYY 46 11 19 100 2570 CSP NMPNDPNR 323 8 19 100 2571 CSP NNEDNEKIR 98 9 19 100 2572 CSP NNEDNEXLRK 98 10 19 100 2373 CSP NNEEPSDK 346 8 19 100 2574 CSP NNEEPSDKH 346 9 19 100 2575 CSP NNGDNGREGK 81 10 19 100 2576 CSP NNNEEPSDK 345 9 19 100 2577 CSP NNNEEPSDKH 345 10 19 100 2578 CSP NNNGDNGR 80 8 19 100 2579 CSP NNNGDNGREGK 80 11 19 100 2580 CSP NNNNEEPSDK 344 10 19 100 2581 CSP NNNNEEPSDKH 344 11 19 100 2582 CSP NNNNGDNGR 79 9 19 100 2583 CSP NNQGNGQGH 314 9 19 100 2584 CSP NTRVLNELNY 31 10 19 100 0.0002 2585 CSP PNANPNANPNK 303 11 19 100 2586 CSP PSDKHIEQY 346 9 15 79 2587 CSP PSDKHIEQYLK 346 11 15 79 2588 CSP QCYGSSSNTR 24 10 19 100 2589 CSP QGHNMPNDPNR 320 11 19 100 2590 CSP RDGNNEDNEK 95 10 19 100 0.0002  2591 CSP RVLNELNY 33 8 19 100 2592 CSP SDICHIEQY 347 8 15 79 2593 CSP SDKHIEQYLK 347 10 15 79 2594 CSP SDKHIEQYLKK 347 11 15 79 2595 CSP SNIRVLNELNY 30 11 19 100 2596 CSP SVTCGNGIQVR 374 11 19 100 2597 CSP TCGNGIQVR 376 9 19 100 2598 CSP TCGNGIQVRDC 376 11 19 100 2599 CSP VTCGNGIQVR 375 10 19 100 0.0340 2600 CSP YDNAGINLY 40 9 18 95 2601 CSP YGKQENWY 56 8 19 100 2602 CSP YGKQENWYSLK 56 11 19 100 2603 CSP YGSSSNTR 26 8 19 100 2604 CSP YNELEMNY 48 8 19 100 2605 CSP YNELEMNYY 48 9 19 100 2606 CSP YNELEMNYYGK 48 11 19 100 2607 CSP YSLKKNSR 63 8 19 100 2608 EXP ALFFIIFNK 10 9 1 100 1.2000 2609 EXP DDNNLVSGPEH 152 11 1 100 2610 EXP DLISDMIK 52 8 1 100 2611 EXP DLISDMIKK 52 9 1 100 0.0003 2612 EXP DNNLVSGPEH 153 10 1 100 2613 EXP DVHDLISDMIK 49 11 1 100 2614 EXP ELVEVNKR 63 8 1 100 2615 EXP ELVEVNKRK 63 9 1 100 0.0002 2616 EXP ELVEVNKRKSK 63 11 1 100 2617 EXP EMADCTNK 19 9 1 100 0.0002 2618 EXP EVNKRKSK 66 8 1 100 2619 EXP EVNKRKSKY 66 9 1 100 0.0002 2620 EXP EVNKRKSKYK 66 10 1 100 0.0002 2621 EXP FLALFFIIFNK 8 11 1 100 2622 EXP FNKESLAEK 16 9 1 100 2623 EXP GGVGLVLY 94 8 1 100 2624 EXP GLVLYNIEK 97 9 1 100 0.0055 2625 EXP GLVLYNTEKGR 97 11 1 100 2626 EXP GSGEPLIDVH 42 10 1 00 0.0002 2627 EXP GSGVSSKK 30 8 1 00 2628 EXP GSOVSSKKK 30 9 1 00 0.0065 2629 EXP GSGVSSKKKNK 30 11 1 00 2630 EXP GTGSGVSSK 28 9 1 00 0.0180 2631 EXP GTGSGVSSKK 28 10 1 00 0.0340 2632 EXP GTGSGVSSKKK 28 11 1 00 2633 EXP GVGLVLYNIEK 95 11 1 00 2634 EXP GVSSKKKNK 32 9 1 00 0.0002 2635 EXP GVSSKKKNKK 32 10 1 00 0.0002 2636 EXP HDLISDMIK 51 9 1 00 0.0002 2637 EXP HDLISDMIKK 51 10 1 00 0.0002 2638 EXP IFNKESLAEK 15 10 1 00 0.0003 2639 EXP IIFNKESLAEK 14 11 1 00 2640 EXP KGSGEPLDVH 41 11 1 00 2641 EXP KGTGSGVSSK 27 10 1 00 0.0009 2642 EXP KGTGSGVSSKK 27 11 1 00 2643 EXP LALFFIIFNK 9 10 1 00 0.0530 2644 EXP LFFIIFNK 11 8 1 00 2645 EXP LGGVGLVLY 93 9 1 00 0.0002 2646 EXP LISDMIKK 53 8 1 00 2647 EXP LLGGVGLVLY 92 10 1 00 0.0003 2648 EXP LVEVNKRK 64 8 1 00 2649 EXP LVEVNKRKSK 64 10 1 00 0.0002 2650 EXP LVEVNKRKSKY 64 11 1 00 2651 EXP LVLYNIEK 98 8 1 00 2652 EXP LVLYNTEKGR 98 10 1 00 0.0002 2653 EXP LVLYNTEKGRH 98 11 1 00 2654 EXP NLVSGPEH 155 8 1 00 2655 EXP NNLVSGPEH 154 9 1 00 2656 EXP NTEKGRHPFK 102 10 1 00 0.0080 2657 EXP SGEPLIDVH 43 9 1 00 0.0002 2658 EXP SGVSSKKK 31 8 1 00 2659 EXP SGVSSKKKNK 31 10 1 00 0.0002 2660 EXP SGVSSKKKNKK 31 11 1 00 2661 EXP SLAEKTNK 20 8 1 00 2662 EXP SSKKKNKK 34 8 1 00 2663 EXP TGSGVSSK 29 8 1 00 2664 EXP TGSGVSSKK 29 9 1 00 0.0016 2665 EXP TGSGVSSKKK 29 10 1 00 0.0002 2666 EXP VGLVLYNTEK 96 10 1 00 0.0052 2667 EXP VLLGGVGLVLY 91 11 1 00 2668 EXP VLYNTEKGR 99 9 1 00 0.0007 2669 EXP VLYNTEXGRH 99 10 1 00 0.0002 2670 EXP VNKRKSKY 67 8 1 00 2671 EXP VNKFRKSKYK 67 9 1 00 2672 EXP VSSKKKNK 33 8 1 00 2673 EXP VSSKKKNKK 33 9 1 00 0.0002 2674 EXP YNTEKGRH 101 8 1 00 2675 EXP YNTEKGRHPFK 101 11 1 00 2676 LSA ADTKKNLER 1632 9 1 00 2677 LSA ADTKKNLERK 1632 10 1 00 0.0003 2678 LSA ADTKKNLERKK 1632 11 1 00 2679 LSA AIELPSENER 1660 10 1 00 0.0002 2680 LSA ANEKLQBQQR 1531 10 1 00 2681 LSA DDDDKKKY 130 8 1 00 2682 LSA DDDDKKKYIK 130 10 1 100 0.0002 2683 LSA DDDKKKYIK 131 9 1 100 0.0002 2684 LSA DDEDLDEFK 1778 9 1 100 0.0002 2685 LSA DDKKKYIK 132 8 1 100 2686 LSA DDLDEGIEK 1817 9 1 100 0.0002 2687 LSA DGSIKPEQK 1724 9 1 100 0.0002 2688 LSA DIHKGHLEEK 1713 10 1 100 0.0002 2689 LSA DIHKGHLEEXK 1713 11 1 100 2690 LSA DITKYFMK 1901 8 1 100 2691 LSA DLDEFKPIVQY 1781 11 1 100 2692 LSA DLDEOIEK 1818 8 1 100 2693 LSA DLEEKAAK 148 8 1 100 2694 LSA DLEQDRLAK 1388 9 1 100 0.0002 2695 LSA DLEQDRLAKEK 1388 11 1 100 2696 LSA DLEQDRLAK 1609 9 1 100 0.0002 2697 LSA DLEQERLAKEK 1609 11 1 100 2698 LSA DLEQERLANEK 1524 11 1 100 2699 LSA DLEQBIRAK 1575 9 1 100 0.0002 2700 LSA DLEQERRAKEK 1575 11 1 100 2701 LSA DLEQRKADTK 1626 10 1 100 0.0002 2702 LSA DLEQRKADTKK 1626 11 1 100 2703 LSA DLERTKASK 1184 9 1 100 0.0002 2704 LSA DNNFKPNDK 1846 9 1 100 2705 LSA DNRGNSRDSK 1682 10 1 100 2706 LSA DSEQERLAK 521 9 1 100 0.0002 2707 LSA DSEQERLAKEK 521 11 1 100 2708 LSA DSKEISIIEK 1689 10 1 100 0.0002 2709 LSA DTKKNLER 1633 8 1 100 2710 LSA DTKKNLERK 1633 9 1 100 0.0002 2711 LSA DTKKNLERKK 1633 10 1 100 0.0002 2712 LSA DVLAEDLY 1646 8 1 100 2713 LSA DVLAEDLYGR 1646 10 1 100 0.0002 2714 LSA DVNDFQISK 1751 9 1 100 0.0018 2715 LSA DVNDFQISKY 1751 10 1 100 0.0002 2716 LSA EDDEDLDEFK 1777 10 1 100 0.0002 2717 LSA EDEISAEY 1761 8 1 !CO 2718 LSA EDMCYFMK 1900 9 1 100 0.0003 2719 LSA EDKSADIQNH 1733 10 1 100 2720 LSA EDLEEKAAK 147 9 1 100 0.0002 2721 LSA EFKPIVQY 1784 8 1 100 2722 LSA EGRRDIHK 1709 8 1 100 2723 LSA EGRRDIHKGH 1709 10 1 100 0.0002 2724 LSA EIIKSNLR 33 8 1 100 2725 LSA EISIIEKTNR 1692 10 1 100 0.0002 2726 LSA ELEDLIEK 1805 8 1 100 2727 LSA ELPSENER 1662 8 1 100 2728 LSA ELPSENERGY 1662 10 1 100 0.0002 2729 LSA ELPSENERGYY 1662 11 1 100 2730 LSA ELSEDDK 1897 8 1 100 2731 LSA ELSEDITKY 1897 9 1 100 0.0002 2732 LSA ELSEEKIK 1829 8 1 100 2733 LSA ELSEEKIKK 1829 9 1 100 0.0002 2734 LSA ELSEEKIKKGK 1829 11 1 100 2735 LSA ELTMSNVK 83 8 1 100 2736 LSA ENERGYYIPH 1666 10 1 100 2737 LSA ENIFLKENK 108 9 1 100 2738 LSA ENKLNKEGK 114 9 1 100 2739 LSA ENNKFFDK 73 8 1 100 2740 LSA ENNKFFDKDK 73 10 1 100 2741 LSA ENRQEDLEEK 143 10 1 100 2742 LSA ESITINVEGR 1702 10 1 100 0.0002 2743 LSA ESITTNVEGRR 1702 11 1 100 2744 LSA FILVNLLIFH 11 10 1 100 0.0060 2745 LSA FLKENKLNK 111 9 1 100 0.0005 2746 LSA GDVLAEDLY 1645 9 1 100 2747 LSA GDVLAEDLYGR 1645 11 1 100 2748 LSA GSIKPEQK 1725 8 1 100 2749 LSA GSIKPEQKEDK 1725 11 1 100 2750 LSA GSSNSRNR 42 8 1 100 2751 LSA GVSENIFLK 105 9 1 100 0.6600 2752 LSA HGDVLAEDLY 1644 10 1 100 0.0002 2753 LSA HIINDDDDK 126 9 1 100 0.0002 2754 LSA HIINDDDDKK 126 10 1 100 0.0002 2755 LSA HIINDDDDKKK 126 11 1 100 2756 LSA HIKKYKNDK 1860 9 1 100 0.0002 2757 LSA HILYISFY 3 8 1 100 2758 LSA HINGKIIK 20 8 1 100 2759 LSA HLEEKDGSIK 1718 11 1 100 2760 LSA HNSYEKTK 63 8 1 100 2761 LSA HVLSHNSY 59 8 1 100 2762 LSA HVLSHNSYEK 59 10 1 100 0.0140 2763 LSA IFHINGKIIK 18 10 1 100 0.0006 2764 LSA IFLKENIQNK 110 10 1 100 0.0002 2765 LSA IINDDDDK 127 8 1 100 2766 LSA IINDDDDKK 127 9 1 100 0.0002 2767 LSA IINDDDDKKK 127 10 1 100 0.0002 2768 LSA IINDDDDKKKY 127 11 1 100 2769 LSA ILVNLLIFH 12 9 1 100 0.0008 2770 LSA INDDDDKK 128 8 1 100 2771 LSA INDDDDKKK 128 9 1 100 2772 LSA INDDDDKKKY 128 10 1 100 2773 LSA INEEKHSC 50 8 1 100 2774 LSA INEEKHEKK 50 9 1 100 2775 LSA INEEKNEKKH 50 10 1 100 2776 LSA INGKIIKNSEK 21 11 1 100 2777 LSA ISDVNDFQISK 1749 11 1 100 2778 LSA ISIIEKTNR 1693 9 1 100 0.0008 2779 LSA ITTNVEGR 1704 8 1 100 2780 LSA ITTNVEGRR 1704 9 1 100 0.0007 2781 LSA IVDELSEDMC 1894 11 1 100 2782 LSA KADTKKNLER 1631 10 1 100 0.0002 2783 LSA KADTKKNLERK 1631 11 1 100 2784 LSA KDEIIKSTILR 31 10 1 100 2785 LSA KDGSIKPEQK 1723 10 1 100 0.0002 2786 LSA KDKELIMSNVK 80 11 1 100 2787 LSA KDNNFKPNDK 1845 10 1 100 0.0002 2788 LSA KFIKSLFH 1876 8 1 100 2789 LSA KGHLEEKK 1716 8 1 100 2790 LSA KGKKYEKIK 1837 9 1 100 0.0002 2791 LSA KIIKNSEK 24 8 1 100 2792 LSA KIKKGKKY 1834 8 1 100 2793 LSA KIKKGKKYEK 1834 10 1 100 0.0007 2794 LSA KLNKEGKLIEH 116 11 1 100 2795 LSA KLQEQQSDLER 1177 11 1 100 2796 LSA KNDKQVNK 1865 8 1 100 2797 LSA KNDKQVNKEK 1865 10 1 100 2798 LSA KNLERKKEH 1636 9 1 100 2799 LSA KNNENNKFFDK 70 11 1 100 2800 LSA KNSEKDEIIK 27 10 1 100 2801 LSA KNVSQTNFK 90 9 1 100 2802 LSA KSADIQNH 1735 8 1 100 2803 LSA KSLYDEHIIK 1854 9 1 100 0.0340 2804 LSA KSLYDEHIKK 1854 10 1 100 0.0490 2805 LSA KSLYDEHIIKKY 1854 11 1 100 2806 LSA KSSEELSEEK 1825 10 1 100 0.0009 2807 LSA KTKDNNFK 1843 8 1 100 2808 LSA KTKNNENNK 68 9 1 100 0.0038 2809 LSA LAEDLYGR 1648 8 1 100 2810 LSA LAKEKLQEQQR 1615 11 1 100 2811 LSA LANEKLQEQQR 1530 11 1 100 2812 LSA LDDLDEGIEK 1816 10 1 100 0.0002 2813 LSA LDEFKPIVQY 1782 10 1 100 2814 LSA LGVSENTIFLK 104 10 1 100 0.0063 2815 LSA LIFHINGK 17 8 1 100 2816 LSA LIFHINGKIIK 17 11 1 100 2817 LSA LLIFHINGK 16 9 1 100 0.0100 2818 LSA LNKEGKLIEH 117 10 1 100 2819 LSA LSEDITKY 1898 8 1 100 2820 LSA LSEDITKYFMK 1898 11 1 100 2821 LSA LSEEKIKK 1830 8 1 100 2822 LSA LSEEKIKKGK 1830 10 1 100 0.0002 2823 LSA LSEEKIKKGKK 1830 11 1 100 2824 LSA LSHNSYEK 61 8 1 100 2825 LSA LSHNSYEKTK 61 10 1 100 0.0002 2826 LSA LVNLLIFH 13 8 1 100 2827 LSA NDDDDKKK 129 8 1 100 2828 LSA NDDDDKKKY 129 9 1 100 2829 LSA NDDDDKKKYIK 129 11 1 100 2830 LSA NDFQISKY 1753 8 1 100 2831 LSA NDKQVNKEK 1866 9 1 100 0.0002 2832 LSA NDKQVNKEKEK 1866 11 1 100 2833 LSA NDKSLYDEH 1852 9 1 100 2834 LSA NDKSLYDEHIIK 1852 11 1 100 2835 LSA NFKPNDKSLY 1848 10 1 100 2836 LSA NFQDEENIGIY 1793 11 1 100 2837 LSA NGKIIKNSEK 22 10 1 100 0.0002 2838 LSA NIFLKENK 109 8 1 100 2839 LSA NIFLKENKLNK 109 11 1 100 2840 LSA NLDDLDEGIEK 1815 11 1 100 2841 LSA NLERKKEH 1637 8 1 100 2842 LSA NLGVSENIFLK 103 11 1 100 2843 LSA NLLIFHINGK 15 10 1 100 0.0008 2844 LSA NLRSGSSNSR 38 10 1 100 0.0002 2845 LSA NNENNFFDK 71 10 1 100 2846 LSA NNFKPNDK 1847 8 1 100 2847 LSA NNFKPNDKSLY 1847 11 1 100 2848 LSA NNKFFDKDK 74 9 1 100 2849 LSA NSEKDEIIK 28 9 1 100 0.0002 2850 LSA NSRNRINEEK 45 10 1 100 0.0002 2851 LSA NSRNRINEEKH 45 11 1 100 2852 ISA NVEGRRDIH 1707 9 1 100 0.0002 2853 ISA NVEGRRDIHK 1707 10 1 100 0.0002 2854 LSA NVKNVSQTNFK 88 11 1 100 2855 LSA NVSQTNFK 91 8 1 100 2856 LSA PAIELPSENER 659 11 1 100 2857 LSA PNDKSLYDEFI 851 10 1 100 2858 LSA PSENERGY 664 8 1 100 2859 LSA PSENERGYY 664 9 1 100 0.0002 2860 LSA QDEENIGIY 795 9 1 100 2861 LSA QDEENIGIYK 795 10 1 100 0.0002 2862 LSA QDNRGNSR 681 8 1 100 2863 LSA QDNRGNSRDSK 681 11 1 100 2864 LSA QDRLAKEK 391 8 1 100 2865 LSA QGQQSDLEQER 128 11 1 100 2866 LSA QSDLEQDR 386 8 1 100 2867 LSA QSDLEQDRLAK 386 11 1 100 2868 ISA QSDSEQER 590 8 1 100 2869 LSA QSDLEQERLAK 590 11 1 100 2870 LSA QSDLEQERR 573 9 1 100 0.0002 2871 LSA QSDLEQERRAK 573 11 1 100 2872 LSA QSDLERTK 182 8 1 100 2873 LSA QSDLERTKASK 182 11 1 100 2874 LSA QSDSEQER 519 8 1 100 2875 LSA QSDSEQERLAK 519 11 1 100 2876 ISA QSSLPQDNR 1676 9 1 100 0.0013 2877 ISA QTNFKSLLR 94 9 1 100 0.0440 2878 LSA QVNKEKEK 1869 8 1 100 2879 LSA QVNKEKEKFIK 1869 11 1 100 2880 ISA RDIHKGHLEEK 1712 11 1 100 2881 ISA RDLEQERLAK 1608 10 1 100 0.0002 2882 LSA RDLEQERR 1540 8 1 100 2883 LSA RDLEQERRAK 1540 10 1 100 0.0002 2884 ISA RDLEQRKADTK 1625 11 1 100 2885 ISA RDSKEISIIEK 1688 11 1 100 2886 LSA RGNSRDSK 1684 8 1 100 2887 LSA RINEEKHEK 49 9 1 100 0.0370 2888 LSA RINEEKHEKK 49 10 1 100 0.0018 2889 ISA RINEEKHEKKH 49 11 1 100 2890 LSA RNRINEEK 47 8 1 100 2891 LSA RNRINEEKH 47 9 1 100 2892 LSA RNRINEEKHEK 47 11 1 100 2893 ISA RSGSSNSR 40 8 1 100 2894 LSA RSGSSNSRNR 40 10 1 100 0.0002 2895 LSA SDLEQDRLAK 387 10 1 100 0.0002 2896 ISA SDLEQERLAK 591 10 1 100 0.0002 2897 LSA SDLEQERR 574 8 1 100 2898 LSA SDLEQERRAK 574 10 1 100 0.0002 2899 LSA SDLERTKASK 183 10 1 100 0.0002 2900 ISA SDSEQERLAK 520 10 1 100 0.0002 2901 LSA SDVNDFQISK 750 10 1 100 0.0002 2902 ISA SDVNDFQISKY 750 11 1 100 2903 ISA SGSSNSRNR 41 9 1 100 0.0030 2904 ISA SIIEKTNR 694 8 1 100 2905 ISA SIKPEQKEDK 726 10 1 100 0.0002 2906 LSA SITTNVEGR 703 9 1 100 0.0027 2907 LSA SITTNVEGRR 703 10 1 100 0.0002 2908 LSA SLPQDNRGNSR 678 11 1 100 2909 LSA SLYDEHIK 835 8 1 100 2910 LSA SLYDEHIKK 855 9 1 100 0.4100 2911 LSA SLYDEHRKY 855 10 1 100 0.0045 2912 LSA SLYDEHIKKVK 835 11 1 100 2913 LSA SNLRSGSSNSR 37 11 1 100 2914 LSA SNSRNRINEEK 44 11 1 100 2915 LSA SSEELSEEK 1826 9 1 100 0.0017 2916 ISA SSEELSEEKIK 1826 11 1 100 2917 LSA SSLPQDNR 1677 8 1 100 2918 LSA TNFKSLLR 95 8 1 100 2919 LSA TNVEGRRDIH 1706 10 1 100 2920 LSA TNVEGRRDIHK 1706 11 1 100 2921 LSA TTNVEGRR 1705 8 1 100 2922 LSA TINVEGRRDIH 1705 11 1 100 2923 LSA VDELSEDTK 1895 10 1 100 0.0002 2924 LSA VDELSEDITKY 1895 11 1 100 2925 LSA VLAEDLYGR 1647 9 1 100 0.0004 2926 LSA VLSHNSYEK 60 9 1 100 0.0280 2927 LSA VLSHNSYEKTK 60 11 1 100 2928 LSA VNDFQISK 1752 8 1 100 2929 LSA VNDFQISKY 1752 9 1 100 2930 LSA VNKEKEKFIK 1870 10 1 100 2931 LSA VNLLIFHINGK 14 11 1 100 2932 LSA VSENIFLK 106 8 1 100 2933 LSA VSEMFLKENK 106 11 1 100 2934 LSA VSQTNFKSLLR 92 11 1 100 2935 LSA YDEHIKKY 1857 8 1 100 2936 LSA YDEHIKKYK 1857 9 1 100 0.0002 2937 LSA YFILVNLLIFH 10 11 1 100 2938 LSA YIKGQDENR 137 9 1 100 0.0002 2939 SSP2 ACAGLAYK 512 8 10 100 2940 SSP2 ADSAWENVK 216 9 10 100 0.0009 2941 SSP2 AFNRFLVGCH 197 10 10 100 2942 SSP2 ALLACAGLAY 509 10 10 100 0.0110 2943 SSP2 ALIACAGLAYK 509 11 10 100 2944 SSP2 ALLQVRKH 136 8 9 90 2945 SSP2 AVCVEVEK 233 8 10 100 2946 SSP2 CGKGTRSR 257 8 10 100 2947 SSP2 CGKGTRSRK 257 9 10 100 0.0002 2948 SSP2 CCKGIRSRKR 257 10 10 100 0.0002 2949 SSP2 CNDEVDLY 43 8 8 80 2950 SSP2 CSGSIRRH 55 8 10 100 2951 SSP2 CSVTCGKGTR 253 10 10 100 0.0002 2952 SSP2 DALLQVRK 135 8 9 90 2953 SSP2 DALLQVRKH 135 9 9 90 0.0002 2954 SSP2 DASKNIUEK 106 8 10 100 2955 SSP2 DCSGSIRR 54 8 10 100 2956 SSP2 DCSGSIRRH 54 9 10 100 2957 SSP2 DDREENFDIPK 385 11 10 100 2958 SSP2 DIPKKPENK 392 9 10 100 0.0002 2959 SSP2 DIPKKPENKH 392 10 10 100 0.0002 2960 SSP2 DLDEPEQFR 546 9 10 100 0.0002 2961 SSP2 DLFLVNGR 19 8 10 100 2962 SSP2 DNQNNLPNDK 402 10 10 100 2963 SSP2 CGAVIENVK 217 8 10 100 2964 SSP2 DSIQDSLK 166 8 10 100 2965 SSP2 DSIQDSLKESR 166 11 10 100 2966 SSP2 DSLKESRK 170 8 9 90 2967 SSP2 DVPKNPEDDR 378 10 10 100 0.0002 2968 SSP2 DVQNNIVDEIK 27 11 10 100 2969 SSP2 EDDQPRPR 300 8 10 100 2970 SSP2 EDRETRPH 450 8 9 90 2971 SSP2 EDRETRPHGR 450 10 9 90 2972 SSP2 EIIRLHSDASK 99 11 10 100 2973 SSP2 ELQEQCEEER 276 10 8 80 0.0002 2974 SSP2 ENFDIPKK 389 8 10 100 2975 SSP2 ENRSYNRK 462 8 10 100 2976 SSP2 ETLGEEDK 538 8 10 100 2977 SSP2 EVCNDEVDLY 41 10 8 80 0.0002 2978 SSP2 EVPSDVPK 374 8 10 100 2979 SSP2 FDEILGEEDK 536 10 10 100 0.0002 2980 SSP2 FDIPKKPENK 391 10 10 100 0.0002 2981 SSP2 FDIPKKPENKH 391 11 10 100 2982 SSP2 FDLFLVNGR 18 9 10 100 2983 SSP2 FFDLFLVNGR 17 10 10 100 2984 SSP2 FLVGCHPSDGK 201 11 10 100 2985 SSP2 FMKAVCVEVEK 230 11 10 100 2986 SSP2 FNRFLVGCH 198 9 10 100 2987 SSP2 FVVPGAATPY 520 10 8 80 0.0002 2988 SSP2 GCHPSDGK 204 8 10 100 2989 SSP2 GDNFAVEK 308 8 9 90 2990 SSP2 GINVAFNR 193 8 10 100 2991 SSP2 GIPDSIQDSLK 163 11 10 100 2992 SSP2 GNRHVPNSEDR 442 11 10 100 2993 SSP2 GSIRRHNWVNH 57 11 8 80 2994 SSP2 GIRSRKREILH 260 11 10 100 2995 SSP2 HAVPLAMK 67 8 10. 100 2996 SSP2 HDNQNNLPNDK 401 11 10 100 2997 SSP2 HGRNNENR 457 8 10 100 2998 SSP2 HORNNENRSY 457 10 10 100 0.0002 2999 SSP2 HLNDRINR 143 8 10 100 3000 SSP2 HSDASKNK 104 8 10 100 3001 SSP2 HSDASKNKEK 104 10 10 100 0.0002 3002 SSP2 HVPNSEDR 445 8 10 100 3003 SSP2 HVPNSEDRETR 445 11 9 90 3004 SSP2 IFFDLFLVNGR 16 11 10 100 3005 SSP2 IGQGINVAFNR 190 11 10 100 3006 SSP2 IIRLHSDASK 100 10 10 100 0.0002 3007 SSP2 IVDEIKYR 32 8 9 90 3008 SSP2 KAVCVEVEK 232 9 10 100 0.0076 3009 SSP2 KDLDEPEQFR 545 10 10 100 3010 SSP2 KFVVPGAATPY 519 11 8 80 3011 SSP2 KGTRSRKR 259 8 10 100 3012 SSP2 KNVIGPFMK 224 9 10 100 3013 SSP2 KVLDNERK 421 8 8 80 3014 SSP2 LACAGLAY 511 8 10 100 3015 SSP2 LACAGLAYK 511 9 10 100 0.0290 3016 SSP2 LALLACAOLAY 508 11 10 100 3017 SSP2 LDEPEQFR 547 8 10 100 3018 SSP2 LLACAGLAY 510 9 10 100 0.0005 3019 SSP2 LLACAGLAYK 510 10 10 100 0.0870 3020 SSP2 LLMDCSGSIR 51 10 10 100 0.0005 3021 SSP2 LLMDCSGSIRR 51 11 10 100 3022 SSP2 LLQVRKHLNDR 137 11 9 90 3023 SSP2 LLSTNLPY 121 8 9 90 3024 SSP2 LLSTNLPYGR 121 10 8 80 0.0025 3025 SSP2 LMDCSGSIR 52 9 10 100 0.0002 3026 SSP2 LMDCSGSIRR 52 10 10 100 0.0002 3027 SSP2 LMDCSGSIRRH 52 11 10 100 3028 SSP2 LSTNLPYGR 122 9 8 80 0.0100 3029 SSP2 LVGCHPSDGK 202 10 10 100 0.0002 3030 SSP2 MDCSGSIR 53 8 10 100 3031 SSP2 MDCSGSIRR 53 9 10 100 3032 SSP2 MDCSGSIRRH 53 10 10 100 3033 SSP2 MNHLGNVK 1 8 10 100 3034 SSP2 MNHLGNVKY 1 9 10 100 3035 SSP2 NFDIPKKPENK 390 11 10 100 3036 SSP2 NIPEDSEK 366 8 10 100 3037 SSP2 NIVDEIKY 31 8 10 100 3038 SSP2 NIVDEIKYR 31 9 9 90 0.0002 3039 SSP2 NLPNDKSDR 406 9 10 100 0.0002 3040 SSP2 NNENFtSYNR 460 9 10 100 3041 SSP2 NNENRSYNRK 460 10 10 100 3042 SSP2 NNIVDEIK 30 8 10 100 3043 SSP2 NNIVDEIKY 30 9 10 100 3044 SSP2 NNIVDEIKYR 30 10 9 90 3045 SSP2 NNLPNDKSDR 405 10 10 100 3046 SSP2 NSEDRETR 448 8 9 90 3047 SSP2 NSEDRETPPH 448 10 9 90 0.0002 3048 SSP2 NVIGPFMK 225 8 10 100 3049 SSP2 NVKNVIGPFMK 222 11 10 100 3050 SSP2 PCSVTCGK 252 8 10 100 3051 SSP2 PCSVTCGKGTR 252 11 10 100 3052 SSP2 PDSIQDSLK 165 9 10 100 0.0002 3053 SSP2 PFDETLGEEDK 535 11 10 100 3054 SSP2 PNIPEDSEK 365 9 10 100 3055 SSP2 PNSEDRETR 447 9 9 90 3056 SSP2 PNSEDREMPFI 447 11 9 90 3057 SSP2 PSDGKCNLY 207 9 10 100 0.0002 3058 SSP2 PSPNPEEGK 328 9 10 100 0.0002 3059 SSP2 QCEEERCPPK 280 10 8 80 0.0002 3060 SSP2 QDNNGNRH 438 8 10 100 3061 SSP2 QDSLKESR 169 8 10 100 3062 SSP2 QDSLKESRK 169 9 9 90 0.0002 3063 SSP2 QGINVAFNR 192 9 10 100 0.0780 3064 SSP2 QNNIVDEIK 29 9 10 100 3065 SSP2 QNNIVDEIKY 29 10 10 100 3066 SSP2 QNNIVDBKYR 29 11 9 90 3067 SSP2 QNNLPNDK 404 8 10 100 3068 SSP2 QNNLPNDKSDR 404 11 10 100 3069 SSP2 QSQDNNGNR 436 9 10 100 0.0002 3070 SSP2 QSQDNNGNRH 436 10 10 100 0.0002 3071 SSP2 QVRKHLNDR 139 9 9 90 0.0002 3072 SSP2 RGDNFAVEK 307 9 9 90 0.0240 3073 SSP2 FILHSDASK 102 8 10 100 3074 SSP2 RLHSDASKNK 102 10 10 100 0.0002 3075 SSP2 RNNENRSY 459 8 10 100 3076 SSP2 RNNENRSYNR 459 10 10 100 3077 SSP2 RNNENRSYNRK 459 11 10 100 3078 SSP2 RSRKREILH 262 9 10 100 0.0002 3079 SSP2 SDASKNKEK 105 9 10 100 0.0002 3080 SSP2 SDGKCNLY 208 8 10 100 3081 SSP2 SDVPKNPEDDR 377 11 10 100 3082 SSP2 SIQDSLKESR 167 10 10 100 0.0009 3083 SSP2 SIQDSLKESRK 167 11 9 90 3084 SSP2 SIRRHNWVNH 58 10 8 80 0.0002 3085 SSP2 SLLSTNLPY 120 9 9 90 0.0046 3086 SSP2 SLLSTNLPYGR 120 11 8 80 3087 SSP2 STNLPYGR 123 8 8 80 3088 SSP2 SVTCGKOTFt 254 9 10 100 0.0009 3089 SSP2 SVTCGKGTRSR 254 11 10 100 3090 SSP2 TCGKGTRSR 256 9 10 100 3091 SSP2 TCGKGIRSRK 256 10 10 100 0.0002 3092 SSP2 TCGKGTRSRKR 256 11 10 100 3093 SSP2 VAFNRFLVGCH 196 11 10 100 3094 SSP2 VCNDEVDLY 42 9 8 80 3095 SSP2 VGCHPSDGK 203 9 10 100 0.0003 3096 SSP2 VNHAVPLAMK 65 10 8 80 3097 SSP2 VTOGKGIR 255 8 10 100 3098 SSP2 VTCGKGTRSR 255 10 10 100 0.0017 3099 SSP2 VTCGKGIRSRK 255 11 10 100 3100 SSP2 VVPGAATPY 521 9 8 80 0.0002 3101 SSP2 WSPCSVTCGK 250 10 10 100 0.0002 3102 SSP2 WVNHAVPLAMK 64 11 8 80 3103 SSP2 YADSAWENVK 215 10 10 100 0.0002 3104 SSP2 YLLMDCSGSIR 50 11 10 100 3105

TABLE XVIII Malaria A24 Motif Peptides With Binding Information No. of Sequence Conservancy Protein Sequence Position Amino Acids Frequency (%) A*2401 Seq. Id CSP CYGSSSNTRVL 25 11 19 100 3106 CSP DYENDREKKI 398 10 18 95 3107 CSP EMNYYGKQENW 52 11 19 100 3108 CSP IMVLSFLF 427 8 19 100 3109 CSP IMVLSFLFL 427 9 19 100 0.0008 3110 CSP KMEKCSSVF 409 9 19 100 3111 CSP MMRKLAIL 1 8 19 100 3112 CSP NYDNAGINL 39 9 18 100 0.0004 3113 CSP NYYGKQENW 54 9 19 100 3114 CSP SFLFVEAL 12 8 19 100 3115 CSP SFLFVEALF 12 9 19 100 3116 CSP VFNVVNSSI 416 9 19 100 3117 CSP VFNVVNSSIGL 416 11 19 100 3118 CSP WYSLKKNSRSL 62 11 19 100 3119 CSP YYGKQENW 55 8 19 100 3120 CSP YYGKQENWYSL 55 11 19 100 3121 EXP DMIKKEEEL 56 9 1 100 3122 EXP FFIIFNKESL 12 10 1 100 3123 EXP FFLALFFI 7 8 1 100 3124 EXP FFLALFFII 7 9 1 100 3125 EXP FFLALFFIIF 7 10 1 100 3126 EXP KYKLATSVL 73 9 1 100 0.0960 3127 EXP LFFIIFNKESL 11 11 1 100 3128 EXP LYNTEKGRHPF 100 11 1 100 3129 EXP VFFLALFF 6 8 1 100 3130 EXP VFFLALFFI 6 9 1 100 3131 EXP VFFLALFFII 6 10 1 100 3132 EXP VFFLALFFIIF 6 11 1 100 3133 LSA DFQISKYEDEI 1754 11 1 100 3134 LSA EFKPIVQYDNF 1784 11 1 100 3135 LSA FFDKDKEL 77 8 1 100 3136 LSA FYFILVNL 9 8 1 100 3137 LSA FYFILVNLL 9 9 1 100 7.5000 3138 LSA FYFILVNLLI 9 10 1 100 3139 LSA FYFILVNLLIF 9 11 1 100 3140 LSA GYYIPHQSSL 1670 10 1 100 0.0074 3141 LSA IFDGDNEI 1884 8 1 100 3142 LSA IFDGDNEIL 1884 9 1 100 3143 LSA IFDGDNEILQI 1884 11 1 100 3144 LSA IFHINGKI 18 8 1 100 3145 LSA IFHINGKII 18 9 1 100 3146 LSA IFLKENKL 110 8 1 100 3147 LSA IYKELEDL 1802 8 1 100 3148 LSA IYKELEDLI 1802 9 1 100 3149 LSA KFFDKDKEL 76 9 1 100 3150 LSA KFIKSLFHI 1876 9 1 100 3151 LSA KFIKSLFHIF 1876 10 1 100 3152 LSA KYEKTKDNNF 1840 10 1 100 0.0004 3153 LSA LFHIFDGDNEI 1881 11 1 100 3154 LSA LYGRLETPAI 1652 10 1 100 3155 LSA LYISFYFI 5 8 1 100 3156 LSA LYISFYFIL 5 9 1 100 0.0088 3157 LSA NFKPNDKSL 1848 9 1 100 3158 LSA NFKSLLRNL 96 9 1 100 3159 LSA NFQCEENI 1793 8 1 100 3160 LSA NFQDEENIGI 1793 10 1 100 3161 LSA QYDNFQDEENI 1790 11 1 100 3162 LSA SFYFILVNL 8 9 1 100 3163 LSA SFYFILVNLL 8 10 1 100 3164 LSA SFYFILVNLLI 8 11 1 100 3165 LSA YFILVNLL 10 8 1 100 3166 LSA YFILVNLLI 10 9 1 100 3167 LSA YFILVNLLIF 10 10 1 100 3168 LSA YYIPHQSSL 1671 9 1 100 4.3000 3169 SSP2 AMKLIQQL 72 8 10 100 3170 SSP2 AMKLIQQLNL 72 10 10 100 0.0006 3171 SSP2 AWENVKNVI 219 9 10 100 3172 SSP2 KYKIAGGI 497 8 9 90 3173 SSP2 KYLVIVFL 8 8 10 100 3174 SSP2 KYLVIVFLI 8 9 10 100 4.6000 3175 SSP2 KYLVIVFLIF 8 10 10 100 0.0003 3176 SSP2 KYLVIVFLIFF 8 1 1 10 100 3177 SSP2 LMDCSGSI 52 8 10 100 3178 SSP2 LYLLMDCSGSI 49 11 9 90 3179 SSP2 NWVNHAVPL 63 9 8 80 3180 SSP2 PYAGEPAPF 528 9 8 80 0.0370 3181 SSP2 QFRLPEENEW 552 1 0 10 100 3182 SSP2 VFGIGQGI 187 8 10 100 3183 SSP2 VFLIFFDL 13 8 10 100 3184 SSP2 VFLIFFDLF 13 9 10 100 3185 SSP2 VFLIFFDLFL 13 10 10 100 3186

TABLE XIXa Core Core Core SeqID Core Conservancy Exemplary Protein Sequence Num Frequency (%) Sequence CSP FLFVEALFQ 3187 19 100 VSSFLFVEALFQEYQ CSP FNVVNSSIG 3188 19 100 SSVFNVVNSSIGLIM CSP FQEYQCYGS 3189 19 100 EALFQEYQCYGSSSN CSP IEKKICKME 3190 19 100 ENDIEKKICKMEKCS CSP IGLIMVLSF 3191 19 100 NSSIGLIMVLSFLFL CSP ILSVSSFLF 3192 19 100 KLAILSVSSFLFVEA CSP LAILSVSSF 3193 19 100 MRKLAILSVSSFLFV CSP MEKCSSVFN 3194 19 100 ICKMEKCSSVFNVVN CSP VVNSSIGLI 3195 19 100 VFNVVNSSIGLIMVL CSP YQCYGSSSN 3196 19 100 FQEYQCYGSSSNTRV CSP YNELEMNYY 3197 19 100 INLYNELEMNYYGKQ CSP YDNAGINLY 3198 18  95 ELNYDNAGINLYNEL CSP IQNSLSTEW 3199 15  79 LKKIQNSLSTEWSPC CSP WSPCSVTCG 3200 10 100 STEWSPCSVTCGNGI LSA FILVNLLIF 3201  1 100 SFYFILVNLLIFHIN LSA FYFILVNLL 3202  1 100 YISFYFILVNLLIFH LSA IHKGHLEEK 3203  1 100 RRDIHKGHLEEKKDG LSA IIKSNLRSG 3204  1 100 KDEIIKSNLRSGSSN LSA ILVNLLIFH 3205  1 100 FYFILVNLLIFHING LSA INGKIIKNS 3206  1 100 IFHINGKIIKNSEKD LSA IPAIELPSE 3207  1 100 RLEIPAIELPSENER LSA IPHQSSLPQ 3208  1 100 QYYIPHQSSLPQDNR LSA IQNHTLETV 3209  1 100 SADIQNHTLETVNIS LSA ISFYFILVN 3210  1 100 ILYISFYFILVNLLI LSA LDEFKPIVQ 3211  1 100 DEDLDEFKPIVQYDN LSA LEEKAAKET 3212  1 100 QEDLEEKAAKETLQG LSA LEEPAIELP 3213  1 100 YGRLEEPAIELPSEN LSA LEQRKADTK 3214  1 100 QRDLEQRKADTKKNL LSA LERTKASKE 3215  1 100 QSDLERTKASKETLQ LSA LETVNISDV 3216  1 100 NHTLETVNISDVNDF LSA LIEFIENDD 3217  1 100 EGKLIEHIINDDDDK LSA LKENKLNKE 3218  1 100 NIFLKENKLNKEGKL LSA LLIFHINGK 3219  1 100 LVNLLIFHINGKIIK LSA LQEQQSDLE 3220  1 100 KETLQEQQSDLEQER LSA LQEQQSDSE 3221  1 100 KEKLQEQQSDSEQER LSA LQGQQSDLE 3222  1 100 KETLQGQQSDLEQER LSA LRNLGVSEN 3223  1 100 KSLLRNLGVSENIFL LSA LRSGSSNSR 3224  1 100 KSNLRSGSSNSRNRI LSA LTMSNVKNV 3225  1 100 DKELTMSNVKNVSQT LSA LVNLLXFHI 3226  1 100 YFILVNLLIFHINGK LSA VLSHNSYEK 3227  1 100 KKHVLSHNSYEKTKN LSA VNDFQISKY 3228  1 100 ISDVNDFQISKYEDE LSA VNISDVNDF 3229  1 100 LETVNISDVNDFQIS LSA YDDSLIDEE 3230  1 100 SAEYDDSLIDEEEDD LSA YGRLEIPAI 3231  1 100 EDLYGRLEIPAIELP LSA YIPHQSSLP 3232  1 100 RGYYIPHQSSLPQDN EXP FIUGSSDPA 3233  1 100 RHPFKIGSSDPADNA EXP IDVHDLISD 3234  1 100 EPLIDVHDLISDMIK EXP IFNKESLAE 3235  1 100 FFIIFNKESLAEKTN EXP IGSSDPADN 3236  1 100 PFIUGSSDPADNANP EXP LALFFIIFN 3237  1 100 VFFLALFFIIFNKES EXP LATSVLAGL 3238  1 100 KYKLATSVLAGLLGN EXP LGGVGLVLY 3239  1 100 TVLLGGVGLVLYNTE EXP LGNVSTVLL 3240  I 100 AGLLGNVSTVLLGGV EXP LLGNVSTVL 3241  1 100 LAGLLGNVSTVLLGG EXP LSVFFLALF 3242  1 100 MKILSVFFLALFFII EXP LVLYNTEKG 3243  1 100 GVOLVLYNTEKGRHP EXP VFFLALFFI 3244  1 100 ILSVFFLALFFIIFN EXP VHDLISDMI 3245  1 100 LIDVHDLISDMIKKE EXP VLAGLLGNV 3246  1 100 ATSVLAGLLGNVSTV EXP VLLGGVGLV 3247  1 100 VSTVLLGGVGLVLYN EXP VNKRKSKYK 3248  1 100 LVEVNKRKSKYKLAT EXP VSTVLLGGV 3249  1 100 LGNVSTVLLGGVGLV EXP VTAQDVTPE 3250  1 100 DPQVTAQDVTPEQPQ EXP YKLATSVLA 3251  1 100 KSKYKLATSVLAGLL SSP2 FDLFLVNGR 3252 10 100 LIFFDLFLVNGRDVQ SSP2 FFDLFLVNG 3253 10 100 FLIFFDLFLVNGRDV SSP2 FMKAVCVEV 3254 10 100 IGPFMKAVCVEVEKT SSP2 FNRFLVGCH 3255 10 100 NVAFNRFLVGCHPSD SSP2 IAGGLALLA 3256 10 100 AGGIAGGLALLACAG SSP2 IAVFGIGQG 3257 10 100 GVKIAVFGIGQGINV SSP2 LACAGLAYK 3258 10 100 LALLACAGLAYKFVV SSP2 LALLACAGL 3259 10 100 AGGLALLACAGLAYK SSP2 LAMKLIQQL 3260 10 100 AVPLAMKLIQQLNLN SSP2 LAYKFVVPG 3261 10 100 CAGLAYKFVVPGAAT SSP2 LIFFDLFLV 3262 10 100 IVFLIFFDLFLVNGR SSP2 LTDGIPDSI 3263 10 100 VVILTDGIPDSIQDS SSP2 LVGCHPSDG 3264 10 100 NRFLVGCHPSDGKCN SSP2 LVIVFLIFF 3265 10 100 VKYLVTVFLIFFDLF SSP2 LVVILTDGI 3266 10 100 ANQLVVILTDGIPDS SSP2 MDCSGSIRR 3267 10 100 YLLMDCSGSIRRHNW SSP2 MKAVCVEVE 3268 10 100 GPFMKAVCVEVEKTA SSP2 VEKTASCGV 3269 10 100 CVEVEKTASCGVWDE SSP2 VGCHPSDGK 3270 10 100 RFLVGCHPSDGKCNL SSP2 VIGPFMKAV 3271 10 100 VKNVIGPFMKAVCVE SSP2 VIVFLIFFD 3272 10 100 KYLVIVFLIFFDLFL SSP2 VKYLVIVFL 3273 10 100 LGNVKYLVIVFLIFF SSP2 VNGRDVQNN 3274 10 100 LFLVNGRDVQNNIVD SSP2 WDEWSPCSV 3275 10 100 CGVWDEWSPCSVTCG SSP2 IAGGIAGGL 3276 10 100 KYKIAGGIAGGLALL SSP2 VQNNIVDEI 3277 10 100 GRDVQNNIVDEIKYR SSP2 YLLMDCSGS 3278 10 100 VDLYLLMDCSGSIRR SSP2 FVVPGAATP 3279 10 100 AYKFVVPGAATPYAG SSP2 YKFVVPGAA 3280 10 100 GLAYKFVVPGAATPY SSP2 IIRLHSDAS 3281 10 100 AKEIIRLHSDASKNK SSP2 IIDNNPQEP 3282 10 100 EENIIDNNPQEPSPN SSP2 VDLYLLMDC 3283  9  90 NDEVDLYLLMDCSGS SSP2 LLSTNLPYG 3284  9  90 IKSLLSTNLPYGRTN SSP2 LHEGCTSEL 3285  8  80 REILHEGCTSELQEQ SSP2 VNHAVPLAM 3286  8  80 HNWVNHAVPLAMKLI SSP2 VPGAATPYA 3287  8  80 KFVVPGAATPYAGEP SSP2 VVPGAATPY 3288  8  80 YKFVVPGAATPYAGE SSP2 WVNHAVPLA 3289  8  80 REINWYNHAVPLAMKL SSP2 LSTNLPYGR 3290  8  80 KSLLSTNLPYGRTNL Position  Exemplary Exemplary  Exemplary In PF Sequence Sequence Protein SeqID Num Poly-Protein Frequency Conservancy (%) CSP 3291 10 19 100 CSP 3292 440 19 100 CSP 3293 17 19 100 CSP 3294 426 19 100 CSP 3295 447 19 100 CSP 3296 4 19 100 CSP 3297 2 19 100 CSP 3298 433 19 100 CSP 3299 442 19 100 CSP 3300 20 19 100 CSP 3301 45 18 95 CSP 3302 37 18 95 CSP 3303 385 15 79 CSP 3304 393 19 100 LSA 3305 8 1 100 LSA 3306 6 1 100 LSA 3307 1711 1 100 LSA 3308 31 1 100 LSA 3309 9 1 100 LSA 3310 18 1 100 LSA 3311 1655 1 100 LSA 3312 1670 1 100 LSA 3313 1736 1 100 LSA 3314 4 1 100 LSA 3315 1779 1 100 LSA 3316 146 1 100 LSA 3317 1653 1 100 LSA 3318 1624 1 100 LSA 3319 1182 1 100 LSA 3320 1741 1 100 LSA 3321 120 1 100 LSA 3322 109 1 100 LSA 3323 13 1 100 LSA 3324 1192 1 100 LSA 3325 512 1 100 LSA 3326 155 I 100 LSA 3327 98 1 100 LSA 3328 36 1 100 LSA 3329 81 1 100 LSA 3330 10 1 100 LSA 3331 57 1 100 LSA 3332 1749 1 100 LSA 3333 1744 1 100 LSA 3334 1765 1 100 LSA 3335 1650 1 100 LSA 3336 1669 1 100 EXP 3337 107 1 100 EXP 3338 45 1 100 EXP 3339 12 1 100 EXP 3340 109 1 100 EXP 3341 6 1 100 EXP 3342 73 1 100 EXP 3343 90 1 100 EXP 3344 82 1 100 EXP 3345 81 1 100 EXP 3346 1 1 100 EXP 3347 95 1 100 EXP 3348 3 1 100 EXP 3349 47 1 100 EXP 3350 77 1 100 EXP 3351 88 1 100 EXP 3352 64 1 100 EXP 3353 85 1 100 EXP 3574 136 1 100 EXP 3354 71 1 100 SSP2 3355 15 10 100 SSP2 3356 14 10 100 SSP2 3357 227 10 100 SSP2 3358 195 10 100 SSP2 3359 513 10 100 SSP2 3360 182 10 100 SSP2 3361 520 10 100 SSP2 3362 517 10 100 SSP2 3363 68 10 100 SSP2 3364 525 10 100 SSP2 3365 12 10 100 SSP2 3366 157 10 100 SSP2 3367 199 10 100 SSP2 3368 7 10 100 SSP2 3369 153 10 100 SSP2 3370 50 10 100 SSP2 3371 228 10 100 SSP2 3372 235 10 100 SSP2 3373 200 10 100 SSP2 3374 223 10 100 SSP2 3375 8 10 100 SSP2 3376 4 10 100 SSP2 3377 20 10 100 SSP2 3378 244 10 100 SSP2 3379 509 9  90 SSP2 3380 25 9  90 SSP2 3381 47 9  90 SSP2 3382 529 8  80 SSP2 3383 527 8  80 SSP2 3384 97 6  60 SSP2 3385 317 4  40 SSP2 3386 44 8  80 SSP2 3387 118 5  50 SSP2 3388 266 8  80 SSP2 3389 62 8  80 SSP2 3390 531 8  80 SSP2 3391 530 8  80 SSP2 3392 61 8  80 SSP2 3393 119 5  50

TABLE XIXb Malaria Super Motif Peptides With Binding Data Core Core SeqID Exemplary Exemplary Sequence Num Sequence SeqID Num DR1 DR2w2β1 FLFVEALFQ 3187 VSSFLFVEALFQEYQ 3291 FNVVNSSIG 3188 SSVFNVVNSSIGLIM 3292 0.1200 0.0290 FQEYQCYGS 3189 EQLFQEYQCYGSSSN 3293 0.0001 IEKKICKME 3190 ENDIEKKICKMEKCS 3294 IGLIMVLSF 3191 NSSIGLIMVLSFLFL 3295 0.0040 0.0250 ILSVSSFLF 3192 KLAILSVSSFLFVEA 3296 LAILSVSSF 3193 MRKLAILSVSSFLFV 3297 0.1000 0.5000 MEKCSSVFN 3194 ICKMEKCSSVFNVVN 3298 VVNSSGILI 3195 VFNVVNSSIGLIMVL 3299 0.0310 0.0021 YQCYGSSSN 3196 FQEYQCYGSSSNTRV 3300 YNELEMNYY 3197 INLYNELEMNYYGKQ 3301 YDNAGINLY 3198 ELNYDNAGINLYNEL 3302 0.0003 IQNSLSTEW 3199 LKKIQNSLSTEWSPC 3303 WSPSCSVTCG 3200 STEWSPCSVTCGNGI 3304 FILVNLLIF 3201 SFYFILVNLLIFHIN 3305 0.0009 0.0100 FYFILVNLL 3202 YISFYFILVNLLIGH 3306 0.0029 0.0040 IHKGHLEEK 3203 RRDIHKGHLEEKKDG 3307 IIKSNLRSG 3204 KDEIIKSNLRSGSSN 3308 ILVNLLIFH 3205 FYFILVNLLIFHING 3309 INGKIIKNS 3206 IFHINGKIIKNSEKD 3310 0.0320 0.0220 IPAIELPSE 3207 RLEIPAIELPSENER 3311 IPHQSSLPQ 3208 GYYIPHQSSLPQDNR 3312 IQNHTLETV 3209 SADIQNHTLETVNIS 3313 0.0001 ISFYFILVN 3210 ILYISFYFILVNLLI 3314 LDEFKPIQ 3211 DEDLDEFKPIVQYDN 3315 LEEKAAKET 3212 QEDLEEKAAKETLQG 3316 0.0001 LEIPAIELP 3213 YGRLEIPAIELPSEN 3317 LEQRKADTK 3214 QRDLEQRKADTKKNL 3318 LERTKASKE 3215 QDDLERTKASKETLQ 3319 LETVNISDV 3216 NGTLETVNISDVNDF 3320 0.0001 LIEHIINDD 3217 EGKLIEHIINDDDDK 3321 LKENKLNKE 3218 NIFLKEKLNKEGKL 3322 LLIFHINGK 3219 LVNLLIFHINGKIIK 3323 0.0640 0.7100 LQEQQSDLE 3220 KETLQEQQSDLEQER 3324 LQEQQSESE 3221 KEKLQEQQSDSEQER 3325 LQGQQSDLE 3222 KETLQGQQSDLEQER 3326 LRNTLGVSEN 3223 KSLLRNLGVSENIFL 3327 0.0150 0.0088 LRSGSSNSR 3224 KSNLRSGSSNSRNRI 3328 LTMSNVKNV 3225 DKELTMSNVKNVSQT 3329 0.0018 0.0003 LVNLLIFHI 3226 YFILVNLLIFHINGK 3330 0.0018 0.0004 VLSHNSYEK 3227 KKHVLSHNSYEKTKN 3331 VNDFQISKY 3228 ISDVNDFQISKYEDE 3332 0.0001 VNISKVNDF 3229 LETVNISDVNDFQIS 3333 YDDSLIDEE 3230 SAEYDDSLIDEEEDD 3334 YGRLEIPAI 3231 EDLYGRLEIPAIELP 3335 0.0004 YIPHQSSLP 3232 RGYYIPHQSSLPQDN 3336 0.2900 0.0004 FKIGSSDPA 3233 RHPFKIGSSDPADNA 3337 0.0044 -0.0004 IDVHDLISH 3234 EPLIDVHDLISDMIK 3338 IFNKESLAE 3235 FFIIFNKESLAEKTN 3339 IGSSDPADN 3236 PFKIGSSDPADNANP 3340 LALFFIIFN 3237 VFFALFFIIFNKES 3341 0.0006 0.0180 LATSVLAGL 3238 KYKLATSVLAGLLGN 3342 1.2000 0.0018 LGGVGLVLY 3239 TVLLGGVGLVLYNTE 3343 0.4900 LGNVSTVLL 3240 AGLLGNVSTVLLGGV 3344 0.0430 0.0240 LLGNVSTVL 3241 LAGLLGNVSTVLLGG 3345 0.0420 0.0110 LSVFFLALF 3242 MKILSVFFLALFFII 3346 0.0017 0.0170 LVLYNTEKG 3243 GVGLVLYNTEKGRHP 3347 VFFLALFFI 3244 ILSVFFLALFFIIFN 3348 0.0016 0.0036 VHDLISDMI 3245 LIDVHDLISDMIKKE 3349 0.0130 VLAGLLGNV 3246 ATSVLAGLLGNVSTV 3350 0.2600 VLLGGVGLV 3247 VSTVLLGGVGLVLYN 3351 0.8800 0.0080 VNKRKSKYK 3248 LVEVNKRKSKYKLAT 3352 VSTVLLGGV 3249 LGNVSTVLLGGVGLV 3353 0.0140 0.0001 VTAQDVTPE 3250 DPQVTAQDVTPEQPQ 3574 YKLATSVLA 3251 KSKYKLATSVLAGLL 3354 1.4000 0.0073 FDLFLVNGR 3252 LIFFDLFLVNGRDVQ 3355 0.0042 FFDLFLVNG 3253 FLIFFDLFLVNGRDV 3356 FMKAVCVEV 3254 IGPFMKAVCVEVEKT 3357 0.0072 0.0003 FNRFLVGCH 3255 NVAFNRFLVGCHPSD 3358 IAGGLALLA 3256 AGGIAGGLALLACAG 3359 0.0160 IAVFGIGQG 3257 GVKIAVFGIGQGINV 3360 LACAGLAYK 3258 LALLACAGLAYKFVV 3361 LALLACAGL 3259 AGGLALLACAGLAYK 3362 0.0018 LAMKLIQQL 3260 AVPLAMKLIQQLNTN 3363 0.0015 LAYKFVVPG 3261 CAGLAYKFVVPGAAT 3364 LIFFDLFLV 3262 IVFLIFFDLFLVNGR 3365 0.0006 0.0048 LTDGIPDSI 3263 VVILTDGIPDSIQDS 3366 0.0001 LVGCHPSDG 3264 NRFLVGCHPSDGKCN 3367 LVTVFLIFF 3265 VKYLVTVFLIFFDLF 3368 0.0001 LVVILTDGI 3266 ANQLVVILTDGIPDS 3379 0.0038 0.0008 MDCSGSIRR 3267 YLLMDCSGSIRRHNW 3370 MKAVCVEVE 3268 GPFMKAVCVEVEKTA 3371 VEKTASCGV 3269 CVEVEKTASCGVWDE 3372 0.0004 VGCHPSDGK 3270 RFLVGCHPSDGKCNL 3373 VIGPFMKAV 3271 VKNVIGPFMKAVCVE 3374 0.0900 0.0430 VIVFLIFFD 3272 KYVTVFLIFFDLFL 3375 0.0012 0.0057 VKYLVTVFL 3273 LGNVKYLVTVFLIFF 3376 0.0006 0.0033 VNGRDVQNN 3274 LFLVNGRDVQNNTVD 3377 WDEWSPCSV 3275 CGVWDEWSPCSVTCG 3378 0.0001 IAGGIAGGL 3276 KYKIAGGIAGGLALL 3389 0.0380 0.0001 YQNNIVDEI 3277 GRDVQNNIVDEIKYR 3380 0.0001 0.0001 YLLMDCSGS 3278 VDLYLLMDCSGSIRR 3381 0.0015 FVVPGAATP 3279 AYKFVVPGAATPYAG 3382 0.3600 -0.0009 YKFVVPGAA 3280 GLAYKFVVPGAATPY 3383 1.6000 0.0001 IIRLHSDAS 3281 AKEIIRLHSDASKNK 3384 IIDNNPQEP 3282 EENIIDNNPQEPSPN 3385 VDLYLLMDC 3283 NDEVDLYLLMDCSGS 3386 0.0001 LLSTNLPYG 3284 IKSLSSTNLPYGRTN 3387 LHEGCTSEL 3285 REILHEGCTSELQEQ 3388 0.0001 VNHAVPLAM 3286 HNWVNHAVPLAMKLI 3389 0.3500 0.0250 VPGAATPYA 3287 KFVVPGAATPYAGEP 3390 0.0230 0.0001 VVPGAATPY 3288 YKFVVPGAATPYAGE 3391 0.1100 0.0008 WVNHAVPLA 3289 RHNWVNHAVPLAMKL 3392 0.1900 0.0350 LSTNLPYGR 3290 KSLLSTNLPYGRTNL 3393 0.0012 Core Sequence DR2w2β2 DR3 DR4w4 DR4w15 DR5w11 DR5w12 FLFVEALFQ FNVVNSSIG 0.0050 -0.0043 0.1000 0.230 0.0170 0.0051 FQEYQCYGS -0.0005 0.0053 -0.0009 -0.0002 0.0001 IEKKICKME IGLIMVLSF 0.0024 -0.0043 0.0120 0.0035 -0.0005 0.0340 ILSVSSFLF LAILSVSSF 0.0130 -0.0043 0.0078 0.0270 0.0370 0.1200 MEKCSSVFN VVNSSGILI 0.0006 0.0021 0.0079 0.0056 0.0002 0.0015 YQCYGSSSN YNELEMNYY YDNAGINLY -0.0005 0.0091 -0.0009 -0.0009 -0.0002 0.0001 IQNSLSTEW WSPSCSVTCG FILVNLLIF -0.0020 -0.0043 0.0250 0.0038 -0.0005 0.0009 FYFILVNLL 0.0044 -0.0008 0.0210 -0.0009 0.0011 0.0006 IHKGHLEEK IIKSNLRSG ILVNLLIFH INGKIIKNS 0.0660 0.0120 -0.0007 0.0038 0.0380 0.0055 IPAIELPSE IPHQSSLPQ IQNHTLETV -0.0005 -0.0041 -0.0007 -0.0014 -0.0002 0.0001 ISFYFILVN LDEFKPIQ LEEKAAKET -0.0005 -0.0009 -0.0009 -0.0002 0.0001 LEIPAIELP LEQRKADTK LERTKASKE LETVNISDV -0.0005 -0.0007 0.0016 -0.0002 0.0015 LIEHIINDD LKENKLNKE LLIFHINGK 0.0070 -0.0043 0.0110 -0.0030 0.2700 0.0410 LQEQQSDLE LQEQQSESE LQGQQSDLE LRNTLGVSEN 0.0006 0.0210 0.0810 0.0033 LRSGSSNSR LTMSNVKNV 0.0009 0.0058 0.0023 0.0074 0.0030 0.0001 LVNLLIFHI 0.0120 -0.008 0.0160 0.0027 0.0015 0.0006 VLSHNSYEK VNDFQISKY -0.0005 -0.0007 -0.0014 -0.0002 0.0001 VNISKVNDF YDDSLIDEE YGRLEIPAI -0.0005 -0.0007 0.0170 -0.0002 0.0002 YIPHQSSLP 0.0029 4.1000 0.2800 0.0064 FKIGSSDPA -0.0003 -0.0008 0.4700 0.0029 0.0056 0.0001 IDVHDLISH IFNKESLAE IGSSDPADN LALFFIIFN -0.0021 -0.0043 0.0047 0.0100 -0.0005 0.0002 LATSVLAGL 0.0700 0.0010 3.2000 0.1200 0.0210 0.0073 LGGVGLVLY -0.005 0.0032 -0.0009 -0.0062 0.0004 LGNVSTVLL 0.0013 0.0059 0.0065 0.0360 0.0005 0.0001 LLGNVSTVL 0.0006 0.0078 0.0160 0.0230 0.0004 0.0003 LSVFFLALF -0.0021 -0.0043 0.0370 -0.0047 -0.0010 0.0023 LVLYNTEKG VFFLALFFI 0.0091 -0.0008 0.0130 -0.0009 0.0012 0.0008 VHDLISDMI 0.0061 0.0100 0.0310 0.0075 0.0037 0.0001 VLAGLLGNV -0.0005 0.0021 -0.0014 0.0008 0.0043 VLLGGVGLV 0.0005 -0.0008 0.0067 -0.0009 0.0003 0.0011 VNKRKSKYK VSTVLLGGV -0.0005 -0.0008 0.0016 -0.0014 -0.0002 0.0005 VTAQDVTPE YKLATSVLA 0.8500 -0.0008 6.3000 0.8100 0.6700 0.0009 FDLFLVNGR 0.0036 FFDLFLVNG FMKAVCVEV 0.0430 -0.0008 -0.0006 0.0086 -0.0004 0.0038 FNRFLVGCH IAGGLALLA 0.0013 0.0014 0.0014 -0.0002 0.0007 IAVFGIGQG LACAGLAYK LALLACAGL 0.0013 -0.0007 -0.0014 -0.0002 0.0051 LAMKLIQQL -0.0006 0.0023 0.0013 0.0002 0.1300 LAYKFVVPG LIFFDLFLV 0.0019 -0.0008 0.0130 -0.0009 0.0019 0.0016 LTDGIPDSI -0.0006 0.1200 -0.0014 -0.0004 0.0001 LVGCHPSDG LVTVFLIFF 0.0030 LVVILTDGI -0.0005 0.0019 0.0460 0.0062 -0.0002 0.0003 MDCSGSIRR MKAVCVEVE VEKTASCGV -0.0009 0.0021 -0.0009 -0.0002 0.0001 VGCHPSDGK VIGPFMKAV 0.0800 -0.0026 -0.0020 -0.0030 0.3420 0.0920 VIVFLIFFD -0.0020 -0.0043 0.0680 -0.0030 -0.0009 0.0021 VKYLVTVFL 0.0012 -0.0008 0.0120 0.0045 0.0018 0.0011 VNGRDVQNN WDEWSPCSV -0.0006 -0.0007 -0.0014 -0.0002 0.0001 IAGGIAGGL 0.0480 0.0250 0.0120 0.0017 0.2300 0.3600 YQNNIVDEI -0.0006 0.0026 -0.0006 -0.0014 -0.0004 0.0001 YLLMDCSGS 0.0096 0.0150 -0.0014 -0.0004 0.0001 FVVPGAATP 0.0620 0.1600 0.0036 0.6400 0.1200 YKFVVPGAA 0.7000 -0.0008 1.0000 0.0270 1.9000 0.3500 IIRLHSDAS IIDNNPQEP VDLYLLMDC -0.0005 0.0028 -0.0009 -0.0002 0.0001 LLSTNLPYG LHEGCTSEL -0.0005 -0.0041 -0.0009 -0.0014 -0.0002 0.0001 VNHAVPLAM 0.1400 0.2300 3.900 0.0400 0.0074 0.6000 VPGAATPYA 0.0010 0.0620 0.1200 0.0067 0.0010 0.0860 VVPGAATPY 0.0053 -0.0008 0.0057 -0.0014 0.0036 0.0061 WVNHAVPLA 0.1600 0.4000 5.0000 0.0360 0.0079 0.0240 LSTNLPYGR 0.0120 Core Seq Exemplary Exemplary Sequence Id. Sequence SeqID Num DR6w19 DR7 DR8w2 DR9 DRw53 FLFVEALFQ 3187 VSSFLFVEALFQEYQ 3291 FNVVNSSIG 3188 SSVFNVVNSSIGLIM 3292 0.3600 0.7600 0.0550 1.2000   FQEYQCYGS 3189 EQLFQEYQCYGSSSN 3293 -0.0003 0.0005 IEKKICKME 3190 ENDIEKKICKMEKCS 3294 IGLIMVLSF 3191 NSSIGLIMVLSFLFL 3295 0.0009 0.0690 -0.0010 0.0042 ILSVSSFLF 3192 KLAILSVSSFLFVEA 3296 LAILSVSSF 3193 MRKLAILSVSSFLFV 3297 0.0930 0.0500 0.0013 0.1100 MEKCSSVFN 3194 ICKMEKCSSVFNVVN 3298 VVNSSGILI 3195 VFNVVNSSIGLIMVL 3299 0.2600 0.1800 0.0012 0.5000 YQCYGSSSN 3196 FQEYQCYGSSSNTRV 3300 YNELEMNYY 3197 INLYNELEMNYYGKQ 3301 YDNAGINLY 3198 ELNYDNAGINLYNEL 3302 -0.0003 -0.0003 IQNSLSTEW 3199 LKKIQNSLSTEWSPC 3303 WSPSCSVTCG 3200 STEWSPCSVTCGNGI 3304 FILVNLLIF 3201 SFYFILVNLLIFHIN 3305 0.0004 0.0084 -0.0007 -0.0018 FYFILVNLL 3202 YISFYFILVNLLIGH 3306 0.0003 0.0020 0.0010 -0.0003 IHKGHLEEK 3203 RRDIHKGHLEEKKDG 3307 IIKSNLRSG 3204 KDEIIKSNLRSGSSN 3308 ILVNLLIFH 3205 FYFILVNLLIFHING 3309 INGKIIKNS 3206 IFHINGKIIKNSEKD 3310 0.0120 0.0150 0.0400 0.0093  0.0020 IPAIELPSE 3207 RLEIPAIELPSENER 3311 IPHQSSLPQ 3208 GYYIPHQSSLPQDNR 3312 IQNHTLETV 3209 SADIQNHTLETVNIS 3313 -0.0003 -0.0003  0.0012 ISFYFILVN 3210 ILYISFYFILVNLLI 3314 LDEFKPIQ 3211 DEDLDEFKPIVQYDN 3315 LEEKAAKET 3212 QEDLEEKAAKETLQG 3316 -0.0003 -0.0002 LEIPAIELP 3213 YGRLEIPAIELPSEN 3317 LEQRKADTK 3214 QRDLEQRKADTKKNL 3318 LERTKASKE 3215 QDDLERTKASKETLQ 3319 0.0010 -0.0003 -0.0005 LETVNISDV 3216 NGTLETVNISDVNDF 3320 LIEHIINDD 3217 EGKLIEHIINDDDDK 3321 LKENKLNKE 3218 NIFLKEKLNKEGKL 3322 0.0530 0.1200 0.0290 0.1800 LLIFHINGK 3219 LVNLLIFHINGKIIK 3323 LQEQQSDLE 3220 KETLQEQQSDLEQER 3324 LQEQQSESE 3221 KEKLQEQQSDSEQER 3325 LQGQQSDLE 3222 KETLQGQQSDLEQER 3326 LRNTLGVSEN 3223 KSLLRNLGVSENIFL 3327 0.5700 0.0770 0.0021 1.6000 LRSGSSNSR 3224 KSNLRSGSSNSRNRI 3328 LTMSNVKNV 3225 DKELTMSNVKNVSQT 3329 0.0430 0.0410 0.0110 0.0710  0.0024 LVNLLIFHI 3226 YFILVNLLIFHINGK 3330 0.0013 0.0059 0.0005 0.0040  0.0290 VLSHNSYEK 3227 KKHVLSHNSYEKTKN 3331 VNDFQISKY 3228 ISDVNDFQISKYEDE 3332 -0.0003 -0.0003 -0.0005 VNISKVNDF 3229 LETVNISDVNDFQIS 3333 YDDSLIDEE 3230 SAEYDDSLIDEEEDD 3334 YGRLEIPAI 3231 EDLYGRLEIPAIELP 3335 -0.0003 0.0021 -0.0005 YIPHQSSLP 3232 RGYYIPHQSSLPQDN 3336 0.0004 0.1700 0.0150 0.1500 FKIGSSDPA 3233 RHPFKIGSSDPADNA 3337 0.0003 -0.0003 0.0380 0.0950 IDVHDLISH 3234 EPLIDVHDLISDMIK 3338 IFNKESLAE 3235 FFIIFNKESLAEKTN 3339 IGSSDPADN 3236 PFKIGSSDPADNANP 3340 LALFFIIFN 3237 VFFALFFIIFNKES 3341 -0.0002 0.0056 -0.0007 -0.0018 LATSVLAGL 3238 KYKLATSVLAGLLGN 3342 0.0072 0.6500 0.1300 2.6000 LGGVGLVLY 3239 TVLLGGVGLVLYNTE 3343 0.0007 -0.0002 LGNVSTVLL 3240 AGLLGNVSTVLLGGV 3344 4.6000 0.4300 0.0012 0.5300  0.0012 LLGNVSTVL 3241 LAGLLGNVSTVLLGG 3345 0.6400 0.3800 0.0006 0.5500 LSVFFLALF 3242 MKILSVFFLALFFII 3346 0.0019 0.0360 0.0023 0.0060 LVLYNTEKG 3243 GVGLVLYNTEKGRHP 3347 VFFLALFFI 3244 ILSVFFLALFFIIFN 3348 0.0005 0.0110 0.0031 -0.0003 VHDLISDMI 3245 LIDVHDLISDMIKKE 3349 0.0004 0.0100 0.0096 0.0430  0.0940 VLAGLLGNV 3246 ATSVLAGLLGNVSTV 3350 -0.0003 0.0005  0.0039 VLLGGVGLV 3247 VSTVLLGGVGLVLYN 3351 0.0002 0.0020 -0.0002 0.0120 VNKRKSKYK 3248 LVEVNKRKSKYKLAT 3352 VSTVLLGGV 3249 LGNVSTVLLGGVGLV 3353 0.0006 -0.0003 -0.0003 -0.0005 -0.0005 VTAQDVTPE 3250 DPQVTAQDVTPEQPQ 3574 YKLATSVLA 3251 KSKYKLATSVLAGLL 3354 0.0082 1.9000 1.1000 2.7000  0.0150 FDLFLVNGR 3252 LIFFDLFLVNGRDVQ 3355 0.0470 FFDLFLVNG 3253 FLIFFDLFLVNGRDV 3356 FMKAVCVEV 3254 IGPFMKAVCVEVEKT 3357 0.0003 0.0019 -0.0003 0.0820  0.0700 FNRFLVGCH 3255 NVAFNRFLVGCHPSD 3358 IAGGLALLA 3256 AGGIAGGLALLACAG 3359 -0.0003 0.0004 -0.0005 IAVFGIGQG 3257 GVKIAVFGIGQGINV 3360 LACAGLAYK 3258 LALLACAGLAYKFVV 3361 LALLACAGL 3259 AGGLALLACAGLAYK 3362 0.0009 0.0003 -0.0005 LAMKLIQQL 3260 AVPLAMKLIQQLNTN 3363 0.0770 0.0400  0.0350 LAYKFVVPG 3261 CAGLAYKFVVPGAAT 3364 LIFFDLFLV 3262 IVFLIFFDLFLVNGR 3365 0.0006 0.0028 0.0007 -0.0003 LTDGIPDSI 3263 VVILTDGIPDSIQDS 3366 -0.0003 -0.0003  0.0114 LVGCHPSDG 3264 NRFLVGCHPSDGKCN 3367 LVTVFLIFF 3265 VKYLVTVFLIFFDLF 3368 0.0010 LVVILTDGI 3266 ANQLVVILTDGIPDS 3379 0.0070 0.0054 -0.0002 0.0420 MDCSGSIRR 3267 YLLMDCSGSIRRHNW 3370 MKAVCVEVE 3268 GPFMKAVCVEVEKTA 3371 VEKTASCGV 3269 CVEVEKTASCGVWDE 3372 0.0095 0.0005 VGCHPSDGK 3270 RFLVGCHPSDGKCNL 3373 VIGPFMKAV 3271 VKNVIGPFMKAVCVE 3374 0.1100 0.0590 0.0230 0.0870 VIVFLIFFD 3272 KYVTVFLIFFDLFL 3375 0.0034 0.0130 0.0065 -0.0018 VKYLVTVFL 3273 LGNVKYLVTVFLIFF 3376 0.0016 0.0040 0.0050 0.0012 VNGRDVQNN 3274 LFLVNGRDVQNNTVD 3377 WDEWSPCSV 3275 CGVWDEWSPCSVTCG 3378 -0.0003 -0.0003 -0.0006 IAGGIAGGL 3276 KYKIAGGIAGGLALL 3389 0.2400 0.0063 1.6000 0.2600 -0.0010 YQNNIVDEI 3277 GRDVQNNIVDEIKYR 3380 0.0810 -0.0003 -0.0003 -0.0005  0.0850 YLLMDCSGS 3278 VDLYLLMDCSGSIRR 3381 0.0046 0.0007 -0.0010 FVVPGAATP 3279 AYKFVVPGAATPYAG 3382 0.1700 0.1800 0.9200 0.1300 YKFVVPGAA 3280 GLAYKFVVPGAATPY 3383 0.4900 0.1500 2.5000 0.6000 0.0190 IIRLHSDAS 3281 AKEIIRLHSDASKNK 3384 IIDNNPQEP 3282 EENIIDNNPQEPSPN 3385 VDLYLLMDC 3283 NDEVDLYLLMDCSGS 3386 -0.0003 -0.0003 LLSTNLPYG 3284 IKSLSSTNLPYGRTN 3387 LHEGCTSEL 3285 REILHEGCTSELQEQ 3388 -0.0003 -0.0003 VNHAVPLAM 3286 HNWVNHAVPLAMKLI 3389 0.9400 0.3800 0.200 4.000  0.0250 VPGAATPYA 3287 KFVVPGAATPYAGEP 3390 0.0460 0.0017 0.0064 0.2500 VVPGAATPY 3288 YKFVVPGAATPYAGE 3391 0.0017 0.0160 0.0026 0.0200 WVNHAVPLA 3289 RHNWVNHAVPLAMKL 3392 0.8900 0.4400 1.8000 4.6000  0.0430 LSTNLPYGR 3290 KSLLSTNLPYGRTNL 3393 0.0005

TABLE XXa Malaria DR3a Motif Peptides Core Ex- Position Core Core  Sequence emplary in Pf Exemplary Exemplary Core SeqID Sequence Conser- Exemplary SeqID Poly- Sequence Conser- Protein Sequence Num Frequency vancy (%) Sequence Num Protein Frequency vancy (%) CSP LFQEYQCYG 3394 19 100 VEALFQEYQCYGSSS 3449   16 19 100 CSP LFVEALFQE 3395 19 100 SSFLFVEALFQEYQC 3450   11 19 100 CSP MPNDPNRNV 3396 19 100 GHNMPNDPNRNVDEN 3451  347 19 100 CSP LYNELEMNY 3397 19 100 GINLYNELEMNYYGK 3452   44 18  95 CSP VLNELNYDN 3398 19 100 NTRVLNELNYDNAGI 3453   31 18  95 CSP YENDIEKKI 3399 19 100 ELDYENDIEKKICKM 3454  422 12  63 CSP LNYDNAGIN 3400 18  95 LNELNYDNAGINLYN 3455   35 18  95 CSP LSTEWSPCS 3401 18  95 QNSLSTEWSPCSVTC 3456  389 15  79 CSP LDYENDIEK 3402 18  95 KDELDYENDIEKKIC 3457  420 12  63 LSA FDGDNEILQ 3403  1 100 FHIFDGDNEILQIVD 3458 1882  1 100 LSA FDKDKELTM 3404  1 100 NKFFDKDKELTMSNV 3459   75  1 100 LSA FQDEENIGI 3405  1 100 YDNFQDEENIGIYKE 3460 1791  1 100 LSA IDEEEDDED 3406  1 100 DSLIDEEEDDEDLDE 3461 1770  1 100 LSA IINDDDDKK 3407  1 100 IEHIINDDDDKKKYI 3462  124  1 100 LSA INDDDDKKK 3408  1 100 EHIINDDDDKKKYIK 3463  125  1 100 LSA ISAEYDDSL 3409  1 100 EDEISAEYDDSLIDE 3464 1761  1 100 LSA IVDELSEDI 3410  1 100 ILQIVDELSEDITKY 3465 1891  1 100 LSA IYKELEDLI 3411  1 100 NIGIYKELEDLIEKN 3466 1799  1 100 LSA LAEDLYGRL 3412  1 100 GDVLAEDLYGRLEIP 3467 1645  1 100 LSA LAKEKLQEQ 3413  1 100 QERLAKEKLQEQQSD 3468 1357  1 100 LSA LAKEKLQGQ 3414  1 100 QERLAKEKLQGQQSD 3469 1119  1 100 LSA LANEKLQEQ 3415  1 100 QERLANEKLQEQQRD 3470 1527  1 100 LSA LEQDRLAKE 3416  1 100 QSDLEQDRLAKEKLQ 3471 1386  1 100 LSA LEQERLAKE 3417  1 100 QSDLEQERLAKEKLQ 3472 1590  1 100 LSA LEQERLANE 3418  1 100 QSDLEQERLANEKLQ 3473 1522  1 100 LSA LIDEEEDDE 3419  1 100 DDSLIDEEEDDEDLD 3474 1769  1 100 LSA LPSENERGY 3420  1 100 AIELPSENERGYYIP 3475 1660  1 100 LSA LSEDITKYF 3421  1 100 VDELSEDITKYFMKL 3476 1895  1 100 LSA LSEEKIKKG 3422  1 100 SEELSEEKIKKGKKY 3477 1827  1 100 LSA LYDEHIKKY 3423  1 100 DKSLYDEHIKKYKND 3478 1853  1 100 LSA VLAEDLYGR 3424  1 100 HGDVLAEDLYGRLEI 3479 1644  1 100 LSA VNKEKEKFI 3425  1 100 DKQVNKEKEKFIKSL 3480 1867  1 100 LSA VQYDNFQDE 3426  1 100 KPIVQYDNFQDEENI 3481 1786  1 100 LSA YEDEISAEY 3427  1 100 ISKYEDEISAEYDDS 3482 1757  1 100 LSA YKNDKQVNK 3428  1 100 IKKYKNDKQVNKEKE 3483 1861  1 100 PfEXP FNKESLAEK 3429  1 100 FIIFNKESLAEKTNK 3484   13  1 100 PfEXP IKKEEELVE 3430  1 100 SDMIKKEEELVEVNK 3485   55  1 100 PfEXP LISDMIKKE 3431  1 100 VHDLISDMIKKEEEL 3486   50  1 100 PfEXP VTPEQPQGD 3432  1 100 AQDVTPEQPQGDDNN 3487  141  1 100 PfEXP YNTEKGRHP 3433  1 100 LVLYNTEKGRHPFKI 3488   98  1 100 SSP2 IFFDLFLVN 3434 10 100 VFLIFFDLFLVNGRD 3489   13 10 100 SSP2 ILTDGIPDS 3435 10 100 LVVILTDGIPDSIQD 3490  156 10 100 SSP2 INRENANQL 3436 10 100 NDRINRENANQLVVI 3491  145 10 100 SSP2 LHSDASKNK 3437 10 100 IIRLHSDASKNKEKA 3492  100 10 100 SSP2 LYADSAWEN 3438 10 100 KCNLYADSAWENVKN 3493  211 10 100 SSP2 VCVEVEKTA 3439 10 100 MKAVCVEVEKTASCG 3494  231 10 100 SSP2 VEVEKTASC 3440 10 100 AVCVEVEKTASCGVW 3495  233 10 100 SSP2 VPSDVPKNP 3441 10 100 EKEVPSDVPKNPEDD 3496  384 10 100 SSP2 VWDEWSPCS 3442 10 100 SCGVWDEWSPCSVTC 3497  243 10 100 SSP2 LLMDCSGSI 3443 10  90 DLYLLMDCSGSIRRH 3498   48  9  90 SSP2 ILHEGCTSE 3444 10  80 KREILHEGCTSELQE 3499  265  8  80 SSP2 IPEDSEKEV 3445 10  80 EPNIPEDSEKEVPSD 3500  376  8  80 SSP2 YREEVCNDE 3446  9  80 EIKYREEVCNDEVDL 3501   35  8  80 SSP2 VCNDEVDLY 3447  8  80 REEVCNDEVDLYLLM 3502   39  8  80 SSP2 YAGEPAPFD 3448  8  80 ATPYAGEPAPFDETL 3503  538  8  80

TABLE XXb DR3a Motif Peptides With Binding Information Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR1 DR2w2β1 DR2w2β2 LFQEYQCYG 3394 VEALFQEYQCYGSSS 3449 LFVEALFQE 3395 SSFLFVEALFQEYQC 3450 MPNDPNRNV 3396 GHNMPNDPNRNVDEN 3451 LYNELEMNY 3397 GINLYNELEMNYYGK 3452 VLNELNYDN 3398 NTRVLNELNYDNAGI 3453 YENDIEKKI 3399 ELDYENDIEKKICKM 3454 LNYDNAGIN 3400 LNELNYDNAGINLYN 3455 LSTEWSPCS 3401 QNSLSTEWSPCSVTC 3456 LDYENDIEK 3402 KDELDYENDIEKKIC 3457 FDGDNEILQ 3403 FHIFDGDNEILQIVD 3458 FDKDKELTM 3404 NKFFDKDKELTMSNV 3459 FQDEENIGI 3405 YDNFQDEENIGIYKE 3460 IDEEEDDED 3406 DSLIDEEEDDEDLDE 3461 IINDDDDKK 3407 IEHIINDDDDKKKYI 3462 INDDDDKKK 3408 EHIINDDDDKKKYIK 3463 ISAEYDDSL 3409 EDEISAEYDDSLIDE 3464 IVDELSEDI 3410 ILQIVDELSEDITKY 3465 0.0001 -0.0005 IYKELEDLI 3411 NIGIYKELEDLIEKN 3466 LAEDLYGRL 3412 GDVLAEDLYGRLEIP 3467 LAKEKLQEQ 3413 QERLAKEKLOEQQSD 3468 LAKEKLQGQ 3414 QERLAKEKLOGQQSD 3469 LANEKLQEQ 3415 QERLANEKLOEQQRD 3470 LEQDRLAKE 3416 QSDLEQDRLAKEKLQ 3471 LEQERLAKE 3417 QSDLEQERLAKEKLQ 3472 LEQERLANE 3418 QSDLEQERLANEKLQ 3473 LIDEEEDDE 3419 DDSLIDEEEDDEDLD 3474 LPSENERGY 3420 AIELPSENERGYYIP 3475 LSEDITKYF 3421 VDELSEDITKYFMKL 3476 LSEEKIKKG 3422 SEELSEEKIKKGKKY 3477 LYDEHIKKY 3423 DKSLYDEHIKKYKND 3478 0.0001 -0.0005 VLAEDLYGR 3424 HGDVLAEDLYGRLEI 3479 VNKEKEKFI 3425 DKOVNKEKEKFIKSL 3480 VQYDNFQDE 3426 KPIVQYDNFQDEENI 3481 YEDEISAEY 3427 ISKYEDEISAEYDDS 3482 0.0001 -0.0005 YKNDKQVNK 3428 IKKYKNDKQVNKEKE 3483 FNKESLAEK 3429 FIIFNKESLAEKTNK 3484 IKKEEELVE 3430 SDMIKKEEELVEVNK 3485 LISDMIKKE 3431 VHDLISDMIKKEEEL 3486 VTPEQPQGD 3432 AQDVTPEQPQGDDNN 3487 YNTEKGRHP 3433 LVLYNTEKGRHPFKI 3488 IFFDLFLVN 3434 VFLIFFDLFLVNGRD 3489 ILTDGIPDS 3435 LVVILTDGIPDSIQD 3490 0.0002 0.0001 -0.0006 INRENANQL 3436 NDRINRENANOLVVI 3491 0.0770 0.0015 LHSDASKNK 3437 IIRLHSDASKNKEKA 3492 LYADSAWEN 3438 KCNLYADSAWENVKN 3493 0.0002 0.0005 -0.0010 VCVEVEKTA 3439 MKAVCVEVEKTASCG 3494 VEVEKTASC 3440 AVCVEVEKTASCGVW 3495 0.0001 -0.0006 VPSDVPKNP 3441 EKEVPSDVPKNPEDD 3496 VWDEWSPCS 3442 SCGVWDEWSPCSVTC 3497 0.0001 -0.0005 LLMDCSGSI 3443 DLYLLMDCSGSIRRH 3498 0.0041 0.0250 Core Sequence DR3 DR4w4 DR4w15 DR5w11 DR5w12 LFQEYQCYG 0.0082 LFVEALFQE 0.0051 MPNDPNRNV -0.0033 LYNELEMNY 0.0270 VLNELNYDN -0.0033 YENDIEKKI LNYDNAGIN LSTEWSPCS -0.0033 LDYENDIEK FDGDNEILQ 0.0640 FDKDKELTM FQDEENIGI -0.0033 IDEEEDDED IINDDDDKK INDDDDKKK ISAEYDDSL -0.0033 IVDELSEDI -0.0041 0.0027 0.0017 -0.0002 0.0001 IYKELEDLI -0.0033 LAEDLYGRL LAKEKLQEQ LAKEKLQGQ LANEKLQEQ -0.0033 LEQDRLAKE 0.0038 LEQERLAKE -0.0033 LEQERLANE LIDEEEDDE LPSENERGY -0.0033 LSEDITKYF LSEEKIKKG -0.0033 LYDEHIKKY -0.0041 -0.0007 -0.0014 -0.0002 0.0001 VLAEDLYGR VNKEKEKFI -0.0033 VQYDNFQDE -0.0033 YEDEISAEY -0.0041 0.0008 -0.0014 -0.0002 0.0001 YKNDKQVNK -0.0033 FNKESLAEK 0.0040 IKKEEELVE -0.0033 LISDMIKKE VTPEQPQGD -0.0033 YNTEKGRHP IFFDLFLVN ILTDGIPDS 0.1400 0.3600 -0.0014 -0.0004 0.0002 INRENANQL 0.0092 0.0011 0.0010 -0.0004 0.0001 LHSDASKNK -0.0033 LYADSAWEN 0.3500 -0.0055 -0.0006 VCVEVEKTA VEVEKTASC -0.0041 0.0030 -0.0014 0.0003 0.0001 VPSDVPKNP -0.0130 VWDEWSPCS -0.0041 -0.0009 -0.0009 -0.0002 0.0001 LLMDCSGSI 0.0300 0.0340 0.0028 -0.0002 0.0001 Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR6w19 DR7 DR8w2 DR9 DRw53 LFQEYQCYG 3394 VEALFQEYQCYQSSS 3449 LFVEALFQE 3395 SSFLFVEALFQEYQC 3450 MPNDPNRNV 3396 GHNMPNDPNRNVDEN 3451 LYNELEMNY 3397 GINLYNELEMNYYGK 3452 VLNELNYDN 3398 NTRVLNELNYDNAGI 3453 YENDIEKKI 3399 ELDYENDIEKKICKM 3454 LNYDNAGIN 3400 LNELNYDNAGINLYN 3455 LSTEWSPCS 3401 QNSLSTEWSPCSVTC 3456 LDYENDIEK 3402 KDELDYENDIEKKIC 3457 FDGDNEILQ 3403 FHIFDGDNEILQIVD 3458 FDKDKELTM 3404 NKFFDKDKELTMSNV 3459 FQDEENIGI 3405 YDNFQDEENIGIYKE 3460 IDEEEDDED 3406 DSLIDEEEDDEDLDE 3461 IINDDDDKK 3407 IEHIINDDDDKKKYI 3462 INDDDDKKK 3408 EHIINDDDDKKKYIK 3463 ISAEYDDSL 3409 EDEISAEYDDSLIDE 3464 IVDELSEDI 3410 ILQIVDELSEDITKY 3465 -0.0003 -0.0003 0.0290 IYKELEDLI 3411 NIGIYKELEDLIEKN 3466 LAEDLYGRL 3412 GDVLAEDLYGRLEIP 3467 LAKEKLQEQ 3413 QERLAKEKLQEQQSD 3468 LAKEKLQGQ 3414 QERLAKEKLQGQQSD 3469 LANEKLQEQ 3415 QERLANEKLQEQQRD 3470 LEQDRLAKE 3416 QSDLEQDRLAKEKLQ 3471 LEQERLAKE 3417 QSDLEQERLAKEKLQ 3472 LEQERLANE 3418 QSDLEQERLANEKLQ 3473 LIDEEEDDE 3419 DDSLIDEEEDDEDLD 3474 LPSENERGY 3420 AIELPSENERGYYIP 3475 LSEDITKYF 3421 VDELSEDITKYFMKL 3476 LSEEKIKKG 3422 SEELSEEKIKKGKKY 3477 LYDEHIKKY 3423 DKSLYDEHIKKYKND 3478 -0.0003 -0.0003 0.0006 VLAEDLYGR 3424 HGDVLAEDLYGRLEI 3479 VNKEKEKFI 3425 DKQVNKEKEKFIKSL 3480 VQYDNFQDE 3426 KPIVQYDNFQDEENI 3481 YEDEISAEY 3427 ISKYEDEISAEYDDS 3482 -0.0003 -0.0003 -0.0005 YKNDKQVNK 3428 IKKYKNDKQVNKEKE 3483 FNKESLAEK 3429 FIIFNKESLAEKTNK 3484 IKKEEELVE 3430 SDMIKKEEELVEVNK 3485 LISDMIKKE 3431 VHDLISDMIKKEEEL 3486 VTPEQPQGD 3432 AQDVTPEQPQGDDNN 3487 YNTEKGRHP 3433 LVLYNTEKGRHPFKI 3488 IFFDLFLVN 3434 VFLIFFDLFLVNGRD 3489 ILTDGIPDS 3435 LVVILTDGIPDSIQD 3490 0.0002 0.0046 -0.0003 0.0014 0.0480 INRENANQL 3436 NDRINRENANQLVVI 3491 -0.0003 -0.0003 0.0096 LHSDASKNK 3437 IIRLHSDASKNKEKA 3492 LYADSAWEN 3438 KCNLYADSAWENVKN 3493 0.0003 -0.0014 -0.0009 VCVEVEKTA 3439 MKAVCVEVEKTASCG 3494 VEVEKTASC 3440 AVCVEVEKTASCGVW 3495 0.0073 0.0006 0.0022 VPSDVPKNP 3441 EKEVPSDVPKNPEDD 3496 VWDEWSPCS 3442 SCGVWDEWSPCSVTC 3497 -0.0003 -0.0003 LLMDCSGSI 3443 DLYLLMDCSGSIRRH 3498 0.0072 0.0014 0.0057 Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR1 DR2w2β1 DR2w2β2 ILHEGCTSE 3444 KREILHEGCTSELQE 3499 IPEDSEKEV 3445 EPNIPEDSEKEVPSD 3500 YREEVCNDE 3446 EIKYREEVCNDEVDL 3501 VCNDEVDLY 3447 REEVCNDEVDLYLLM 3502 0.0003 -0.0006 0.1300 YAGEPAPFD 3448 ATPYAGEPAPFDETL 3503 Core Sequence DR3 DR4w4 DR4w15 DR5w11 DR5w12 ILHEGCTSE IPEDSEKEV -0.0130 YREEVCNDE -0.0033 VCNDEVDLY -0.0006 -0.0014 -0.0004 0.0001 YAGEPAPFD -0.0130 Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR6w19 DR7 DR8w2 DR9 DRw53 ILHEGCTSE 3444 KREILHEGCTSELQE 3499 IPEDSEKEV 3445 EPNIPEDSEKEVPSD 3500 YREEVCNDE 3446 EIKYREEVCNDEVDL 3501 VCNDEVDLY 3447 REEVCNDEVDLYLLM 3502 -0.0003 -0.0003 -0.0010 YAGEPAPFD 3448 ATPYAGEPAPFDETL 3503

TABLE XXc Core Core Core SeqID Core Conservancy Exemplary Protein Sequence Num Frequency (%) Sequence CSP LKKNSRSLG 3504 19 100 WYSLKKNSRSLGEND CSP ANNDVKNNN 3505 3 16 NANANNDVKNNNNEE LSA ADIQNHTLE 3506 1 100 DKSADIQNHTLETVN LSA FHINGKIIK 3507 1 100 LLIFHINGKIIKNSE LSA FKPNDKSLY 3508 1 100 DNNFKPNDKSLYDEH LSA FLKENKLNK 3509 1 100 ENIFLKENKLNKEGK LSA IEKTNRESI 3510 1 100 ISIIEKTNRESITTN LSA IKNSEKDEI 3511 1 100 GKIIKNSEKDEIIKS LSA IKPEQKEDK 3512 1 100 DGSIKPEQKEDKSAD LSA IKSNLRSGS 3513 1 100 DEIIKSNLRSGSSNS LSA INEEKHEKK 3514 1 100 RNRINEEKHEKKHVL LSA LEQERRAKE 3515 1 100 QSDLEQERRAKEKLQ LSA LNKEGKLIE 3516 1 100 ENKLNKEGKLIEHII LSA LPQDNRGNS 3517 1 100 QSSLPQDNRGNSRDS LSA LQEQQRDLE 3518 1 100 NEKLQEQQRDLEQER PfEXP AEKTNKGTG 3519 1 100 ESLAEKTNKGTGSGV PfEXP LYNTEKGRH 3520 1 100 GLVLYNTEKGRHPFK PfEXP VEVNKRKSK 3521 1 100 EELVEVNKRKSKYKL SSP2 AWENVKNVI 3522 10 100 ADSAWENVKNVIGPF SSP2 FLVNGRDVQ 3523 10 100 FDLFLVNGRDVQNNI SSP2 LGEEDKDLD 3524 10 100 DETLGEEDKDLDEPE SSP2 LDNERKQSD 3525 10 80 PKVLDNERKQSDPQS SSP2 VLDNERKQS 3526 10 70 PPKVLDNERKQSDPQ SSP2 IQDSLKESR 3527 10 60 PDSIQDSLKESRKLN SSP2 IVDEIKYSE 3528 9 90 QNNIVDEIKYREEVC SSP2 ALLQVRKHL 3529 9 60 LTDALLQVRKHLNDR SSP2 LKESRKLND 3530 6 50 QDSLKESRKLSDRGV SSP2 FSNNAKEII 3531 6 40 VNVFSNNAKEIIRLH SSP2 YNDTPKHPE 3532 5 50 NRKYNDTPKHPEREE SSP2 FSNNAREII 3533 4 20 LNIFSNNAREIIRLH SSP2 LKESRKLSD 3534 3 30 QDSLKESRKLSDRGV SSP2 YNDTPKYPE 3535 2 20 NRKYNDTPKYPEREE SSP2 AGSDNKYKI 3536 1 10 KKKAGSDNKYKIAGG SSP2 ALLEVRKHL 3537 1 10 LTDALLEVRKHLNDR SSP2 IVDEIKYSE 3538 1 10 QNNIVDEIKYSEEVC Exemplary Position  Exemplary  Exemplary  SeqID In PF Sequence Sequence Protein Num Poly-Protein Frequency Conservancy (%) CSP 3539 62 19 100 CSP 3540 361 3  16 LSA 3541 1734 1 100 LSA 3542 16 1 100 LSA 3543 1846 1 100 LSA 3544 108 1 100 LSA 3545 1693 1 100 LSA 3546 23 1 100 LSA 3547 1724 1 100 LSA 3548 32 1 100 LSA 3549 47 1 100 LSA 3550 1573 1 100 LSA 3551 114 1 100 LSA 3552 1676 1 100 LSA 3553 1532 1 100 PfEXP 3554 19 1 100 PfEXP 3555 97 1 100 PfEXP 3556 62 1 100 SSP2 3557 216 10 100 SSP2 3558 18 10 100 SSP2 3559 549 10 100 SSP2 3560 435 8  80 SSP2 3561 434 7  70 SSP2 3562 165 6  60 SSP2 3563 29 9  90 SSP2 3564 133 6  60 SSP2 3565 169 5  50 SSP2 3566 90 4  40 SSP2 3567 479 5  50 SSP2 3568 90 2  20 SSP2 3569 169 3  30 SSP2 3570 479 2  20 SSP2 3571 501 1  10 SSP2 3572 133 1  10 SSP2 3573 29 1  10

TABLE XXd Malaria DR3b Motif Peptides With Binding Information Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR1 DR2w2β1 DR2w2β2 LKKNSRSLG 3504 WYSLKKNSRSLGEND 3539 ANNDVKNNN 3505 NANANNDVKNNNNEE 3540 ADIQNHTLE 3506 DKSADIQNHTLETVN 3541 FHINGKIIK 3507 LLIFHINGKIIKNSE 3542 0.5700 0.2900 0.2500 FKPNDKSLY 3508 DNNFKPNDKSLYDEH 3543 FLKENKLNK 3509 ENIFLKENKLNKEGK 3544 IEKTNRESI 3510 ISIIEKTNRESITIN 3545 IKNSEKDEI 3511 GKIIKNSEKDEIIKS 3546 0.0002 -0.0021 -0.0160 IKPEQKEDK 3512 DGSIKPEQKEDKSAD 3547 IKSNLRSGS 3513 DEIIKSNLRSGSSNS 3548 INEEKHEKK 3514 RNRINEEKHEKKHVL 3549 LEQERRAKE 3515 QSDLEQERRAKEKLQ 3550 LNKEGKLIE 3516 ENKLNKEGKLIEHII 3551 0.0001 -0.0021 LPQDNRGNS 3517 QSSLPQDNRGNSRDS 3552 LQEQQRDLE 3518 NEKLQEQQRDLEQER 3553 AEKTNKGTG 3519 ESLAEKTNKGTGSGV 3554 LYNTEKGRH 3520 GLVLYNTEKGRHPFK 3555 VEVNKRKSK 3521 EELVEVNKRKSKYKL 3556 AWENVKNVI 3522 ADSAWENVKNVIGPF 3557 FLVNGRDVQ 3523 FDLFLVNGRDVQNNI 3558 LGEEDKDLD 3524 DETLGEEDKDLDEPE 3559 LDNERKQSD 3525 PKVLDNERKQSDPQS 3560 VLDNERKQS 3526 PPKVLDNERKQSDPQ 3561 IQDSLKESR 3527 PDSIQDSLKESRKLN 3562 -0.0001 0.0040 -0.0018 IVDEIKYRE 3528 QNNIVDEIKYREEVC 3563 ALLQVRKHL 3529 LTDALLQVRKHLNDR 3564 LKESRKLND 3530 QDSLKESRKLNDRGV 3565 FSNNAKEll 3531 VNVFSNNAKEIIRLH 3566 YNDTPKHPE 3532 NRKYNDTPKHPEREE 3567 FSNNAREII 3533 LNIFSNNAREIIRLH 3568 LKESRKLSD 3534 QDSLKESRKLSDRGV 3569 YNDTPKYPE 3535 NRKYNDTPKYPEREE 3570 AGSDNKYKI 3536 KKKAGSDNKYKIAGG 3571 ALLEVRKHL 3537 LTDALLEVRKHLNDR 3572 IVDEIKYSE 3538 QNNIVDEIKYREEVC 3573 Core Sequence DR3 DR4w4 DR4w15 DR5w11 DR5w12 LKKNSRSLG ANNDVKNNN ADIQNHTLE FHINGKIIK 0.5300 0.0060 -0.0030 0.3600 0.0230 FKPNDKSLY 0.1700 FLKENKLNK 0.0950 IEKTNRESI 0.1300 IKNSEKDEI -0.0017 0.0030 -0.0010 -0.0003 IKPEQKEDK -0.0033 IKSNLRSGS 0.0050 INEEKHEKK 0.0420 LEQERRAKE LNKEGKLIE -0.0140 -0.0017 -0.0047 -0.0005 -0.0003 LPQDNRGNS -0.0033 LQEQQRDLE AEKTNKGTG -0.0033 LYNTEKGRH VEVNKRKSK 0.0880 AWENVKNVI -0.0130 FLVNGRDVQ -0.0033 LGEEDKDLD -0.0130 LDNERKQSD -0.0130 VLDNERKQS -0.0130 IQDSLKESR 0.8400 -0.0055 -0.0006 IVDEIKYRE ALLQVRKHL -0.0033 LKESRKLND FSNNAKEll YNDTPKHPE FSNNAREII LKESRKLSD YNDTPKYPE AGSDNKYKI ALLEVRKHL IVDEIKYSE Core Exemplary Core SeqID Exemplary SeqID Sequence Num Sequence Num DR6w19 DR7 DR8w2 DR9 DRw53 LKKNSRSLG 3504 WYSLKKNSRSLGEND 3539 ANNDVKNNN 3505 NANANNDVKNNNNEE 3540 ADIQNHTLE 3506 DKSADIQNHTLETVN 3541 FHINGKIIK 3507 LLIFHINGKIIKNSE 3542 0.0330 0.1300 0.1400 0.1500 FKPNDKSLY 3508 DNNFKPNDKSLYDEH 3543 FLKENKLNK 3509 ENIFLKENKLNKEGK 3544 IEKTNRESI 3510 ISIIEKTNRESITTN 3545 IKNSEKDEI 3511 GKIIKNSEKDEIIKS 3546 -0.0011 -0.0007 IKPEQKEDK 3512 DGSIKPEQKEDKSAD 3547 IKSNLRSGS 3513 DEIIKSNLRSGSSNS 3548 INEEKHEKK 3514 RNRINEEKHEKKHVL 3549 LEQERRAKE 3515 QSDLEQERRAKEKLQ 3550 LNKEGKLIE 3516 ENKLNKEGKLIEHII 3551 -0.0009 -0.0007 LPQDNRGNS 3517 QSSLPQDNRGNSRDS 3552 LQEQQRDLE 3518 NEKLQEQQRDLEQER 3553 AEKTNKGTG 3519 ESLAEKTNKGTGSGV 3554 LYNTEKGRH 3520 GLVLYNTEKGRHPFK 3555 VEVNKRKSK 3521 EELVEVNKRKSKYKL 3556 AWENVKNVI 3522 ADSAWENVKNVIGPF 3557 FLVNGRDVQ 3523 FDLFLVNGRDVQNNI 3558 LGEEDKDLD 3524 DETLGEEDKDLDEPE 3559 LDNERKQSD 3525 PKVLDNERKQSDPQS 3560 VLDNERKQS 3526 PPKVLDNERKQSDPQ 3561 IQDSLKESR 3527 PDSIQDSLKESRKLN 3562 -0.0002 -0.0014 0.0012 IVDEIKYRE 3528 QNNIVDEIKYREEVC 3563 ALLQVRKHL 3529 LTDALLQVRKHLNDR 3564 LKESRKLND 3530 QDSLKESRKLNDRGV 3565 FSNNAKEII 3531 VNVFSNNAKEIIRLH 3566 YNDTPKHPE 3532 NRKYNDTPKHPEREE 3567 FSNNAREII 3533 LNIFSNNAREIIRLH 3568 LKESRKLND 3534 QDSLKESRKLNDRGV 3569 YNDTPKYPE 3535 NRKYNDTPKYPEREE 3570 AGSDNKYKI 3536 KKKAGSDNKYKIAGG 3571 ALLEVRKHL 3537 LTDALLEVRKHLNDR 3572 IVDEIKYSE 3538 QNNIVDEIKYREEVC 3573

TABLE XXI Population coverage with combined HLA Supertypes PHENOTYPIC FREQUENCY North American HLA-SUPERTYPES Caucasian Black Japanese Chinese Hispanic Average a. Individual Supertypes A2 45.8 39.0 42.4 45.9 43.0 43.2 A3 37.5 42.1 45.8 52.7 43.1 44.2 B7 38.6 52.7 48.8 35.5 47.1 44.7 A1 47.1 16.1 21.8 14.7 26.3 25.2 A24 23.9 38.9 58.6 40.1 38.3 40.0 B44 43.0 21.2 42.9 39.1 39.0 37.0 B27 28.4 26.1 13.3 13.9 35.3 23.4 B62 12.6 4.8 36.5 25.4 11.1 18.1 B58 10.0 25.1 1.6 9.0 5.9 10.3 b. Combined Supertypes A2, A3, B7 83.0 86.1 87.5 88.4 86.3 86.2 A2, A3, B7, A24, B44, A1 99.5 98.1 100.0 99.5 99.4 99.3 A2, A3, B7, A24, B44, A1, 99.9 99.6 100.0 99.8 99.9 99.8 B27, B62, B58

TABLE XXII  Fixed analogs of P. falciparum CTL epitopes SEQ SEQ Supertype ID Alleles Fixing Fixed ID (or allele) Peptide Sequence NO: Source bounda strategy sequence NO: A2 1167.21 FLIFFDLFLV 3610 Pf SSP2 14 5 V2 FLIFFDLFLV 3803 supertype 1167.16 FMKAVCVEV 3611 Pf SSP2 230 5 V2 FVKAVCVEV 3804 1167.08 GLIMVLSFL 3612 Pf CSP 425 4 Vc GLIMVLSFV 3805 V2 GVIMVLSFL 3806 V2Nc GVIMVLSFV 3807 1167.12 VLAGLLGNV 3613 Pf EXP1 80 4 V2 VLAGLLGNV 3808 1167.13 KILSVFFLA 3614 Pf EXP1 2 3 L2 KLLSVFFLA 3809 V2 KVLSVFFLA 3810 Vc KILSVFFLV 3811 L2/Vc KLLSVFFLV 3812 V2/Vc KVLSVFFLV 3813 1167.10 GLLGNVSTV 3615 Pf EXP1 83 3 V2 GVLGNVSTV 3814 1167.18 ILSVSSFLFV 3616 Pf CSP 7 2 V2 IVSVSSFLFV 3815 1167.19 VLLGGVGLVL 3617 Pf EXP1 91 2 Vc VLLGGVGLVV 3816 V2 VVLGGVGLVL 3817 V2/Vc VVLGGVGLVV 3818 A3- 1167.36 LACAGLAYK 3718 Pf SSP2 511 4 V2 LVCAGLAYK 3819 supertype 1167.32 QTNFKSLLR 3619 Pf LSA1 94 4 V2 QVNFKSLLR 3820 1167.43 VTCGNGIQVR 3620 Pf CSP 375 4 V2 VVCGNGIQVR 3821 1167.24 ALFFIIFNK 3621 Pf EXP1 10 3 V2 AVFFIIFNK 3822 1167.28 GVSENIFLK 3622 Pf LSA1 105 3 — 1167.47 HVLSHNSYEK 3623 Pf LSA1 59 3 — 1167.51 LLACAGLAYK 3624 Pf SSP2 510 3 V2 LVACAGLAYK 3823 1167.46 FILVNLLIFH 3625 Pf LSA1 11 2 V2 FVLVNLLIFH 3824 Rc FILVNLLIFR 3825 Kc FILVNLLIFK 3826 V2/Rc FVLVNLL1FR 3827 V2/Kc FVLVNLLIFK 3828 B7- 1167.61 TPYAGEPAPF 3626 Pf SSP2 539 4 Ic TPYAGEPAPI 3829 supertype 19.0051 LPYGRTNL 3627 Pf SSP2 126 3 Ic LPYGRTNI 3830 A1 16.0245 FQDEENIGIY 3628 Pf LSA1 1794 1 T2 FTDEENIGIY 3831 16.0040 FVEALFQEY 3629 Pf CSP 15 1 D3 FVEALFQEY 3832 T2 FTEALFQEY 3833 15.0184 LPSENERGY 3630 Pf LSA1 1663 1 D3 LPDENERGY 3834 T2 LTSENERGY 3835 16.0130 PSDGKCNLY 3631 Pf SSP2 207 1 T2 PTDGKCNLY 3836 A24 1167.54 FYFILVNLL 3632 Pf LSA1 9 1 Fc FYFILVNLF 3837 1167.53 KYKLATSVL 3633 Pf EXP1 73 1 Fc KYKLATSVF 3838 1167.56 KYLVIVFLI 3634 Pf SSP2 8 1 Fc KYLVIVFLF 3839 1167.55 YYIPHQSSL 3635 Pf LSA1 1671 1 Fc YYIPHQSSF 3840 aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding ato A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101, and A*2402, respectively.

TABLE XXIII Plasmodium falciparum CTL-inducing epitopes SEQ ID HLA- Epitope NO: Antigen Residues restriction GLIMVLSFL 3636 CSP 386-394 A2-supertype ILSVSSFLFV 3637 CSP   7-16 A2-supertype VLAGLLGNV 3638 Exp-1  80-88 A2-supertype KILSVFFLA 3639 Exp-1   2-10 A2-supertype GLLGNVSTV 3640 Exp-1  83-91 A2-supertype VLLGGVGLVL 3641 Exp-1  91-100 A2-supertype FLIFFDLFLV 3642 SSP2  14-23 A2-supertype VTCGNGIQVR 3643 CSP 336-345 A3-supertype ALFFIIFNK 3644 Exp-1  10-18 A3-supertype QTNFKSLLR 3645 LSA-1  94-102 A3-supertype GVSENIFLK 3646 LSA-1 105-113 A3-supertype HVLSHNSYEK 3647 LSA-1  59-68 A3-supertype FILVNLLIFH 3648 LSA-1  11-20 A3-supertype TPYAGELPAPF 3649 SSP2 539-548 B7-supertype MPLETQLAI 3650 s16  77-85 B7-supertype MRKLAILSVSSFLVF 3651 CSP   2-16 DR-supermotif MNYYGKQENWYSLICK 3652 CSP  53-67 DR-supermotif RHNWVNHAVPLAMKLI 3653 SSP2  61-76 DR-supermotif VKNVIGPFMKAVCVE 3654 SSP2 223-237 DR-supermotif SSVFNVVNSSIGLIM 3655 CSP 410-424 DR-supermotif AGLLGNVSTVSTVLLGGV 3656 EXP1  82-96 DR-supermotif KSKYKLATSVLAGLL 3657 EXP1  71-85 DR-supermotif GLAYKFVVPGAATPY 3658 SSP2 512-526 DR-supermotif KYKIAGGIAGGLALL 3659 SSP2 494-508 DR-supermotif

TABLE XXIV MHC-peptide binding assays: cell lines and radiolabeled ligands. A. Class I binding assays Radiolabeled peptide Species Antigen Allele Cell line Source Sequence SEQ ID NO: Human A1 A*0101 Steinlin Hu. J chain 102-110 YTAVVPLVY 3660 A2 A*0201 JY HBVc 18-27 F6->Y FLPSDYFPSV 3661 A2 A*0202 P815  HBVc 18-27 F6->Y FLPSDYFPSV 3662 (transfected) A2 A*0203 FUN HBVc 18-27 F6->Y FLPSDYFPSV 3663 A2 A*0206 CLA HBVc 18-27 F6->Y FLPSDYFPSV 3664 A2 A*0207 721.221  HBVc 18-27 F6->Y FLPSDYFPSV 3665 (transfected) A3 GM3107 non-natural (A3CON1) KVFPYALINK 3666 A11 BVR non-natural (A3CON1) KVFPYALINK 3667 A24 A*2402 KAS116 non-natural (A24CON1) AYIDNYNKF 3668 A31 A*3101 SPACH non-natural (A3CON1) KVFPYALINK 3669 A33 A*3301 LWAGS non-natural (A3CON1) KVFPYALINK 3670 A28/68 A*6801 C1R HBVc 141-151 T7->Y STLPETYVVRR 3671 A28/68 A*6802 AMAI HBV pol 646-654 C4->A FTQAGYPAL 3672 B7 B*0702 GM3107 A2 sigal seq. 5-13  APRTLVYLL 3673 (L7->Y) B8 B*0801 Steinlin HIVgp 586-593 Y1->F,  FLKDYQLL 3674 Q5->Y B27 B*2705 LG2 R 60s FRYNGLIHR 3675 B35 B*3501 C1R, BVR non-natural (B35CON2) FPFKYAAAF 3676 B35 B*3502 TISI non-natural (B35CON2) FPFKYAAAF 3677 B35 B*3503 EHM non-natural (B35CON2) FPFKYAAAF 3678 B44 B*4403 PITOUT EF-1 G6->Y AEMGKYSFY 3679 B51 KAS116 non-natural (B35CON2) FPFKYAAAF 3680 B53 B*5301 AMAI non-natural (B35CON2) FPFKYAAAF 3681 B54 B*5401 KT3 non-natural (B35CON2) FPFKYAAAF 3682 Cw4 Cw*0401 CIR non-natural (C4CON1) QYDDAVYKL 3683 Cw6 Cw*0602 721.221  non-natural (C6CON1) YRHDGGNVL 3684 transfected Cw7 Cw*0702 721.221  non-natural (C6CON1) YRHDGGNVL 3685 transfected Mouse Db EL4 Adenovirus ElA P7->Y SGPSNTYPEI 3686 Kb EL4 VSV NP 52-59 RGYVFQGL 3687 Dd P815 HIV-IIIB ENV 04->Y RGPYRAFVTI 3688 Kd P815 non-natural (KdCON1) KFNPMKTYI 3689 Ld P815 HBVs 28-39 IPQSLDSYWTSL 3690 B. Class II binding assays Radiolabeled peptide Species Antigen Allele Cell line Source Sequence SEQ ID NO: Human DR1 DRB1*0101 LG2 HA Y307-319 YPKYVKQNTLKLAT 3691 DR2 DRB1*1501 L466.1 MBP 88-102Y VVHFFKNIVTPRTPPY 3692 DR2 DRB1*1601 L242.5 non-natural (760.16) YAAFAAAKTAAAFA 3693 DR3 DRB1*0301 MAT MT 65kD Y3-13 YKTIAFDEEARR 3694 DR4w4 DRB1*0401 Preiss non-natural (717.01) YARFQSQTTLKQKT 3695 DR4w10 DRB1*0402 YAR non-natural (717.10) YARFQRQTTLKAAA 3696 DR4w14 DRB1*0404 BIN 40 non-natural (717.01) YARFQSQTTLKQKT 3697 DR4w15 DRB1*0405 KT3 non-natural (717.01) YARFQSQTTLKQKT 3698 DR7 DRB1*0701 Pitout Tet. tox. 830-843 QYIKANSKFIGITE 3699 DR8 DRB1*0802 OLL Tet. tox. 830-843 QYIKANSKFIGITE 3700 DR8 DRB1*0803 LUY Tet. tox. 830-843 QYIKANSKFIGITE 3701 DR9 DRB1*0901 HID Tet. tox. 830-843 QYIKANSKFIGITE 3702 DR11 DRB1*1101 Sweig Tet. tox. 830-843 QYIKANSKFIGITE 3703 DR12 DRB1*1201 Herluf unknown eluted peptide EALIHQLKINPYVLS 3704 DR13 DRB1*1302 H0301 Tet. tox. 830-843 S->A QYIKANAKFIGITE 3705 DR51 DRB5*0101 GM3107  Tet. tox. 830-843 QYIKANAKFIGITE 3706 or  L416.3 DR51 DRB5*0201 L255.1 HA 307-319 PKYVKQNTLKLAT 3707 DR52 DRB3*0101 MAT Tet. tox. 830-843 NGQIGNDPNRDIL 3708 DR53 DRB4*0101 L257.6 non-natural (717.01) YARFQSQTTLKQKT 3709 DQ3.1 QA1*0301/ PF non-natural (ROIV) YAHAAHAAHAAHAAHAA 3710 DQB1*03( Mouse IAb DB27.4 non-natural (ROIV) YAHAAHAAHAAHAAHAA 3711 IAd A20 non-natural (ROIV) YAHAAHAAHAAHAAHAA 3712 IAk CH-12 HEL 46-61 YNTDGSTDYGILQINSR 3713 IAs LS102.9 non-natural (ROIV) YAHAAHAAHAAHAAHAA 3714 IAu 91.7 non-natural (ROIV) YAHAAHAAHAAHAAHAA 3715 IEd A20 Lambda repressor 12-26 YLEDARRKKAIYEKKK 3716 lEk CH-12 Lambda repressor 12-26 YLEDARRKKAIYEKKK 3717

TABLE XXV Monoclonal antibodies used in MHC purification. Monoclonal antibody Specificity W6/32 HLA-class I B123.2 HLA-B and C IVD12 HLA-DQ LB3.1 HLA-DR M1/42 H-2 class I 28-14-8S H-2 Db and Ld 34-5-8S H-2 Dd B8-24-3 H-2 Kb SF1-1.1.1 H-2 Kd Y-3 H-2 Kb 10.3.6 H-2 IAk 14.4.4 H-2 IEd, IEK MKD6 H-2 IAd Y3JP H-2 IAb, IAs, IAu

TABLE XXVI P. falciparum A2-supermotif CTL epitopes SEQ ID A2-supertype binding capacity (IC50 nM) Alleles Peptide AA Sequence NO: Source A*0201 A*0202 A*0203 A*0206 A*6802 bounda 1167.21 10 FLIFFDLFLV 3718 Pf SSP2 14 12 10 5.9 11 333 5 1167.16  9 FMKAVCVEV 3719 Pf SSP2 230 63 307 2.9 389 143 5 1167.12  9 VLAGLLGNV 3720 Pf EXP1 80 19 24 0.67 31 606 4 1167.08  9 GLIMVLSFL 3721 Pf CSP 425 22 20 3.6 74 4396 4 1167.13  9 KILSVFFLA 3722 Pf EXP1 2 5.0 172 3448 8.0 9524 3 1167.10  9 GLLGNVSTV 3723 Pf EXP1 83 24 1194 1.2 25 21053 3 1167.19 10 VLLGGVGLVL 3724 Pf EXP1 91 94 — 2500 420 16000 2 1167.18 10 ILSVSSFLFV 3725 Pf CSP 7 208 3583 19 587 2105 2 * A dash indicates IC50 nM > 30000.

TABLE XXVII  P. falciparum A3-supermotif CTL epitopes A3-supertype binding capacity (IC50 nm) SEQ ID Alleles Peptide AA Sequence NO: Source A*301 A-1101 A*3101 A*3301 A*6801 bounda 1167.32  9 QTNFKSLLR 3726 Pf LSA1 94 50 14 180 617 4 4 1167.36  9 LACAGLAYK 3727 Pf SSP2 511 423 143 5294 64 32 4 1167.43 10 VTCGNGIQVR 3728 Pf CSP 375 6875 11 15 64 444 4 1167.24  9 ALFFIIFNK 3729 Pf EXP1 10 9.2 2.2 720 1261 73 3 1167.51 10 LLACAGLAYK 3730 Pf SSP2 510 22 73 692 1526 24 3 1167.28  9 GVSENIFLK 3731 Pf LSA1 105 151 5.0 2250 8286 10 3 1167.47 10 HVLSHNSYEK 3732 Pf LSA1 59 407 200 — — 114 3 1167.46 10 FILVNLLIFH 3733. Pf LSA1 11 733 1333 1957 397 154 2 * A dash indicates IC50 nM > 30000.

TABLE XXVIII  P. falciparum B7-supermotif CTL epitopes SEQ ID B7-supertype binding capacity (IC50 nM) Alleles Peptide AA Sequence NO: Source B*0702 B*3501 B*5101 B*5301 B*5401 bounda 1167.61 10 TPYAGEPAPF 3734 Pf SSP2 539 31 14 15   158 25000 4 19.0051  8 LPYGRTNL 3735 Pf SSP2 126 50 — 32 15500   417 3 * A dash indicates 1050 nM > 30000.

TABLE XXIX P. falciparum HLA-A*0101 and A*2402 binding peptides Binding capacity (IC50 nM) Motif Peptide AA Sequence SEQ ID NO: Source A*0101 A*2401 A1 16.0040 9 FVEALFQEY 3736 Pf CSP 15   7.4 16.0245 10 FQDEENIGIY 3737 Pf LSA1 1794 23 15.0184 9 LPSENERGY 3738 37 16.0130 9 PSDGKCNLY 3739 Pf SSP2 207 46 A24 1167.55 9 YYPHQSSL 3740 Pf LSA1 1671   2.4 1167.54 9 FYFILVNLL 3741 Pf LSA1 9 25 1167.56 9 KYLVIVFLI 3742 Pf SSP2 8 34 1167.53 9 KYKLATSVL 3743 Pf EXP1 73 75

TABLE XXX HLA-DR screening panels Screening Representative Assay Phenotypic Frequencies Panel Antigen Alleles Allele Alias Cauc. Blk. Jpn. Chn. Hisp. Avg. Primary DR1 DRB1*0101-03 DRB1*0101 (DR1) 18.5 8.4 10.7 4.5 10.1 10.4 DR4 DRB1*0401-12 DRB1*0401 (DR4w4) 23.6 6.1 40.4 21.9 29.8 24.4 DR7 DRB1*0701-02 DRB1*0701 (DR7) 26.2 11.1 1.0 15.0 16.6 14.0 Panel total 59.6 24.5 49.3 38.7 51.1 44.6 Secondary DR2 DRB1*1501-03 DRB1*1501 (DR2w2 β1) 19.9 14.8 30.9 22.0 15.0 20.5 DR2 DRB5*0101 DRB5*0101 (DR2w2 β2) — — — — — — DR9 DRB1*09011, 09012 DRB1*0901 (DR9) 3.6 4.7 24.5 19.9 6.7 11.9 DR13 DRB1*1301-06 DRB1*1302 (DR6w19) 21.7 16.5 14.6 12.2 10.5 15.1 Panel total 42.0 33.9 61.0 48.9 30.5 43.2 Tertiary DR4 DRB1*0405 DRB1*0405 (DR4w15) — — — — — — DR8 DRB1*0801-5 DRB1*0802 (DR8w2) 5.5 10.9 25.0 10.7 23.3 15.1 DR11 DRB1*1101-05 DRB1*1101 (DR5w11) 17.0 18.0 4.9 19.4 18.1 15.5 Panel total 22.0 27.8 29.2 29.0 39.0 29.4 Quartemary DR3 DRB1*0301-2 DRB1*0301 (DR3w17) 17.7 19.5 0.4 7.3 14.4 11.9 DR12 DRB1*1201-02 DRB1*1201 (DR5w12) 2.8 5.5 13.1 17.6 5.7 8.9 Panel total 20.2 24.4 13.5 24.2 19.7 20.4

TABLE XXXI P. falciparum derived HTL candidate epitopes SEQ ID Binding capacity (IC50 nM) Peptide Sequence NO: Source DR1 DR2w2β1 DR2w2β2 DR4w4 DR4w15 F125.04 RHNWVNHAVPLAMKLI 3744 Pf SSP2 61 26 260 83 14 317 1188.34 HNWVNHAVPLAMKLI 3745 Pf SSP2 62 14 364 143 12 950 1188.16 KSKYKLATSVLAGLL 3746 Pf EXP1 71 3.6 1247 24 7.1 47 LVNLLIFHINGKIIKNSE 3747 Pf LSA1 13 F125.02 LVNLLIFHINGKIIKNS 3748 Pf LSA1 13 78 13 426 — 1810 27.0402 LLIFHINGKIIKNSE 3749 Pf LSA1 16 8.8 80 7500 1188.32 GLAYKFVVPGAATPY 3750 Pf SSP2 512 3.1 - 29 45 1407 27.0392 SSVFNVVNSSIGLIM 3751 Pf CSP 410 42 314 2500 450 1652 27.0417 VKNVIGPFMKAVCVE 3752 Pf SSP2 223 56 212 250 — — 27.0388 MRKLAILSVSSFLFV 3753 Pf CSP 2 50 18 1538 5769 1407 27.0387 MNYYGKQENWYSLKK 3754 Pf CSP 53 6.4 9100 435 21 292 1188.38 KYKIAGGIAGGLALL 3755 Pf SSP2 494 132 - 417 3750 22353 1188.13 AGLLGNVSTVLLGGV 3756 Pf EXP1 82 116 379 15,385 6923 1056 27.0408 QTNFKSLLRNLGVSE 3757 Pf LSA1 94 91 8273 5405 2500 1900 35.0171 PDSIQDSLKESRKLN 3758 Pf SSP2 165 - 2285 - - 35.0172 KCNLYADSAWENVKN 3759 Pf SSP2 211 23425 18200 - - Binding capacity (IC50 nM) Alleles Peptide DR5w11 DR6w19 DR7 DR8w2 DR9 DR3 DR5w12 bound2 F125.04 282 3.9 23 41 33 8751 441 11 1188.34 2703 3.7 66 68 19 1304 497 10 1188.16 30 427 13 45 28 — —  9 F125.02 408 66 260 766 625 19722 11610  8 27.0402 56 106 192 350 500 566 12957  8 1188.32 11 7.1 167 20 125 — 851  9 27.0392 1176 9.7 33 891 63 — —  7 27.0417 476 32 424 2130 862 — 3239  7 27.0388 541 38 500 — 682  6 27.0387 351 3182 3788 538 22059  6 1188.38 87 15 3968 31 288  6 1188.13 — 0.76 58 — 142  5 27.0408 51 47 7813 69 —  4 35.0171 — — — — — 357  1 35.0172 — 11061 — — — 857  1 A dash (—) indicates IC50 > 20 μM.

TABLE XXXII PBMC responses of individuals from the Irian Java endemic malaria region. Percent individuals yielding positive responses (n) Peptide IFNγ TNFα Proliferation CSP.2 11% (7) 59% (39)  9% (11) LSA1.13 16% (9) 30% (21)  8% (10) CSP.53  7% (4) 53% (40) 3% (4) SSP2.61  7% (4) 45% (36) 7% (9) SSP2.223 15% (9) 42% (31) 5% (6) CSP.410 16% (9) 47% (33) 12% (14) EXP1.82  29% (17) 43% (32) 6% (7) EXP1.71  9% (5) 49% (36) 12% (14) SSP2.512 14% (8) 41% (30) 3% (4) SSP2.62 11% (6) 42% (31) 12% (14) SSP2.494  7% (4) 36% (26) 2% (3)

TABLE XXXIII  P. falciparum CTL epitopes Supertype SEQ ID Alleles (or allele) Peptide AA Sequence NO: Source bounda A2- 1167.08  9 GLIMVLSFL 3760 Pf CSP 425 4 supertype 1167.10  9 GLLGNVSTV 3761 Pf EXP1 83 3 1167.12  9 VLAGLLGNV 3762 Pf EXP1 80 4 1167.13  9 KILSVFFLA 3763 Pf EXP1 2 3 1167.16  9 FMKAVCVEV 3764 Pf SSP2 230 5 1167.18 10 ILSVSSFLFV 3765 Pf CSP 7 2 1167.19 10 VLLGGVGLVL 3766 Pf EXP1 91 2 1167.21 10 FLIFFDLFLV 3767 Pf SSP2 14 5 A3- 1167.24  9 ALFFIIFNK 3768 PF EXP1 10 3 supertype 1167.28  9 GVSENIFLK 3769 Pf LSA1 105 3 1167.32  9 QTNFKSLLR 3770 Pf LSA1 94 4 1167.36  9 LACAGLAYK 3771 Pf SSP2 511 4 1167.43 10 VTCGNGIQVR 3772 Pf CSP 375 4 1167.46 10 FILVNLLIFH 3773 Pf LSA1 11 2 1167.47 10 HVLSHNSYEK 3774 Pf LSA1 59 3 1167.51 10 LLACAGLAYK 3775 Pf SSP2 510 3 B7- 19.0051  8 LPYGRTNL 3776 Pf SSP2 126 3 supertype 1167.61 10 TPYAGEPAPF 3777 Pf SSP2 539 4 A1 15.0184  9 LPSENERGY 3778 Pf LSA1 1663 1 16.0040  9 FVEALFQEY 3779 Pf CSP 15 1 16.0130  9 PSDGKCNLY 3780 Pf SSP2 207 1 16.0245 10 FQDEENIGIY 3781 Pf LSA1 1794 1 A24 1167.53  9 KYKLATSVL 3782 Pf EXP1 73 1 1167.54  9 FYFILVNLL 3783 Pf LSA1 9 1 1167.55  9 YYIPHQSSL 3784 Pf LSA1 1671 1 1167.56  9 KYLVIVFLI 3785 Pf SSP2 8 1 aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding to A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101 and A*2402, respectively.

TABLE XXXIV  P. falciparum HTL epitopes SEQ ID Alleles Motif Peptide Sequence NO: Source bounda DR- F125.04 RHNWVNHAVPLAMKLI 3786 Pf SSP2 61 11 supermotif 1188.16 KSKYKLATSVLAGLL 3787 Pf EXP1 71  9 27.0402 LLIFHINGKIIKNSE 3788 Pf LSA1 16 9(DR3) 1188.32 GLAYKFVVPGAATPY 3789 Pf SSP2 512 9 27.0392 SSVFNVVNSSIGLIM 3790 Pf CSP 410 7 27.0417 VKNVIGPFMKAVCVE 3791 Pf SSP2 223 7 27.0388 MRKLAILSVSSFLFV 3792 Pf CSP 2 6 27.0387 MNYYGKQENWYSLKK 3793 PF CSP53 6 1188.38 KYKIAGGIAGGLALL 3794 Pf SSP2 494 6 1188.13 AGLLGNVSTVLLGGV 3795 Pf EXP1 82 5 27.0408 QTNFKSLLRNLGVSE 3796 Pf LSA1 94 4 DR3 35.0171 PDSIQDSLKESRKLN 3797 Pf SSP2 165 DR3 35.0172 KCNLYADSAWENVKN 3798 Pf SSP2 211 DR3 aHLA-DR supermotif peptides are screened for binding to a panel alleles representing the 10 most common HLA antigens, including DR1, DR2w2 β1, DR2w2 β2, DR4w4, DR4w15, DR5w11, DR6w19, DR7, DR8w2, and DR9. Additional alleles that are tested include DR3, DR5w12, DR52a, and DR53. DR3-motif peptides are tested for binding to DR3.

TABLE XXXV Estimated population coverage by a panel of P. falciparum derived HTL epitopes Representative No. of Population coverage (phenotypic frequency) Antigen Alleles assay epitopes2 Cauc. Blk. Jpn. Chn. Hisp. Avg. DR1 DRB1*0101-03 DR1 11 18.5 8.4 10.7 4.5 10.1 10.4 DR2 DRB1*1501-03 DR2w2 β1 6 19.9 14.8 30.9 22.0 15.0 20.5 DR2 DRB5*0101 DR2w2 β2 7 — — — — — — DR3 DRB1*0301-2 DR3 3 17.7 19.5 0.40 7.3 14.4 11.9 DR4 DRB1*0401-12 DR4w4 5 23.6 6.1 40.4 21.9 29.8 24.4 DR4 DRB1*0401-12 DR4w15 3 — — — — — — DR7 DRB1*0701-02 DR7 8 26.2 11.1 1.0 15.0 16.6 14.0 DR8 DRB1*0801-5 DR8w2 8 5.5 10.9 25.0 10.7 23.3 15.1 DR9 DRB1*09011, 09012 DR9 9 3.6 4.7 24.5 19.9 6.7 11.9 DR11 DRB1*1101-05 DR5w11 9 17.0 18.0 4.9 19.4 18.1 15.5 DR12 DRB1*1201-2 DR5w12 2 2.8 5.5 13.1 17.6 5.7 8.9 DR13 DRB1*1301-06 DR6w19 10 21.7 16.5 14.6 12.2 10.5 15.1 Total 97.0 83.9 98.8 95.5 95.6 94.7

Claims

1-40. (canceled)

41. An isolated peptide less than 13 amino acids in length comprising the oligopeptide: LLACAGLAY (SEQ ID NO: 3019), FLIFFDLFLV (SEQ ID NO: 3718), FMKAVCVEV (SEQ ID NO: 3719), VLAGLLGNV (SEQ ID NO: 3720), GLIMVLSFL (SEQ ID NO: 3721), KILSVFFLA (SEQ ID NO: 3722), GLLGNVSTV (SEQ ID NO: 3723), VLLGGVGLVL (SEQ ID NO: 3724), ILSVSSFLFV (SEQ ID NO: 3725), QTNFKSLLR (SEQ ID NO: 3726), LACAGLAYK (SEQ ID NO: 3727), ALFFIIFNK (SEQ ID NO: 3729), LLACAGLAYK (SEQ ID NO: 3730), HVLSHNSYEK (SEQ ID NO: 3732), FILVNLLIFH (SEQ ID NO: 3733), FQDEENIGIY (SEQ ID NO: 3737), PSDGKCNLY (SEQ ID NO: 3739), YYIPHQSSL (SEQ ID NO: 3740), FYFILVNLL (SEQ ID NO: 3741), KYLVIVFLI (SEQ ID NO: 3742) or KYKLATSVL (SEQ ID NO: 3743).

42. The isolated peptide of claim 41, wherein the peptide is LLACAGLAY (SEQ ID NO: 3019), FLIFFDLFLV (SEQ ID NO: 3718), FMKAVCVEV (SEQ ID NO: 3719), VLAGLLGNV (SEQ ID NO: 3720), GLIMVLSFL (SEQ ID NO: 3721), KILSVFFLA (SEQ ID NO: 3722), GLLGNVSTV (SEQ ID NO: 3723), VLLGGVGLVL (SEQ ID NO: 3724), ILSVSSFLFV (SEQ ID NO: 3725), QTNFKSLLR (SEQ ID NO: 3726), LACAGLAYK (SEQ ID NO: 3727), ALFFIIFNK (SEQ ID NO: 3729), LLACAGLAYK (SEQ ID NO: 3730), HVLSHNSYEK (SEQ ID NO: 3732), FILVNLLIFH (SEQ ID NO: 3733), FQDEENIGIY (SEQ ID NO: 3737), PSDGKCNLY (SEQ ID NO: 3739), YYIPHQSSL (SEQ ID NO: 3740), FYFILVNLL (SEQ ID NO: 3741), KYLVIVFLI (SEQ ID NO: 3742) or KYKLATSVL (SEQ ID NO: 3743).

43. A conjugate of an isolated peptide less than 13 amino acids in length comprising an oligopeptide selected from a group consisting of LLACAGLAY (SEQ ID NO: 3019), FLIFFDLFLV (SEQ ID NO: 3718), FMKAVCVEV (SEQ ID NO: 3719), VLAGLLGNV (SEQ ID NO: 3720), GLIMVLSFL (SEQ ID NO: 3721), KILSVFFLA (SEQ ID NO: 3722), GLLGNVSTV (SEQ ID NO: 3723), VLLGGVGLVL (SEQ ID NO: 3724), ILSVSSFLFV (SEQ ID NO: 3725), QTNFKSLLR (SEQ ID NO: 3726), LACAGLAYK (SEQ ID NO: 3727), ALFFIIFNK (SEQ ID NO: 3729), LLACAGLAYK (SEQ ID NO: 3730), HVLSHNSYEK (SEQ ID NO: 3732), FILVNLLIFH (SEQ ID NO: 3733), FQDEENIGIY (SEQ ID NO: 3737), PSDGKCNLY (SEQ ID NO: 3739), YYIPHQSSL (SEQ ID NO: 3740), FYFILVNLL (SEQ ID NO: 3741), KYLVIVFLI (SES ID NO: 3742) and KYKLATSVL (SEQ ID NO: 3743) and a T helper peptide, wherein the T helper peptide is less than about 50 amino acids in length and wherein the T helper peptide comprises a pan-DR binding epitope.

44. The conjugate of claim 43, wherein the isolated peptide is LLACAGLAY (SEQ ID NO: 3019), FLIFFDLFLV (SEQ ID NO: 3718), FMKAVCVEV (SEQ ID NO: 3719), VLAGLLGNV (SEQ ID NO: 3720), GLIMVLSFL (SEQ ID NO: 3721), KILSVFFLA (SEQ ID NO: 3722), GLLGNVSTV (SEQ ID NO: 3723), VLLGGVGLVL (SEQ ID NO: 3724), ILSVSSFLFV (SEQ ID NO: 3725), QTNFKSLLR (SEQ ID NO: 3726), LACAGLAYK (SEQ ID NO: 3727), ALFFIIFNK (SEQ ID NO: 3729), LLACAGLAYK (SEQ ID NO: 3730), HVLSHNSYEK (SEQ ID NO: 3732), FILVNLLIFH (SEQ ID NO: 3733), FQDEENIGIY (SEQ ID NO: 3737), PSDGKCNLY (SEQ ID NO: 3739), YYIPHQSSL (SEQ ID NO: 3740), FYFILVNLL (SEQ ID NO: 3741), KYLVIVFLI (SEQ ID NO: 3742) or KYKLATSVL (SEQ ID NO: 3743).

45. The conjugate of claim 43, wherein said pan-DR binding epitope is aKXVWANTLKAAa (SEQ ID NO: 3802), wherein “X” is either cycloexylalanine, phenylalanine, or tyrosine, and “a” is either D-alanine or L-alanine.

46. The conjugate of claim 45, wherein “X” is cycloexylalanine.

47. The conjugate of claim 45, wherein “X” is phenylalanine.

48. The conjugate of claim 45, wherein “X” is tyrosine.

49. The conjugate of claim 45, wherein “a” is D-alanine.

50. The conjugate of claim 45, wherein “a” is L-alanine.

51. A composition comprising the isolated peptide of claim 41.

52. A composition comprising the isolated peptide claim 42.

53. The composition of claim 51, further comprising a carrier.

54. A composition comprising the conjugate of claim 43.

55. A composition comprising the conjugate of claim 44.

56. The composition of claim 54, further comprising a carrier.

Patent History
Publication number: 20160193316
Type: Application
Filed: Dec 28, 2015
Publication Date: Jul 7, 2016
Applicant: Epimmune Inc. (San Diego, CA)
Inventors: Alessandro Sette (La Jolla, CA), John Sidney (San Diego, CA), Scott Southwood (Santee, CA), Brian D. Livingston (San Diego, CA), Robert Chestnut (Cardiff-by-the-Sea, CA), Denise Marie Baker (San Diego, CA), Esteban Celis (Rochester, MN), Ralph T. Kubo (Carlsbad, CA), Howard M. Grey (La Jolla, CA)
Application Number: 14/980,150
Classifications
International Classification: A61K 39/015 (20060101); C07K 14/74 (20060101); C07K 14/445 (20060101);