Abstract: Methods and compositions for detecting molecular interactions, particularly protein-protein interactions, using at least two inactive, weakly-complementing ?-lactamase fragments are provided. The invention allows detection of such interactions in eukaryotic and mammalian cells, in situ or in vitro. Detection of molecular interactions in mammalian cells is not limited to the nuclear compartment, but can be accomplished in the cytoplasm, cell surface, organelles, or between these entities. Methods provided utilize novel compositions comprising fusion proteins between molecules of interest and inactive, weakly-complementing ?-lactamase fragments. Association of the molecules of interest brings the corresponding complementary ?-lactamase fragments into close enough proximity for complementation to occur and ?-lactamase activity to be observed. The invention is useful in the study of protein-protein interactions, functional genomics, agonist and antagonist screening and drug discovery.

Abstract: Interaction-activated circularly permutated proteins are disclosed that depend for their functional reassembly into the parent protein on the interaction of heterologous polypeptides or other molecules which have been genetically or chemically conjugated to the break-point termini of engineered enzymes. In addition, methods are provided for identifying circularly permutated marker proteins that will optimally reassemble into a functional parent protein, and which are dependent on the association of heterologous interactor domains. The invention is exemplified by circular permutations of a Class A ?-lactamase (TEM-1 of E. coli).

Abstract: The invention provides methods for generating human antibodies with the specificity of a reference antibody by replacement of portions of the VH and VL sequences of the reference antibody with sequences from human antibody repertoires. The invention also provides novel compositions comprising hybrid immunoglobulin variable domains containing a combination of frameworks (FRs) and CDRs from different antibody clones.

Abstract: The present invention provides methods of making antibodies having the binding specificity of a reference antibody. Antibodies generated by the methods of the inventions have at least one minimal essential binding specificity determinant from a heavy chain or light chain CDR3 from the reference antibody. The method can be used, e.g., in humanization procedures. The invention also provides libraries and antibodies made in accordance with the methods.

Abstract: This invention provides for a novel means for obtaining human idiologs for any non-human antibody to any target by epitope guided replacement of variable regions using competitive cell-based methods in which the competitor can be either the reference antibody or a ligand that binds to the same epitope on the target as the reference antibody.

Abstract: This invention provides methods of obtaining a binding molecule, e.g., an antibody, that has enhanced affinity for a binding partner relative to a reference binding molecule.

Abstract: Fragment pairs of a Class A &bgr;-lactamase (TEM-1 of E. coli) are disclosed that depend for their functional reassembly into the parent protein on the interaction of heterologous polypeptides or other molecules which have been genetically or chemically conjugated to the break-point termini of the fragment pairs. In addition, methods are provided for identifying fragment pairs that will optimally reassemble into a functional parent protein.

Abstract: This invention provides methods and systems for linking the functional activation of a responder molecule to the interaction of two or more binding ensemble members of interest either in vitro or in vivo, and thereby producing a signal, phenotype, or other functional output in response to the interaction of the binding ensemble members. The systems comprise a responder, an inhibitor of the responder, and an inhibitor of the inhibitor, or “reactivator” of the responder, and interacting components. Two binding ensemble members are complexed to the other components of the system in such a way that interaction of the binding ensemble members, either directly or via additional ensemble members, causes a shift in the equilibrium of inhibitor binding from the responder to the reactivator, thereby functionally activating the responder.

Abstract: The current invention provides methods and systems for detecting the presence of a target molecule either in vitro or in vivo. The systems of the invention comprise interacting components, a reporter and a low-affinity inhibitor of the reporter, each of which is fused to a member of a binding pair. A target molecule that interferes with binding of the binding pair members can therefore be identified by detecting activation of the reporter molecule.