PHASE-SENSITIVELY DETECTED REDUCED DIMENSIONALITY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY FOR RAPID CHEMICAL SHIFT ASSIGNMENT AND SECONDARY STRUCTURE DETERMINATION OF PROTEINS

Abstract

The present invention discloses eleven reduced dimensionality (RD) triple resonance nuclear magnetic resonance (NMR) experiments for measuring chemical shift values of certain nuclei in a protein molecule, where the chemical shift values encoded in a peak pair of an NMR spectrum are detected in a phase sensitive manner. The RD 3D HA,CA,(CO),N,HN NMR and RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiments are designed to yield “sequential” connectivities, while the RD 3D Hα/β,Cα/β, CO,HA NMR and RD 3D Hα/β,Cα/β,N,HN NMR experiments provide “intraresidue” connectivities. The RD 3D H,C,C,H-COSY NMR, RD 3D H,C,C,H-TOCSY NMR, and RD 2D H,C,H-COSY NMR experiments allow one to obtain assignments for aliphatic and aromatic side chain chemical shifts, while the RD 2D HB,CB,(CG,CD),HD NMR experiment provide information for the aromatic side chain chemical shifts. In addition, methods of conducting suites of RD triple resonance NMR experiments for high-throughput resonance assignment of proteins and determination of secondary structure elements are disclosed.

Description

The present invention is a divisional of U.S. patent application Ser. No. 10/628,818, filed Jul. 28, 2003, which claims the benefit of U.S. Provisional Patent Application Ser. No. 60/399,332, filed Jul. 26, 2002, which is hereby incorporated by reference in its entirety.

This invention arose out of research sponsored by the National Science Foundation (Grant No. MCB 0075773) and National Institutes of Health (Grant No. P50 GM62413-01). The U.S. Government may have certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates to methods of using phase sensitively-detected reduced dimensionality nuclear magnetic resonance (NMR) spectroscopy for obtaining chemical shift assignment and for structure determination of proteins.

BACKGROUND OF THE INVENTION

The use of triple resonance (TR) nuclear magnetic resonance (NMR) experiments for the resonance assignment of polypeptide chains via heteronuclear scalar connectivities (Montelione et al., J. Am. Chem. Soc., 111:5474-5475 (1989); Montelione et al., J. Magn. Reson., 87:183-188 (1989); Kay et al., J. Magn. Reson., 89:496-514 (1990); Ikura et al., Biochemistry, 29:4659-8979 (1990); Edison et al., Methods Enzymol., 239:3-79 (1994)) is a standard approach which neatly complements the assignment protocol based on ¹H—¹H nuclear Overhauser effects (NOE) (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986)). In addition, triple resonance NMR spectra are highly amenable to a fast automated analysis (Friedrichs et al., J. Biomol. NMR, 4:703-726 (1994); Zimmerman et al., J. Biomol. NMR, 4:241-256 (1994); Bartels et al., J. Biomol. NMR, 7:207-213 (1996); Morelle et al., J. Biomol. NMR, 5:154-160 (1995); Buchler et al., J. Magn. Reson., 125:34-42 (1997); Lukin et al., J. Biomol. NMR, 9:151-166 (1997)), yielding the ¹³C^α/β chemical shifts at an early stage of the assignment procedure. This enables both the identification of regular secondary structure elements without reference to NOEs (Spera et al., J. Am. Chem. Soc., 113: 5490-5491 (1991)) and the derivation of (φ,ψ)-angle constraints which serve to reduce the number of cycles consisting of nuclear Overhauser enhancement spectroscopy (NOESY) peak assignment and structure calculation (Luginbühl et al., J. Magn. Reson., B 109:229-233 (1995)).

NMR assignments are prerequisite for NMR-based structural biology (Wüthrich, NMR of Proteins and Nucleic Acid, Wiley:New York (1986)) and, thus, for highthroughput (HTP) structure determination in structural genomics (Rost, Structure, 6:259-263 (1998); Montelione et al., Nature Struct. Biol., 6:11-12. (1999); Burley, Nature Struc Biol., 7:932-934 (2000)) and for exploring structure-activity relationships (SAR) by NMR for drug discovery (Shuker et al., Science, 274:1531-1534 (1996)). The aims of structural genomics are to (i) explore the naturally occurring “protein fold space” and (ii) contribute to the characterization of function through the assignment of atomic resolution three-dimensional (3D) structures to proteins. It is now generally acknowledged that NMR will play an important role in structural genomics (Montelione et al., Nature Struc. Biol., 7:982-984 (2000)). The resulting demand for HTP structure determination requires fast and automated NMR data collection and analysis protocols (Moseley et al., Curr. Opin. Struct. Biol., 9:635-642 (1999)).

The establishment of a HTP NMR structural genomics pipeline requires two key objectives in data collection. Firstly, the measurement time should be minimized in order to (i) lower the cost per structure and (ii) relax the constraint that NMR samples need to be stable over a long period of measurement time. The recent introduction of commercial cryogenic probes (Styles et al., J. Magn. Reson., 60:397-404 (1984); Flynn et al., J. Am. Chem. Soc., 122:4823-4824 (2000)) promises to reduce measurement times by about a factor of ten or more, and will greatly impact the realization of this first objective. Secondly, reliable automated spectral analysis requires recording of a “redundant” set of multidimensional NMR experiments each affording good resolution (which requires appropriately long maximal evolution times in all indirect dimensions). Concomitantly, it is desirable to keep the total number of NMR spectra small in order to minimize “interspectral” variations of chemical shift measurements, which may impede automated spectral analysis. Straightforward consideration of this second objective would suggest increasing the dimensionality of the spectra, preferably by implementing a suite of four- or even higher-dimensional NMR experiments. Importantly, however, the joint realization of the first and second objectives is tightly limited by the rather large lower bounds of higher-dimensional TR NMR measurement times if appropriately long maximal evolution times are chosen.

Hence, “sampling limited” and “sensitivity limited” data collection regimes are distinguished, depending on whether the sampling of the indirect dimensions or the sensitivity of the multidimensional NMR experiments “per se” determines the minimally achievable measurement time. As a matter of fact, the ever increasing performance of NMR spectrometers will soon lead to the situation where, for many protein samples, the sensitivity of the NMR spectrometers do not constitute the prime bottleneck determining minimal measurement times. Instead, the minimal measurement times encountered for recording conventional higher-dimensional NMR schemes will be “sampling limited,” particularly as high sensitivity cryoprobes become generally available. As structure determinations of proteins rely on nearly complete assignment of chemical shifts, which are obtained using multidimensional ¹³C, ¹⁵N, ¹H-TR NMR experiments (Montelione et al., J. Am. Chem. Soc., 111:5474-5475 (1989); Montelione, et al., J. Magn. Reson., 87:183-188 (1989); Ikura et al., Biochemistry, 29:4659-8979 (1990)), the development of TR NMR techniques that avoid the sampling limited regime represents a key challenge for future biomolecular NMR methods development.

Reduced dimensionality (RD) TR NMR experiments (Szyperski et al., J. Biomol. NMR, 3:127-132 (1993); Szyperski et al., J. Am. Chem. Soc., 115:9307-9308 (1993); Szyperski et al., J. Magn. Reson., B 105:188-191 (1994); Brutscher et al., J. Magn. Reson., B 105:77-82 (1994); Szyperski et al., J. Magn. Reson., B 108: 197-203 (1995); Brutscher et al., J. Biomol. NMR, 5:202-206 (1995); Löhr et al., J. Biomol. NMR, 6:189-197 (1995); Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996); Szyperski et al., J. Magn. Reson., 28:228-232 (1997); Bracken et al., J. Biomol. NMR, 9:94-100 (1997); Sklenar et al., J. Magn. Reson., 130:119-124 (1998); Szyperski et al., J. Biomol. NMR, 11:387-405 (1998)), designed for simultaneous frequency labeling of two spin types in a single indirect dimension, offer a viable strategy to circumvent recording NMR spectra in a sampling limited fashion. RD NMR is based on a projection technique for reducing the spectral dimensionality of TR experiments: the chemical shifts of the projected dimension give rise to a cosine-modulation of the transfer amplitude, yielding in-phase peak pairs encoding n chemical shifts in a n−1 dimensional spectrum (Szyperski et al., J. Biomol. NMR, 3:127-132 (1993); Szyperski et al., J. Am. Chem. Soc., 115:9307-9308 (1993)). As a key result, this allows recording projected four-dimensional (4D) NMR experiments with maximal evolution times typically achieved in the corresponding conventional 3D NMR experiments (Szyperski et al., J. Biomol. NMR, 3:127-132 (1993); Szyperski et al., J. Am. Chem. Soc., 115:9307-9308 (1993); Szyperski et al., J. Magn. Reson. B 105:188-191 (1994); Szyperski et al., J. Magn. Reson., B 108: 197-203 (1995); Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996); Szyperski et al., J. Magn. Reson., 28:228-232 (1997); Bracken et al., J. Biomol. NMR, 9:94-100 (1997); Sklenar et al., J. Magn. Reson., 130:119-124 (1998); Szyperski et al., J. Biomol. NMR, 11:387-405 (1998)). Furthermore, axial coherences, arising from either incomplete insensitive nuclei enhanced by polarization transfer (INEPT) or heteronuclear magnetization, can be observed as peaks located at the center of the in-phase peak pairs (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996)). This allows both the unambiguous assignment of multiple doublets with degenerate chemical shifts in the other dimensions and the identification of peak pairs by symmetrization of spectral strips about the position of the central peak (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996); Szyperski et al., J. Biomol. NMR, 11:387-405 (1998)). Hence, observation of central peaks not only restores the dispersion of the parent, higher-dimensional experiment, but also provides access to reservoir of axial peak magnetization (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996)). Historically, RD NMR experiments were first designed to simultaneously recruit both ¹H and heteronuclear magnetization (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996)) for signal detection, a feature that has also gained interest for improving transverse relaxation-optimized spectroscopy (TROSY) pulse schemes (Pervushin et al., Proc. Natl. Acad. Sci. USA, 94:12366-12371 (1997); Salzmann et al., J. Am. Chem. Soc., 121:844-848 (1999); Pervushin et al., J. Biomol. NMR, 12:345-348, (1998)). Moreover, RD two-spin coherence NMR spectroscopy (Szyperski et al., J. Biomol. NMR, 3:127-132 (1993)) subsequently also called zero-quantum/double-quantum (ZQ/DQ) NMR spectroscopy (Rexroth et al., J. Am. Chem. Soc., 17:10389-10390 (1995)), served as a valuable radio-frequency (r.f.) pulse module for measurement of scalar coupling constants (Rexroth et al., J. Am. Chem. Soc., 17: 10389-10390 (1995)) and cross-correlated heteronuclear relaxation (Reif et al., Science, 276:1230-1233 (1997); Yang et al., J. Am. Chem. Soc., 121:3555-3556 (1999); Chiarparin et al., J. Am. Chem. Soc., 122:1758-1761 (2000); Brutscher et al., J. Magn. Reson., 130:346-351 (1998); Brutscher, Concepts Magn. Reson., 122:207-229 (2000)).

Recently, a suite of RD ¹³C,¹⁵N,¹H-triple resonance NMR experiments was presented for rapid and complete protein resonance assignment (Szyperski et al., Proc. Natl. Acad. Sci. USA, 99:8009-8014 (2002)). Even when using short measurement times, these experiments allow one to retain the high spectral resolution required for efficient automated analysis. “Sampling limited” and “sensitivity limited” data collection regimes were defined, respectively, depending on whether the sampling of the indirect dimensions or the sensitivity of a multidimensional NMR experiments per se determines the minimally required measurement time. It was shown that RD NMR spectroscopy is a powerful approach to avoid the “sampling limited regime”, i.e., a standard set of experiments allows one to effectively adapt minimal measurement times to sensitivity requirements. It would be advantageous to implement those RD NMR experiments in a manner that allows frequency discrimination of the projected chemical shifts.

The present invention is directed to achieving these objectives.

SUMMARY OF THE INVENTION

The present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) HA,CA,(CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) an α-proton of amino acid residue i−1, ¹H^α_i−1; (2) an α-carbon of amino acid residue i−1, ¹³C^α_i; (3) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (4) a polypeptide backbone amide proton of amino acid residue i, ¹H^N_i, where the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i−1 and ¹³C^α_i−1, of amino acid residue i−1 are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i of amino acid residue i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i−1 and ¹⁵N_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the ¹³C^α_i−1 chemical shift evolution in t₁(¹³C^α) with the chemical shift evolution of ¹H^α_i−1. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with an anti-phase peak pair derived from the sine modulating, where (1) the chemical shift values of ¹⁵N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) the chemical shift values of ¹H^a_i−1 and ¹³C^α_i−1 are measured in a frequency domain dimension, ω₁(¹³C^α), by the frequency difference between the two peaks forming the anti-phase peak pair and the frequency at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H^α_i−1 in a phase sensitive manner.

The present invention also relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,(C-TOCSY-CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) aliphatic protons of amino acid residue i−1, ¹H^ali_i−1; (2) aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1; (3) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (4) a polypeptide backbone amide proton of amino acid residue i, ¹H^N_i, where the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^ali_i−1 and ¹³C^ali_i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i, of amino acid residue i, under conditions effective (1) to generate a NMR signal encoding the chemical shifts of ¹³C^ali_i−1 and ¹⁵N_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^ali) and t₂(¹⁵N), respectively, and the chemical shift of ¹H^N_i in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the chemical shift evolutions of ¹³C^ali_i−1 in t₁(¹³C^ali) with the chemical shift evolutions of ¹H^ali_i−1. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹⁵ N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 are measured in a frequency domain dimension, ω₁(¹³C^ali), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H^ali_i−1 in a phase sensitive manner.

Another aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H^α/β,C^α/β,CO,HA nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, ¹H^β_i; (2) a β-carbon of amino acid residue i, ¹³C^β_i; (3) an α-proton of amino acid residue i, ¹H^α_i; (4) an α-carbon of amino acid residue i, ¹³C^α_i; and (5) a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i, where the chemical shift values of ¹H^α_i/¹³C^α_i, and ¹H^β_i/¹³C^β_i which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i, ¹H^β_i, ¹³C^α_i, and ¹³C^β_i are connected to the chemical shift evolution of ¹³C′_i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹³C′_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α/β) and t₂(¹³C′), respectively, and the chemical shift value of ¹H^α_i in a direct time domain dimension, t₃(¹H^α), and (2) to sine modulate the chemical shift evolutions of ¹³C^α_i and ¹³C^α_i in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i, respectively. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³C′_i and ¹H^α_i are measured in two frequency domain dimensions, ω₂(¹³C′) and ω₃(¹H^α), respectively, and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs, and (ii) the chemical shift values of ¹³C^α_i and ¹³C^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the anti-phase peak pairs, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift values of ¹H^α_i and ¹H^β_i in a phase sensitive manner.

A further aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H^α/β,C^α/β,N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, ¹H^β_i; (2) a β-carbon of amino acid residue i, ¹³C^β_i; (3) an α-proton of amino acid residue i, ¹H^α_i; (4) an α-carbon of amino acid residue i, ¹³C^α_i; (5) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (6) a polypeptide backbone amide proton of amino acid residue i, ¹H^N, where the chemical shift values of ¹H^α_i/¹³C^α_i and ¹H^α_i/¹³C^β_i, which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i, ¹H^β_i, ¹³C^α_i, and ¹³C^β_i are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹⁵N_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α/β) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i, in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the chemical shift evolutions of ¹³C^α_i and ¹³C^β_i in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i, respectively. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹⁵N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs, and (ii) the chemical shift values of ¹³C^α_i and ¹³C^α_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the anti-phase peak pairs, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift values of ¹H^α_i and ¹H^β_i in a phase sensitive manner.

The present invention also relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, ¹Hⁿ, and ¹³Cⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups that are linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m, which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effects a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolutions of ¹Hⁿ and ¹³Cⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ, in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^m) and t₂(¹³Cⁿ), respectively, and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₃(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H_m. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³Cⁿ and ¹Hⁿ are measured in two frequency domain dimensions, ω₂(¹³Cⁿ) and ω₃(¹Hⁿ), respectively, and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

Another aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-TOCSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, ¹Hⁿ, and ¹³Cⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups that may or may not be directly linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolutions of ¹Hⁿ and ¹³Cⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^m) and t₂(¹³Cⁿ), and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₃(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³Cⁿ and ¹Hⁿ are measured in two frequency domain dimensions, ω₂(¹³Cⁿ) and ω₃(¹Hⁿ), respectively, and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

A further aspect of the present invention relates to a method of conducting a reduced dimensionality two-dimensional (2D) HB,CB,(CG,CD),HD nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule: (1) a β-proton of an amino acid residue with an aromatic side chain, ¹H^β; (2) a β-carbon of an amino acid residue with an aromatic side chain, ¹³C^β; and (3) a δ-proton of an amino acid residue with an aromatic side chain, ¹H^δ, where the chemical shift values of ¹H^β and ¹³C^β which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^β and ¹³C^β are connected to the chemical shift evolution of ¹H⁶⁷, under conditions effective (1) to generate NMR signals encoding the chemical shift value of ¹³C^β in a phase sensitive manner in an indirect time domain dimension, t₁(¹³C^β), and the chemical shift value of ¹H^δ in a direct time domain dimension, t₂(¹H⁶⁷), and (2) to sine modulate the chemical shift evolution of ¹³C^β in t₁(¹³C^β) with the chemical shift evolution of ¹H^β. Then, the NMR signals are processed to generate a sine-modulated 2D NMR spectrum with an anti-phase peak pair derived from the sine modulating where (1) the chemical shift value of ¹H^δ is measured in a frequency domain dimension, ω₂(¹H^δ), and (2) the chemical shift values of ¹H^β and ¹³C^β are measured in a frequency domain dimension, ω₁(¹³C^β), by the frequency difference between the two peaks forming the anti-phase peak pair and the frequency at the center of the two peaks, respectively, where the sine-modulated 2D NMR spectrum enables detection of the chemical shift value of ¹H^β in a phase sensitive manner.

The present invention also relates to a method of conducting a reduced dimensionality two-dimensional (2D) H,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, and ¹Hⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolution of ¹Hⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift value of ¹³C^m in a phase sensitive manner in an indirect time domain dimension, t₁(¹³C^m), and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₂(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m. Then, the NMR signals are processed to generate a sine-modulated 2D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift value of ¹Hⁿ is measured in a frequency domain dimension, ω₂(¹Hⁿ), and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 2D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

Another aspect of the present invention relates to a method for sequentially assigning chemical shift values of an α-proton, ¹H^α, an α-carbon, ¹³C^α, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^α and ¹³C^α which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD three-dimensional (3D) HA,CA,(CO),N,HN NMR experiment to measure and connect chemical shift values of the α-proton of amino acid residue i−1, ¹H^α_i−1, the α-carbon of amino acid residue i−1, ¹³C^α_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 with the chemical shift values of ¹H^α_i and ¹³C^α_i, (ii) using the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain.

Yet another aspect of the present invention relates to a method for sequentially assigning chemical shift values of a β-proton, ¹H^β, a β-carbon, ¹³C^β, an α-proton, ¹H^α, an α-carbon, ¹³C^α, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^α/β and ¹³C^α/β which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H^α/βC^α/β (CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, ¹H^β_i−1, the β-carbon of amino acid residue i−1, ¹³C^β_i−1, the α-proton of amino acid residue i−1, ¹H^α_i−1, the α-carbon of amino acid residue i−1, ¹³C^α_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N_i and (2) a RD 3D H^α/β,C^α/β, N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, ¹H^α/β_i−1, and the α- and β-carbons of amino acid residue i−1, ¹³C^α/β_i−1, with the chemical shift values of ¹H^α/β_i and ¹³C^α/β_i, (ii) using the chemical shift values of ¹H^α/β_i−1 and ¹³C^α/β_i−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain.

A further aspect of the present invention involves a method for sequentially assigning chemical shift values of aliphatic protons, ¹H^ali, aliphatic carbons, ¹³C^ali, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^ali and ¹³C^ali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, ¹H^ali_i−1 the aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N_i and (2) a RD 3D H^α/β, C^α/β,N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali, ¹³C^ali, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, ¹H^α/β_i−1, and the α- and β-carbons of amino acid residue i−1, ¹³C^α/β_i−1, with the chemical shift values of ¹H^α/β_i and ¹³C^α/β_i of amino acid residue i, (ii) using the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain.

The present invention also relates to a method for sequentially assigning chemical shift values of aliphatic protons, ¹Ha^ali, aliphatic carbons, ¹³C^ali, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^ali and ¹³C^ali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, ¹H^ali_i−1, the aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali, ¹³C^ali, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α-proton of amino acid residue i−1, ¹H^α_i−1, and the α-carbon of amino acid residue i−1, ¹³C^α_i−1, with the chemical shift values of ¹H^α_i and ¹³C^α_i, (ii) using the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain.

Another aspect of the present invention involves a method for obtaining assignments of chemical shift values of ¹H, ¹³C and ¹⁵N of a protein molecule. The method involves providing a protein sample and conducting four reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H and ¹³C which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner and (1) a first experiment is selected from a RD 3D H^α/βC^α/β(CO)NHN NMR experiment, a RD 3D HA, CA,(CO),N,HN NMR experiment, or a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment for obtaining sequential correlations of chemical shift values; (2) a second experiment is selected from a RD 3D HNNCAHA NMR experiment, a RD 3D H^α/β, C^α/β,N,HN NMR experiment, or a RD 3D HNN<CO,CA> NMR experiment for obtaining intraresidue correlations of chemical shift values; (3) a third experiment is a RD 3D H,C,C,H-COSY NMR experiment for obtaining assignments of sidechain chemical shift values; and (4) a fourth experiment is a RD 2D HB,CB,(CG,CD),HD NMR experiment for obtaining assignments of aromatic sidechain chemical shift values.

The present invention enables one to record an entire suite of RD NMR experiments used for obtaining chemical shift assignments and secondary structure determination of a protein molecule in a manner that enables frequency discrimination for the projected chemical shift and allows one to place the two peaks forming a peak pair into separate spectra. The frequency discrimination allows one to place the radiofrequency carrier in the center of the projected chemical shift range.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic presentation describing cosine-modulated and sine-modulated RD NMR data acquisition and processing, as well as the editing of the peaks forming RD NMR peak pairs into separate spectra. Data sets (1) and (2) correspond to real part and imaginary part, respectively, of a cosine-modulated RD NMR experiment, in which Ω_y is detected in a phase sensitive manner and the evolution of the chemical shift Ω_x effects a cosine modulation. Data sets (3) and (4) correspond to real part and imaginary part, respectively, of a sine-modulated RD NMR experiment, in which Ω_y is detected in a phase sensitive manner and the evolution of Ω_x effects a sine modulation, further enabling the phase sensitive detection of Ω_x. The two data sets as well as the corresponding cosine and sine functions for the cosine-modulated RD NMR and sine-modulated RD NMR are shown in (A) and (B), respectively. Forming the sum and the difference of the cosine-modulated and sine-modulated RD NMR spectra allows one to edit the two peaks forming the peak pairs into separate spectra. The data sets that need to be linearly combined in the time domain to achieve such editing are shown in (C) and (D).

FIGS. 2A-K show the polarization transfer pathways (top) and stick diagrams of the in-phase peak pattern observed along ω₁(¹³C) (bottom) for the cosine-modulated RD NMR experiments implemented for the present invention (the 3D H^α/βC^α/β(CO)NHN experiment, the 3D HACA(CO)NHN experiment, the 3D HC(C-TOCSY-CO)NHN experiment, the 3D HNNCAHA experiment, the 3D H^α/βC^α/βCOHA experiment, the 3D H^α/βC^α/βNHN experiment, the 3D HNN<CO,CA> experiment, the 3D HCCH-COSY experiment, the 3D HCCH-TOCSY experiment, the 2D HBCB(CGCD)HD experiment, and the 2D ¹H-TOCSY-relayed-HCH-COSY experiment, respectively). For the sine-modulated RD NMR experiments, anti-phase peak pairs are observed (see FIG. 1) instead of the in-phase peak pattern for the cosine-modulated RD NMR experiments. The boxes comprise nuclei whose chemical shifts are measured in the common dimension ω₁, and the nuclei which are detected in quadrature in t₁ are marked with an asterisk. Bold solid and hatched boxes indicate intraresidue and sequential connectivities, respectively, and the resulting signals sketched in the stick diagrams are represented accordingly. Those ¹³C nuclei whose magnetization is used to detect central peaks (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996), which is hereby incorporated by reference in its entirety), as well as the resulting subspectrum II shown at the bottom are highlighted in grey. The magnetization is frequency labeled with single-quantum coherence of the encircled nuclei during t₂ and detected on the boxed protons. Except for FIG. 2G, the in-phase splittings 2ΔΩ(¹H) are equal to 2κ·δΩ(¹H)[γ(¹H)/γ(¹³C)], where κ, δΩ(¹H) and γ(X) denote the scaling factor applied for ¹H chemical shift evolution (set to 1.0 for the present study), the chemical shift difference with respect to the apparent ¹H carrier position, and the gyromagnetic ratio of nucleus X, respectively. In FIG. 2G, the in-phase splittings 2ΔΩ(¹³C^α) are equal to 2κ·δΩ(¹³C^α), where κ and δΩ(¹³C^α) are the scaling factor applied for ¹³C^α chemical shift evolution¹³ (set to 0.5 for the present study) and the chemical shift difference with respect to the apparent ¹³C^α carrier position, respectively.

FIG. 3A illustrates the experimental scheme for the 3D H^α/βC^α/β(CO)NHN experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high-power 90° pulse lengths were: 5.9 μs for ¹H, 15.4 μs for ¹³C, and 38 μs for ¹⁵N. Pulses on ¹³C prior to t₁(¹³C) are applied at high power, and ¹³C decoupling during t₁(¹H) is achieved using a (90_x-180_y-90_x) composite pulse. Subsequently, the 90° and 180° pulse lengths applied for ¹³C^α/β are adjusted to 47.5 μs and 42.5 μs, respectively, to minimize perturbation of ¹³CO spins. The width of the 90° pulse applied on ¹³CO pulse is 52 μs and the corresponding 180° pulses are applied with same power. A SEDUCE 180° pulse with a length of 200 μs is used to decouple ¹³CO during t₁ and τ₄. The length of the spin-lock purge pulses SL_x and SL_y are 1.2 ms and 0.6 ms, respectively. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple ¹⁵N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of ¹³C^α during ¹⁵N evolution period (rf=1.0 kHz). The ¹H r.f. carrier is placed at 0 ppm before the start of the semi constant time ¹H chemical shift evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. Initially, the ¹³C and ¹⁵N r. f. carriers are set to 43 ppm and 120.9 ppm, respectively. The ¹³C carrier is set to 56 ppm during the second τ₄/2 delay. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (1 ms, 24 G/cm); G2 (100 μs, 16 G/cm); G3 (250 μs, 29.5 G/cm); G4 (250 μs, 30 G/cm); G5 (1.5 ms, 20 G/cm); G6 (1.25 ms, 30 G/cm); G7 (500 μs, 8 G/cm); G8 (125 μS, 29.5 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=800 μs, τ₂=3.1 ms, τ₃=3.6 ms, τ₄=7.2 ms, τ₅=4.4 ms, τ₆=24.8 ms, τ₇=24.8 ms, τ₈=5.5 ms, τ₉=4.6 ms, τ₁₀=1.0 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^b=19.3 μs, Δt₁^c=−14 μs. Hence, the fractional increase of the semi constant-time period with t₁^a equals to λ=1+Δt₁^c/Δt₁^a=0.58. Phase cycling: φ₁=x; φ₂=x, x, −x, −x; φ₃=x, −x; φ₄=x, −x; φ₅=x; φ₆ x, x, −x, −x; φ₇=x; φ₈ (receiver)=x, −x, −x, x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed, i.e., the sign of G₆ is inverted in concert with a 180° shift of φ₇. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₅, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3B illustrates the experimental scheme for the 3D HACA(CO)NHN experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for ¹H and 15.4 μs for ¹³C, and 38 μs for ¹⁵N. Pulses on ¹³C prior to t₁(¹³C) are applied at high power, and ¹³C decoupling during t₁(¹H) is achieved using a (90_x-180_y-90_x) composite pulse. Subsequently, the 90° and 180° pulse lengths of ¹³C^α are adjusted to 51.5 μs and 46 μs, respectively, to minimize perturbation of the ¹³CO spins. The width of the 90° pulses applied to ¹³CO pulse is 52 μs and the corresponding 180° pulses are applied with same power. A SEDUCE 180° pulse with a length 252 μs is used to decouple ¹³CO during t₁. The length of the spin-lock purge pulses SL_x and SL_y are 2.5 ms and 1 ms, respectively. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple ¹⁵N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of ¹³C^α during the ¹⁵N chemical shift evolution period (r.f.=1.0 kHz). The ¹H r.f. carrier is placed at 0 ppm before the start of the semi constant time ¹H evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. The ¹³C^α and ¹⁵N r.f. carriers are set to 56.1 ppm and 120.9 ppm, respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (1 ms, 24 G/cm); G2 (100 μs, 16 G/cm); G3 (1 ms, 24 G/cm); G4 (250 μs, 30 G/cm); G5 (1.5 ms, 20 G/cm); G6 (1.25 ms, 30 G/cm); G7 (500 μs, 8 G/cm); G8 (125 μs, 29.5 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=1.6 ms, τ₂=3.6 ms, τ₃=4.4 ms, τ₄=τ₅=24.8 ms, τ₆=5.5 ms, τ₇=4.6 ms, τ₈=1 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=60 μs, Δt₁^b=35.4 μs, Δt₁^c=24.6 μs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a=0.58. Phase cycling: φ₁=x; φ₂=x, x, −x, −x; φ₃=x, −x; φ₄=x; φ₅=x, x, −x, −x; φ₆=x; φ₇(receiver)=x, −x, −x, x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed., i.e., the sign of G6 is inverted in concert with a 180° shift of φ₆. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₄, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3C illustrates the experimental scheme for the 3D HC(C-TOCSY-CO)NHN experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for ¹H and 15.5 μs for ¹³C, and 38 μs for ¹⁵N. Pulses on ¹³C prior to t₁(¹³C) are applied at high power, and ¹³C decoupling during t₁(¹H) is achieved using a (90_x-180_y-90_x) composite pulse. Subsequently, the 90° and 180° pulse lengths applied for ¹³C are adjusted to 47.0 μs and 42.5 μs, respectively, to minimize perturbation of ¹³CO spins. The width of the 90° pulses applied to ¹³CO pulse is 52 μs and the corresponding 180° pulses are applied with same power. A SEDUCE 180° pulse with a length 200 μs is used to decouple ¹³CO during t₁ and τ₄ period. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple ¹⁵N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of ¹³C^α during the ¹⁵N chemical shift evolution period (r.f.=1.0 kHz). The ¹H r.f. carrier is placed at 0 ppm before the start of the semi constant time ¹H evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. The ¹³C and ¹⁵N r.f. carriers are set to 43 ppm and 120.9 ppm, respectively. The lengths of the ¹³C spin-lock purge pulses, SL_x, are 2.5 ms and 1.25 ms, respectively, before and after the carbon-carbon total correlation spectroscopy (TOCSY) relay. ¹³C isotropic mixing is accomplished using DIPSI-2 scheme with a r.f. field strength of 8.5 kHz. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (2 ms, 30 G/cm); G2 (100 μs, 8 G/cm); G3 (200 μs, 4 G/cm); G4 (2 ms, 30 G/cm); G5(1.25 ms, 30 G/cm); G6 (500 μs, 5 G/cm); G7 (125 μs, 29.5 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=950 μs, τ₂=3.1 ms, τ₃=3.6 ms, τ₄=7.2 ms, τ₅=4.45 ms, τ₆=24.8 ms, τ₇=24.8 ms, τ₈=5.5 ms, τ₉=4.8 ms, τ₁₀=1 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μS, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^a=19.3 μs, Δt₁^c=−14 μs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a=0.58. Phase cycling: φ₁=x; φ₂=x, =x; φ₃=x, x, −x, −x; φ₄=x, −x; φ₅=x, x, −x, −x; φ₆=x, x, −x, −x; φ₇=x; φ₈=4x,4(−x); φ₉=x; φ₁₀(receiver) x, −x, −x, x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed, i.e., the sign of G5 is inverted in concert with a 180° shift of φ₉. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₇, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3D illustrates the experimental scheme for the 3D HNNCAHA experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₈=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The 90° pulse lengths were: 5.8 μs for ¹H and 21.6 μs for ¹³C^α, and 38 μs for ¹⁵N, where the 90° pulse width for ¹³C^α is adjusted to generate a null of excitation in the center of the CO chemical shift range. The selective 90° ¹H pulse used to flip back the water magnetization is applied for the 1.8 ms with the SEDUCE-1 profile. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple of ¹⁵N (r.f.=1.78 kHz) during acquisition. SEDUCE is used for decoupling of ¹³CO (max. r.f.=3.0 kHz). WURST-2 is used for simultaneous band selective decoupling of ¹³CO and ¹³C^β during τ₄ and the ¹H and ¹³C chemical shift evolution during t₁. 3.0 kHz sweeps at 176 ppm and 30 ppm, respectively, are used for decoupling of ¹³C^βand ¹³C^β (except for Ser, Thr, Ala). A sweep of 600 Hz is used at 14 ppm to decouple ¹³C^β of Ala. The ¹H r.f. carrier is placed at the position of the solvent line at 4.78 ppm for the first three ¹H pulses and the first WALTZ period, then switched to 0 ppm during the first delay τ₄/2, and subsequently switched back to the water line at 4.78 ppm during t₁^c. The ¹³C^α and ¹⁵N carriers are set to 56.1 ppm and 120.9 ppm, respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (500 μs, 8 G/cm); G2 (500 μs, 4 G/cm); G3 (1 ms, 30 G/cm); G4 (150 μs, 25 G/cm); G5 (1.25 ms, 30 G/cm); G6 (500 μs, 8 G/cm); G7 (125 μs, 29.57 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays have the following values: τ₁=4.6 ms, τ₂=5.5 ms, τ₃=24 ms, τ₄=2.0 ms, τ₅=500 μs. ¹³C-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.065 ms, t₁^b(0)=49 μs, t₁^c(0)=984 μs, Δt₁^a=65 μs, Δt₁^b=49 μs, Δt₁^c=−16 μs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a=0.76. Note that the acquisition starts with the second complex point in t₁, while the first one is obtained by linear prediction. This ensures that a zero first-order phase correction is achieved along ω₁. Phase cycling: φ₁=x, −x; φ₂=x, x, −x, −x; φ₃=x, −x, −x, x; φ₄=x; φ₅=4(x), 4(−x); φ₆=x; φ₇(receiver)=x, −x, −x, x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed, i.e., the sign of G5 is inverted in concert with a 180° shift of φ₆. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₄ according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety).

FIG. 3E illustrates the experimental scheme for the 3D H^α/βC^α/βCOHA experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for the ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.9 μs for ¹H, 15.4 μs for ¹³C, and 38.2 μs for ¹⁵N. The 90° and 180° pulse lengths of ¹³C^α/β were adjusted to 47.4 μs and 42.4 μs, respectively, to minimize perturbation of ¹³CO spins. A 200 μs 180° pulse with SEDUCE profile is used to selectively invert ¹³CO magnetization prior to the start of t₁. The 90° and 180° pulses employed for excitation of ¹³CO and subsequent magnetization transfer back to ¹³C^α are of rectangular shape and 52 μs and 103 μs duration, respectively. The length of the spin-lock purge pulses SL_x and SL_y are 2.5 ms and 1 ms, respectively. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers, and for decoupling of ¹⁵N (r.f.=1.78 kHz) during acquisition. GARP is used for decoupling of ¹³C^α (r.f.=2.5 kHz). The ¹H r.f. carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time ¹H evolution period and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. Initially, the ¹³C and ¹⁵N r.f. carriers are set to 43 ppm and 120.9 ppm respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1=G2 (100 μs, 15 G/cm); G3 (2 ms, 25 G/cm); G4 (100 μs, 10 G/cm); G5 (1 ms, 27 G/cm); G6 (3 ms, 30 G/cm); G7 (1.3 ms, 20 G/cm); G8 (130 μs, 14 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=800 μs, τ₂=2.8 ms, τ₃=3.6 ms, τ₄=6.5 ms, τ₅=1.8 ms, τ₆=1 ms, τ₇=2.8 ms, τ₈=3.6 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^b=19.3 μs, Δt₁^c=−14 Ξs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a=0.58. Phase cycling: φ₁=x; φ_x=x, −x; φ₃=x, −x, x, −x; φ₄ x; φ₅(receiver)=x, −x. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₄, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996), which is hereby incorporated by reference in its entirety).

FIG. 3F illustrates the experimental scheme for the 3D H^α/βC^α/β NHN experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for the ¹H chemical shift evolution during t₁ is set to 10. The high power 90° pulse lengths were: 5.9 μs for ¹H and 15.4 μs for ¹³C, and 38 μs for ¹⁵N. Pulses on ¹³C prior to t₁(¹³C) are applied at high power, and ¹³C decoupling during t₁(¹H) is achieved using a (90_x-180_y-90_x) composite pulse. Subsequently, the 90° and 180° pulse lengths of ¹³C^α/β are adjusted to 49 μs and 43.8 μs to minimize perturbation of ¹³CO spins. SEDUCE 180° pulses of 200 μs pulse length are used to decouple ¹³C^β. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers, as well as to decouple ¹⁵N (r.f.=1.78 kHz). The ¹H carrier is placed at the position of the solvent line at 0 ppm during the first semi constant time ¹H evolution period, and then switched to the water line 4.78 ppm after the second 90° ¹H pulse. The ¹³C and ¹⁵N r.f. carriers are set to 43 ppm and 120.9 ppm, respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (1 ms, 24 G/cm); G2 (500 μs, 8 G/cm); G3 (250 μs, 15 G/cm); G4 (1 ms, 11 G/cm); G5 (500 μs, 20 G/cm); G6(500 μs, 4 G/cm); G7 (125 μs, 29.5 G/cm). All PFG pulses are of rectangular shape. The delays are: τ₁=800 μs, τ₂=2.8 ms, τ₃=3.3 ms, τ₄=7.2 ms, τ₅=24 ms, τ₆=5.4 ms, τ₇=4.8 ms, τ₈=1 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^b=19.3 μs, Δt₁=−14 μs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a=0.58. Phase cycling: φ₁=x; φ₂=x; φ₃=x, −x; φ₄=x, x, −x, −x; φ₅=x; φ₆(receiver)=x, −x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed, i.e., the sign of G5 is inverted in concert with a 180° shift of φ₅. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₃, respectively, according to States-TPPI. For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3G illustrates the experimental scheme for the 3D HNN<CO,CA> experiment. Rectangular 900 and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₃=y. The scaling factor κ for ¹³C^α chemical shift evolution during t₂ is set to 0.5. The high power 90° pulse lengths were: 5.8 μs for ¹H and 38.5 μs for ¹⁵N. The 90° and 180° pulse lengths of ¹³C^α were adjusted 54 μs and 48.8 μs to minimize perturbation of ¹³CO spins. The length of the 90° pulses applied on ¹³CO are 102 μs, and they possess the shape of a sinc center lobe. The corresponding 180° pulses are applied with same power and shape. The selective ¹H 90° pulse used for flip-back of water magnetization is applied for 1.8 ms with the SEDUCE-1 profile. WALTZ16 is employed to decouple ¹H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple ¹⁵N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of ¹³C^α during ¹⁵N evolution period (r.f.=0.9 kHz). The ¹³C^α and ¹⁵N r.f. carriers are set to 176.5 ppm and 120.9 ppm respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (500 μs, 30 G/cm); G2 (500 μs, 5 G/cm); G3 (2 ms, 13 G/cm); G4 (750 μs, 20 G/cm); G5 (200 μs, 5 G/cm); G6 (100 μs, 12 G/cm); G7 (1.25 ms, 30 G/cm); G8 (300 μs, 5 G/cm); G9 (200 μs, 10 G/cm); G10 (125 μs, 29.5 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=4.6 ms, τ₂=5.5 ms, τ₃=14=28 ms, τ₅=1 ms. Phase cycling: φ₁=x x, −x, −x; φ₂=x, −x; φ₃=x; φ₄=x; φ₅=4(x), 4(−x); φ₆=x; φ₇(receiver)=x, −x, −x, x. The sensitivity enhancement scheme of Kay (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) is employed, i.e., the sign of G5 is inverted in concert with a 180° shift of φ₆. Quadrature detection in t₁(¹³C) and t₂(¹⁵N) is accomplished by altering the phases φ₂ and φ₄, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). To shift the apparent ¹³C^α carrier position to 82.65 ppm i.e., downfield to all ¹³C^α resonances, φ₃ is incremented in 60° steps according to TPPI. Note, that the acquisition was started with the ninth complex point and the first eight complex points along ω₁(¹³C^β) were obtained by linear prediction. This ensures that a zero first-order phase correction is achieved along ω₁ (Szyperski et al., J. Magn. Reson., B 108: 197-203 (1995), which is hereby incorporated by reference in its entirety).

FIG. 3H illustrates the experimental scheme for the 3D HCCH-COSY experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for ¹H and 15.4 μs for ¹³C, and 38 μs for ¹⁵N. The lengths of the ¹H spin-lock purge pulses are: first SL_x, 2.8 ms; second SL_x, 1.7 ms; SL_y: 4.9 ms. SEDUCE is used for decoupling of ¹³CO during t₁ and t₂ (r.f. field strength=1 kHz). WURST is used for decoupling of ¹³C during acquisition. The ¹H carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time ¹H evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. The ¹³C and ¹⁵N r.f. carriers are set to 38 ppm and 120.9 ppm respectively. The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (500 μs, 6 G/cm); G2 (500 μs, 7 G/cm); G3 (100 μs, 12 G/cm); G4 (100 μs, 12.5 G/cm); G5 (2 ms, 9 G/cm); G6 (500 μs, 5 G/cm); G7 (1.5 ms, 8 G/cm); G8 (400 μs, 6 G/cm). All gradients are applied along z-axis and are of rectangular shape. All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=1.6 ms, τ₂=850 μs, τ₃=2.65 ms, τ₄=3.5 ms, τ₅=7 ms, τ₆=1.6 ms, τ₇=3.2 ms. Phase cycling: φ₁=x; φ₂=x, −x; φ₃=x, −x; φ₄=x; φ₅(receiver)=x, −x. Quadrature detection in t₁(¹³C) and t₂(¹³C) is accomplished by altering the phases φ₂ and φ₃, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3I illustrates the experimental scheme for the 3D HCCH-TOCSY experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for ¹H and 15.4 μs for ¹³C, and 38 μs for ¹⁵N. ¹³C decoupling during t₁(¹H) is achieved using a (90_x-180_y-90_x) composite pulse. The lengths of the ¹H spin-lock purge pulses are: first SL_x, 5.7 ms; second SL_x, 0.9 ms; SL_y, 4.3 ms. SEDUCE is used for decoupling of ¹³CO during t₁ and t₂ (r.f. field strength=1 kHz), and GARP is employed for decoupling of ¹³C during acquisition (r.f.=2.5 kHz). The ¹H r.f carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time ¹H evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. The ¹³C^α and ¹⁵N r.f. carriers are set to 38 ppm and 120.9 ppm, respectively. The length of ¹³C spin-lock purge pulses denoted SL_x are of 2 ms duration. ¹³C isotropic mixing is accomplished using the DIPSI-2 scheme (r.f.=8.5 kHz). The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (100 μs, 16 G/cm); G2 (2 ms, 15 G/cm); G3 (300 μs, 8 G/cm); G4 (500 μs, 30 G/cm); G5 (100 μs, 16 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=850 μs, τ₂=3.2 ms. ¹H-frequency labeling in t₁ is achieved in a semi constant-time fashion with t₁^a(0)=1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^b=19.3 μs, Δt₁^c=−14 μs. ¹³C-frequency labeling in t₂ is achieved in a semi constant-time fashion with t₂^a(0)=1120 μs, t₂^b(0)=62.5 μs, t₂^c(0)=995 μs, Δt₂^a=160 μs, Δt₂^b=125 μs, Δt₂^c=−35 μs. These delays ensure that a 90° first-order phase correction is obtained along ω₂(¹³C). The fractional increases of the semi constant-time period in t₁ equals to λ=1+Δt₂^c/Δt₂^a=0.58, and in t₂ equals to λ=1+Δt₂^c/Δt₂^a=0.78. Phase cycling: φ₁=x; φ₂=x, −x; φ₃=x; φ₄=2(x), 2(−x); φ₅(receiver)=x, −x. Quadrature detection in t₁(¹³C) and t₂(¹³C) is accomplished by altering the phases φ₂ and φ₃, respectively, according to States-TPPI (Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety). For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3J illustrates the experimental scheme for the 2D HBCB(CGCD)HD experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₁=y. The scaling factor κ for ¹H chemical shift evolution during t₁ is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for ¹H and 15.4 μs for ¹³C. The first 180° pulse on ¹³C prior to t₁(¹³C) is applied at high power. Subsequently, the 90° pulse lengths of ¹³C^β is adjusted to 66 μs. The 180° ¹³C^β and ¹³C^aro pulses are of gaussian-3 shape and 375 μs duration. WALTZ16 is used for decoupling of ¹H (r.f. field strength=4.5 kHz) during the magnetization transfer from ¹³C^α to ¹³C^aro, and GARP is employed to decouple ¹³C^aro (r.f.=2.5 kHz) during acquisition. The ¹H r.f. carrier is placed at 0 ppm before the start of the semi constant time ¹H evolution period, and then switched to the water line at 4.78 ppm after the second 90° ¹H pulse. The ¹³C r.f. carrier is set to 38 ppm during ω₁(¹³C^β) and then switched to 131 ppm before the first 90° pulse on ¹³C^aro (pulse labeled with φ₄). The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (500 μs, 2 G/cm); G2 (1 ms, 22 G/cm); G3 (2 ms, 10 G/cm); G4 (1 ms, 5 G/cm); G5 (500 μs, 4 G/cm); G6 (1 ms, −14 G/cm); G7 (500 μs, −2 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=1.8 ms, τ₂=8.8 ms, τ₃=71 μs, τ₄=5.4 ms, τ₅=4.2 ms, τ₆=710 μs, τ₇=2.5 ms. ¹H-frequency labeling is achieved in a semi constant-time fashion with t₁^a(0) 1.7 ms, t₁^b(0)=1 μs, t₁^c(0)=1.701 ms, Δt₁^a=33.3 μs, Δt₁^b=19.3 μs, Δt₁^c=−14 μs. Hence, the fractional increase of the semi constant-time period with t₁ equals to λ=1+Δt₁^c/Δt₁^a, 0.58. Phase cycling: φ₁=x; φ₂=x; φ₃=x, y, −x, −y; φ₄=4(x), 4(−x); φ₅ (receiver) x, −x, x, −x, −x, x, −x, x. Quadrature detection in t₁(¹³C) is accomplished by altering the phases φ₂ respectively, according to States-TPPI. For acquisition of central peaks derived from ¹³C steady state magnetization, a second data set with φ₁=−x is collected. The sum and the difference of the two resulting data sets generate subspectra II and I, respectively, containing the central peaks and peak pairs.

FIG. 3K illustrates the experimental scheme for the 2D ¹H-TOCSY-relayed-HCH-COSY experiment. Rectangular 90° and 180° pulses are indicated by thin and thick vertical bars, respectively, and phases are indicated above the pulses. Where no radio-frequency (r.f.) phase is marked, the pulse is applied along x. In order to accomplish sine modulation, φ₆=y. The high-power 90° pulse lengths were: 5.9 μs for ¹H and 15.4 μs for ¹³C. The ¹H r.f. carrier is placed at the position of the solvent line at 4.78 ppm, and the ¹³C carrier is set to 131 ppm. GARP is used for ¹³C decoupling during acquisition (r.f. field strength 2.5 kHz), and ¹H isotropic mixing is accomplished using the DIPSI-2 scheme (r.f.=16 kHz). The duration and strengths of the pulsed z-field gradients (PFGs) are: G1 (1 ms, −10 G/cm); G2 (500 μs, 6 G/cm); G3 (500 μs, 7.5 G/cm); G4 (1 ms, 22 G/cm). All PFG pulses are of rectangular shape. A recovery delay of at least 100 μs duration is inserted between a PFG pulse and an r.f. pulse. The delays are: τ₁=3.0 ms, τ₂=15.38 ms. Phase cycling: φ₁x, −x; φ₂=x, x, y, y, −x, −x, −y, −y; φ₃=4(x), 4(y), 4(−x), 4(−y); φ₄=x, x, −x, −x; φ₅(receiver) x, −x, x, −x, −x, x, −x, x. Quadrature detection in t₁(¹³C) is accomplished by altering the phase φ₁ according to States-TPPI.

FIG. 4 illustrates the polypeptide chemical shifts correlated by the various spectra constituting the TR NMR experiments identified for efficient HTP resonance assignment of proteins. The nuclei for which the chemical shifts are obtained from a given experiment are boxed and labeled accordingly.

FIG. 5 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^N)]-strips taken from 3D HACA(CO)NHN spectrum obtained for Z-domain protein with a total measurement time of 6.7 hours. The 3D NMR data were acquired with 40(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C^α; ¹H^α)=6.5 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peak” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peak shows opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (113.8 ppm) of Asp 50 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS).

FIG. 6 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^N)]-strips taken from 3D HNNCAHA spectrum obtained for Z-domain protein with a total measurement time of 10.7 hours. The 3D NMR data were acquired with 64(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C^α; ¹H^α)=12.1 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from incomplete INEPT transfer of the ¹³C magnetization. The strip labeled “central peak” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peak shows opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (117.4 ppm) of Leu 35 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to DSS.

FIG. 7 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^N)]-strips taken from 3D H^α/βC^α/β(CO)NHN spectrum obtained for Z-domain protein with a total measurement time of 12.7 hours. The 3D NMR data were acquired with 76(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C^α/β; ¹H^α/β) 6.25 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (117.4 ppm) of Leu 35 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to DSS.

FIG. 8 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^N)]-strips taken from 3D H^α/βC^α/βNHN spectrum obtained for Z-domain protein with a total measurement time of 11.4 hours. The 3D NMR data were acquired with 68(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C^α/β; ¹H^α/β)=5.6 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (117.4 ppm) of Leu 35 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to DSS.

FIG. 9 shows a composite plot of [ω₁(¹³C′/¹³C^α),ω₃(¹H^N]-strips taken from 3D HNN<CO,CA> spectrum obtained for Z-domain protein with a total measurement time of 9.4 hours. The 3D NMR data were acquired with 56(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C′; ¹³C^α)=6.9 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peak” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (170.0 ppm) of Phe 43 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to DSS.

FIG. 10 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^N)]-strips taken from 3D HC(C-TOCSY-CO)NHN spectrum obtained for Z-domain protein with a total measurement time of 12.7 hours. The 3D NMR data were acquired with 76(t₁)×28(t₂)×512(t₃) complex points and t_1max(¹³C; ¹H)=6.3 ms, t_2max(¹⁵N)=20.8 ms, and t_3max(¹H^N)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹⁵N chemical shift (118.8 ppm) of Phe 18 along ω₂(¹⁵N) and centered about the corresponding amide proton shifts detected along ω₃(¹H^N). ¹H, ¹³C, and ¹⁵N chemical shifts are in ppm relative to DSS.

FIG. 11 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^β)]-strips taken from 3D HCCH-COSY spectrum obtained for Z-domain protein with a total measurement time of 10.8 hours. The 3D NMR data were acquired with 90(t₁)×20(t₂)×512(t₃) complex points and t_1max(¹³C; ¹H)=7.4 ms, t_2max(¹³C)=6.1 ms, and t_3max(¹H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference between the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹³C^β chemical shift (37.8 ppm) of Asn 19 along ω₂(¹³C) and centered about the corresponding proton (¹H^β) shifts detected along ω₃(¹H). ¹H and ¹³C chemical shifts are in ppm relative to DSS.

FIG. 12 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^β)]-strips taken from 3D HCCH-TOCSY spectrum obtained for Z-domain protein with a total measurement time of 11.0 hours. The 3D NMR data were acquired with 80(t₁)×20(t₂)×512(t₃) complex points and t_1max(¹³C; ¹H)=6.6 ms, t_2max(¹³C)=6.1 ms, and t_3max(¹H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference of the cosine-modulated 3D NMR spectrum between the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹³C^β chemical shift (37.8 ppm) of Asn 36 along ω₂(¹³C) and centered about the corresponding proton (¹H^β) shifts detected along ω₃(¹H). ¹H and ¹³C chemical shifts are in ppm relative to DSS.

FIG. 13 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^δ)]-strips taken from 2D HBCB(CGCD)HD spectrum obtained for Z-domain protein with a total measurement time of 7.8 hours. The 2D NMR data were acquired with 76(t₁)×512(t₂) complex points and t_1max(¹³C; ¹H)=6.3 ms and t_2max(¹H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from steady state ¹³C magnetization. The strip labeled “central peak” was taken from the 2D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 2D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 2D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 2D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 2D NMR spectrum and the sine-modulated 2D NMR spectrum, and strip (D) from the 2D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference of the cosine-modulated 2D NMR spectrum between the sine-modulated 2D NMR spectrum. All strips have been centered about the aromatic proton (¹H^δ) shifts of Phe 18 detected along ω₂(¹H). ¹H and ¹³C chemical shifts are in ppm relative to DSS.

FIG. 14 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H^α)]-strips taken from 3D H^α/βC^α/βCOHA spectrum obtained for ubiquitin protein with a total measurement time of 12.7 hours. The 3D NMR data were acquired with 76(t₁)×32(t₂)×512(t₃) complex points and t_1max(¹³C^α/β; ¹H^α/β)=6.3 ms, t_2max(¹³C′)=17.2 ms, and t_3max(¹H^α)=72.8 ms. Data acquisition and processing were performed as shown in FIG. 1. The central peaks were acquired from the steady state ¹³C magnetization. The strip labeled “central peaks” was taken from the 3D NMR spectrum comprising the central peaks. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference of the cosine-modulated 3D NMR spectrum between the sine-modulated 3D NMR spectrum. All strips have been taken, respectively, at the ¹³C′ chemical shift (175.2 ppm) of Pro 19 along ω₂(¹³C′) and centered about the corresponding proton shifts detected along ω₃(¹H^α). ¹H and ¹³C chemical shifts are in ppm relative to DSS.

FIG. 15 shows a composite plot of [ω₁(¹³C/¹H),ω₃(¹H)]-strips taken from 2D H-TOCSY-HCH-COSY spectrum obtained for ubiquitin protein with a total measurement time of 1.4 hours. The 2D NMR data were acquired with 100(t₁)×512(t₂) complex points and t_1max(¹³C; ¹H)=9.9 ms and t_2max(¹H)=72.8 ms. Data acquisition and processing were performed as shown in FIG. 1. No central peaks were acquired. The strip labeled (A) was taken from the 3D NMR spectrum comprising in-phase peak pairs arising from cosine modulation; strip (B) from the 3D NMR spectrum comprising anti-phase peak pairs arising from sine modulation (the boxed peaks show opposite peak intensity compared to the others); strip (C) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the sum of the cosine-modulated 3D NMR spectrum and the sine-modulated 3D NMR spectrum, and strip (D) from the 3D NMR spectrum comprising the edited, phase-sensitive peak generated from the difference of the cosine-modulated 3D NMR spectrum between the sine-modulated 3D NMR spectrum. All strips have been centered about the aromatic proton shifts detected along ω₂(¹H). ¹H and ¹³C chemical shifts are in ppm relative to DSS.

DETAILED DESCRIPTION OF THE INVENTION

The present invention discloses eleven RD TR NMR experiments where the chemical shift values encoded in a peak pair of an NMR spectrum are detected in a phase sensitive manner. The present invention also discloses different combinations of those phase-sensitively detected RD NMR experiments which allow one to obtain sequential backbone chemical shift assignments for determining the secondary structure of a protein molecule and nearly complete assignments of chemical shift values for a protein molecule including aliphatic and aromatic sidechain spin systems.

The basic acquisition principle for recording edited, phase sensitive RD NMR spectra is illustrated in FIG. 1 (Brutscher et al., J. Magn Reson., B 109:238-242 (1995), which is hereby incorporated by reference in its entirety). The joint evolution of two chemical shifts, Ω_x and Ω_y, can result in four different time domain NMR data sets, (1), (2), (3), and (4), which are generated from all possible combinations of sine modulation and cosine modulation with either of the two chemical shifts (shown on the left-hand side of the equations for data sets (1)-(4)). According to the addition theorems of trigonometric functions, these products of sine and cosine functions are equal to sums of sine and cosine functions of sums and differences of the two chemical shifts (shown on the right-hand side of the equations for data sets (1)-(4)). To obtain an absorptive NMR signal, two out of the four data sets need to be considered as “real” and “imaginary” parts for cosine-modulated RD NMR and sine-modulated RD NMR. Data sets (1) and (2) correspond to real part and imaginary part, respectively, of a cosine-modulated RD NMR experiment, in which Ω_y is detected in a phase sensitive manner and the evolution of the chemical shift Ω_x effects a cosine modulation (see (A) in FIG. 1). Data sets (3) and (4) correspond to real part and imaginary part, respectively, of a sine-modulated RD NMR experiment, in which Ω_y is detected in a phase sensitive manner and the evolution of Ω_x effects a sine modulation, further enabling the phase sensitive detection of Ω_x (see (B) in FIG. 1). Thus, the phase-sensitively detected sine-modulated RD NMR spectrum contains all information about Ω_x and Ω_y for unambiguous chemical shift assignment. Appropriate linear combination of real and imaginary parts of the cosine-modulated and the sine-modulated RD NMR experiments yields the edited, phase sensitive RD NMR spectra, which also contain all information about Ω_x and Ω_y (see (C) and (D) in FIG. 1).

FIG. 2 provides a survey of (i) the names, (ii) the magnetization transfer pathways and (iii) the peak patterns observed in the projected dimension of specific embodiments of the eleven RD NMR experiments disclosed by the present invention. For simplicity, FIG. 2 shows the in-phase peak pattern from the cosine-modulated RD NMR experiments. When acquiring the sine-modulated congeners, anti-phase peak pairs are observed instead (see (B) in FIG. 1). The group comprising the first three experiments are designed to yield “sequential” connectivities via one-bond scalar couplings: 3D H^α/βC^α/β(CO)NHN (FIG. 2A), 3D HACA(CO)NHN (FIG. 2B), and 3D HC(C-TOCSY-CO)NHN (FIG. 2C). The following three experiments provide “intraresidual” connectivities via one-bond scalar couplings: 3D HNNCAHA (FIG. 2D), 3D H^α/βC^α/βCOHA (FIG. 2E), and 3D H^α/βC^α/βNHN (FIG. 2F). 3D HNN<CO,CA> (FIG. 2G) offers both intraresidual ¹H^N-¹³C^α and sequential ¹H^N—¹³C^α connectivities. Although 3D HNNCAHA (FIG. 2D), 3D H^α/βC^α/β (FIG. 2F) and 3D HNN<CO,CA> (FIG. 2G) also provide sequential connectivities via two-bond ¹³C^α_i−1-¹⁵N_i scalar couplings, those are usually smaller than the one-bond couplings (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety), and obtaining complete backbone resonance assignments critically depends on experiments designed to provide sequential connectivities via one-bond couplings (FIGS. 2D-F). 3D HCCH-COSY (FIG. 2H) and 3D HCCH-TOCSY (FIG. 2I) allow one to obtain assignments for the “aliphatic” side chain spin systems, while 2D HBCB(CDCG)HD (FIG. 2J) and 2D ¹H-TOCSY-relayed HCH-COSY (FIG. 2K) provide the corresponding information for the “aromatic” spin systems.

The RD NMR experiments are grouped accordingly in Table 1, which lists for each experiment (i) the nuclei for which the chemical shifts are measured, (ii) if and how the central peaks are acquired and (iii) additional notable technical features. State-of-the art implementations (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996); Kay, J. Am. Chem. Soc., 115:2055-2057 (1993); Grzesiek et al., J. Magn Reson., 99:201-207 (1992); Montelione et al., J. Am. Chem. Soc., 114:10974-10975 (1992); Boucher et al., J. Biomol. NMR, 2:631-637 (1992); Yamazaki et al., J. Am. Chem. Soc., 115:11054-11055 (1993); Zerbe et al., J. Biomol. NMR, 7:99-106 (1996); Grzesiek et al., J. Biomol. NMR, 3:185-204 (1993), which are hereby incorporated by reference in their entirety) making use of pulsed field z-gradients for coherence selection and/or rejection, and sensitivity enhancement (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) were chosen, which allow executing these experiments with a single transient per acquired free induction decay (FID). Semi (Grzesiek et al., J. Biomol. NMR, 3:185-204 (1993), which is hereby incorporated by reference in its entirety) constant-time (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) chemical shift frequency-labeling modules were used throughout in the indirect dimensions in order to minimize losses arising from transverse nuclear spin relaxation. FIGS. 3A-K provide comprehensive descriptions of the RD NMR r.f. pulse sequences used in the eleven RD NMR experiments.

TABLE 1
Phase-Sensitively Detected Reduced Dimensionality NMR Experiments
Experiment	Nuclei for which the chemical shifts are	Acquisition of
(see FIG. 2)	correlateda,b	central peaksc
3D spectra for sequential backbone connectivities:
(A) Hα/βCα/β(CO)NHN	1Hβi-1, 13Cβi-1, 1Hαi-1, 13Cαi-1, 15Ni, 1HNi	13C
(B) HACA(CO)NHN	1Hαi-1, 13Cαi-1, 15Ni, 1HNi	13C
(C) HC(C-TOCSY—CO)NHN	1Ha1ii-1, 13Calii-1, 15Ni, 1HNi	13C
3D spectra for intraresidual backbone connectivities:
(D) HNNCAHAb,d	1Hαi, 13Cαi, 15Ni, 1HNi	INEPT
(E) Hα/bCα/bCOHA	1Hβi, 13Cβi, 1Hαi, 13Cαi, 13C═Oi	13C
(F) Hα/bCα/bNH	1Hβi, 13Cβi, 1Hαi, 13Cαi, 15Ni, 1HNi	13C
3D spectrum for intra- and sequential backbone connectivities:
(G) HNN<CO,CA>b	13C═Oi−1, 13Cαi, 15Ni, 1HNi	INEPT
3D spectra for assignment of aliphatic resonances:e
(H) HCCH—COSY	1Hm, 13Cm, 1Hn, 13Cn	13C
(I) HCCH-TOCSY	1Hm, 13Cm, 1Hn, 13Cn, 1Hp, 13Cp	13C
2D spectra for assignment of aromatic resonances:e
(J) HBCB(CGCD)HD	1Hβ, 13Cβ, 1Hδ	13C
(K) 1H-TOCSY—HCH—COSY	1Hm, 13Cm, 1Hn,	nonef
ai-1, i: numbers of two sequentially located amino acid residues.
bSequential connectivities via two-bond 13Cαi-1-15Ni scalar couplings are not considered in this table.
capproach-1 (Szyperski et al., J. Am. Chem. Soc., 118: 8146-8147 (1996), which is hereby incorporated by reference in its entirety): use of incomplete INEPT (rows labeled with “INEPT”); approach-2 (Szyperski et al., J. Am. Chem. Soc., 118: 8146-8147 (1996), which is hereby incorporated by reference in its entirety): use of 13C steady state magnetization (rows labeled with “13C”).
dadiabatic 13Cβ-decoupling (Kupce et al., J. Magn. Reson., A 115: 273-277 (1995); Matsuo et al., J. Magn. Reson. B 113: 190-194 (1996), which are hereby incorporated by reference in their entirety) is employed during delays with transverse 13Cα magnetization.
em, n, p: atom numbers in neighboring CH, CH2 or CH3 groups.
facquisition of central peaks is prevented by the use of spin-lock purge pulses (flanking the total correlation relay) to obtain pure phases.

The 3D HA,CA,(CO),N,HN Experiment

The present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) HA,CA,(CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) an α-proton of amino acid residue i−1, ¹H^α_i−1; (2) an α-carbon of amino acid residue i−1, ¹³C^α_i−1; (3) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (4) a polypeptide backbone amide proton of amino acid residue i, ¹H^N_i, where the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i−1 and ¹³C^α_i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i of amino acid residue i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i−1 and ¹⁵N_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the ¹³C^α_i−1 chemical shift evolution in t₁(¹³C^α) with the chemical shift evolution of ¹H^α_i−1. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with an anti-phase peak pair derived from the sine modulating, where (1) the chemical shift values of ¹⁵N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 are measured in a frequency domain dimension, ω₁(¹³C^α), by the frequency difference between the two peaks forming the anti-phase peak pair and the frequency at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H^α_i−1 in a phase sensitive manner.

In addition, the method of conducting a RD 3D HA,CA,(CO),N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i−1 and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^α) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i in t₃(¹H^N) and (2) to cosine modulate the ¹³C^α_i−1 chemical shift evolution in t₁(¹³C^α) with the chemical shift evolution of ¹H^α_i−1 for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with an in-phase peak pair derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D HA,CA,(CO),N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i−1 and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^α) and t₂(¹⁵N) and the chemical shift value of ¹H^N_i in t₃(¹H^N), and (2) to avoid sine modulating the ¹³C^α_i−1 chemical shift evolution in t₁(¹³C^α) with the chemical shift evolution of ¹H^α_i−1 for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with an additional peak located centrally between two peaks forming the primary peak pair which measures the chemical shift value of ¹³C^α_i−1 along ω₁(¹³C^α). That additional peak can be derived from ¹³C^α nuclear spin polarization. One specific embodiment (3D HACA(CO)NHN) of this method is illustrated in FIG. 2B, where the applying radiofrequency pulses effects a nuclear spin polarization transfer where a radiofrequency pulse is used to create transverse ¹H^α_i−1 magnetization, which is transferred to ¹³C^α_i−1, to ¹⁵N_i, and to ¹H^N_i, to generate the NMR signal. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3B to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3B, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the primary peak pair and a second NMR subspectrum derived from the adding which contains the additional peak located centrally between the two peaks forming the primary peak pair.

In an alternate embodiment, the RD 3D HA,CA,(CO),N,HN NMR experiment can be modified to a RD2D HA,CA,(CO,N),HN NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of ¹⁵N_i does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with a peak pair where (1) the chemical shift value of ¹H^N_i is measured in a frequency domain dimension, ω₂(¹H^N), and (2) the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 are measured in a frequency domain dimension, ω₁(¹³C^α), by the frequency difference between the two peaks forming the peak pair and the frequency at the center of the two peaks, respectively.

In an alternate embodiment, the RD 3D HA,CA,(CO),N,HN NMR experiment can be modified to a RD 4D HA,CA,CO,N,HN NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i−1, occurs under conditions effective to generate NMR signals encoding the chemical shift value of ¹³C′_i−1 in a phase sensitive manner in an indirect time domain dimension, t₄(¹³C′). Then, the NMR signals are processed to generate a four dimensional (4D) NMR spectrum with a peak pair where (1) the chemical shift values of ¹⁵N_i, ¹H^N_i and ¹³C′_i−1 are measured in three frequency domain dimensions, ω₂(¹⁵N), ω₃(¹H^N) and ω₄(¹³C′), respectively, and (2) the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 are measured in a frequency domain dimension, ω₁(¹³C^α), by the frequency difference between the two peaks forming the peak pair and the frequency at the center of the two peaks, respectively.

The 3D H,C,(C-TOCSY-CO),N,HN Experiment

The present invention also relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,(C-TOCSY-CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) aliphatic protons of amino acid residue i−1, ¹H^ali_i−1; (2) aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1; (3) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (4) a polypeptide backbone amide proton of amino acid residue i, ¹H^N_i, where the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^ali_i−1 and ¹³C^ali_i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i of amino acid residue i, under conditions effective (1) to generate a NMR signal encoding the chemical shifts of ¹³C^ali_i−1 and ¹⁵N_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^ali) and t₂(¹⁵N), respectively, and the chemical shift of ¹H^N_i in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the chemical shift evolutions of ¹³C^ali_i−1 in t₁(¹³C^ali) with the chemical shift evolutions of ¹H^ali_i−1. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹⁵N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 are measured in a frequency domain dimension, ω₁(¹³C^ali), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H^ali_i−1 in a phase sensitive manner.

In addition, the method of conducting a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^ali_i−1 and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^ali) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i in t₃(¹H^N) and (2) to cosine modulate the chemical shift evolutions of ¹³C^ali_i−1 in t₁(¹³C^ali) with the chemical shift evolutions of ¹H^ali_i−1 for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^ali_i−1 and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^ali) and t₂(¹⁵N) and the chemical shift value of ¹H^N_i in t₃(¹H^N), and (2) to avoid sine modulating the chemical shift evolutions of ¹³C^ali_i−1 in t₁(¹³C^ali) with the chemical shift evolution of ¹H^α_i−1 for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with additional peaks located centrally between two peaks forming the peak pairs which measure the chemical shift values of ¹³C^ali_i−1 along ω₁(¹³C^ali). Those additional peaks can be derived from ¹³C^ali nuclear spin polarization. One specific embodiment (3D HC-(C-TOCSY-CO)NHN) of this method is illustrated in FIG. 2C, where the applying radiofrequency pulses effects a nuclear spin polarization transfer, where a radiofrequency pulse is used to create transverse ¹H^ali_i−1 magnetization, and ¹H^ali_i−1 magnetization is transferred to ¹³C^ali_i−1, to ¹³C^α_i−1, to ¹³C′_i−1, to ¹⁵N_i, and to ¹H^N_i, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3C to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3C, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pairs, and a second NMR subspectrum derived from the adding which contains the additional peaks located centrally between the two peaks forming the peak pairs.

In an alternate embodiment, the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment can be modified to a RD 2D H,C,(C-TOCSY-CO,N),HN NMR experiment, which involves applying radiofrequency pulses so that the chemical shift evolution of ¹⁵N_i does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with peak pairs where (1) the chemical shift value of ¹H^N_i is measured in a frequency domain dimension, ω₂(¹H^N), and (2) the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 are measured in a frequency domain dimension, ω₁(¹³C^ali), by the frequency differences between the two peaks forming the peak pairs and the frequencies at the center of the two peaks, respectively.

In an alternate embodiment, the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment can be modified to a RD 4D H,C,(C-TOCSY),CO,N,HN NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i−1, occurs under conditions effective to generate NMR signals encoding the chemical shift value of ¹³C′_i−1 in a phase sensitive manner in an indirect time domain dimension, t₄(¹³C′). Then, the NMR signals are processed to generate a four dimensional (4D) NMR spectrum with variant peak pairs where (1) the chemical shift values of ¹⁵N_i, ¹H^N_i and ¹³C′_i−1 are measured in three frequency domain dimensions, ω₂(¹⁵N), ω₃(¹H^N), and ω₄(¹³C′), respectively, and (2) the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 are measured in a frequency domain dimension, ω₁(¹³C^ali), by the frequency differences between the two peaks forming the variant peak pairs and the frequencies at the center of the two peaks, respectively.

The 3D H^α/β,C^α/β,CO,HA Experiment

Another aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H^α/β,C^α/β,CO,HA nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, ¹H^β_i; (2) a β-carbon of amino acid residue i, ¹³C^β_i; (3) an α-proton of amino acid residue i, ¹H^α_i; (4) an α-carbon of amino acid residue i, ¹³C′_i; and (5) a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i, where the chemical shift values of ¹H^α_i/¹³C^α_i and ¹H^β_i/¹³C^β_i which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i, ¹H^β_i, ¹³C^α_i, and ¹³C^β_i are connected to the chemical shift evolution of ¹³C′_i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹³C′_i in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α/β) and t₂(¹³C′), respectively, and the chemical shift value of ¹H^α_i in a direct time domain dimension, t₃(¹H^α), and (2) to sine modulate the chemical shift evolutions of ¹³C^α_i and ¹³C^β_i in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i, respectively. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³C′_i and ¹H^α_i are measured in two frequency domain dimensions, ω₂(¹³C′) and ω₃(¹H^α), respectively, and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs, and (ii) the chemical shift values of ¹³C^α_i and ¹³C^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the anti-phase peak pairs, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift values of ¹H^α_i and ¹H^β_i in a phase sensitive manner.

In addition, the method of conducting a RD 3D H^α/β,C^α/β,CO,HA NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹³C′_i in a phase sensitive manner in t₁(¹³C^α/β) and t₂(¹³C′), respectively, and the chemical shift value of ¹H^α_i in t₃(¹H^α) and (2) to cosine modulate the ¹³C^α_i and ¹³ C^β_i chemical shift evolutions in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D H^α/β,C^α/β,CO,HA NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^α/β) and t₂(¹⁵N) and the chemical shift value of ¹H^α_i in t₃(¹H^α), and (2) to avoid cosine modulating the chemical shift evolutions of ¹³C^α_i and ¹³C^β_i in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with additional peaks located centrally between two peaks forming the peak pairs which measure the chemical shift values of ¹³C^α_i and ¹³C^β_i along ω₁(¹³C^α/β). Those additional peaks can be derived from ¹³C^α_i and ¹³C^β_i nuclear spin polarization. One specific embodiment (3D H^α/βC^α/βCOHA) of this method is illustrated in FIG. 2E, where the applying radiofrequency pulses effects a nuclear spin polarization transfer, where a radiofrequency pulse is used to create transverse ¹H^α_i and ¹H^β_i magnetization, and ¹H^α_i and ¹H^β_i polarization is transferred to ¹³C^α_i and ¹³C^β_i, to ¹³C′_i, and back to ¹H^α_i, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3E to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3E, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pairs, and a second NMR subspectrum derived from the adding which contains the additional peaks located centrally between the two peaks forming the peak pairs.

In an alternate embodiment, the RD 3D H^α/β,C^α/β,CO,HA NMR experiment can be modified to a RD 2D H^α/β,C^α/β,(CO),HA NMR experiment, which involves applying radiofrequency pulses so that the chemical shift evolution of ¹³C′_i does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with peak pairs where (1) the chemical shift value of ¹H^α_i is measured in a frequency domain dimension, ω₂(¹H^α), and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between two peaks forming the peak pairs, respectively, and (ii) the chemical shift values of ¹³C^α_i and ¹³C^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the peak pairs.

The 3D H^α/β,C^α/β,N,HN Experiment

A further aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H^α/β,C^α/β,N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, ¹H^β_i; (2) a β-carbon of amino acid residue i, ¹³C^β_i; (3) an α-proton of amino acid residue i, ¹H^α_i; (4) an α-carbon of amino acid residue i, ¹³C^α_i; (5) a polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i; and (6) a polypeptide backbone amide proton of amino acid residue i, ¹H^N_i, where the chemical shift values of ¹H^α_i/¹³C^α_i and ¹H^β_i/¹³C^β_i, which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^α_i, ¹H^β_i, ¹³C^α_i, and ¹³C^α_i are connected to the chemical shift evolutions of ¹⁵N_i and ¹H^N_i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹⁵N_i, in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^α/β) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i, in a direct time domain dimension, t₃(¹H^N), and (2) to sine modulate the chemical shift evolutions of ¹³C^α_i and ¹³C^β_i in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i, respectively. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹⁵N_i and ¹H^N_i are measured in two frequency domain dimensions, ω₂(¹⁵N) and ω₃(¹H^N), respectively, and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs, and (ii) the chemical shift values of ¹³C^α_i, and ¹³C^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the anti-phase peak pairs, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift values of ¹H^α_i and ¹H^β_i in a phase sensitive manner.

In addition, the method of conducting a RD 3D H^α/β, C^α/β,N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^α/β) and t₂(¹⁵N), respectively, and the chemical shift value of ¹H^N_i in t₃(¹H^N) and (2) to cosine modulate the ¹³C^α_i and ¹³C^β_i chemical shift evolutions in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D H^α/β,C^α/β,N,HN NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^α_i, ¹³C^β_i, and ¹⁵N_i in a phase sensitive manner in t₁(¹³C^α/β) and t₂(¹⁵N) and the chemical shift value of ¹H^N_i in t₃(¹H^N), and (2) to avoid cosine modulating the chemical shift evolutions of ¹³C^α_i and ¹³C^β_i, in t₁(¹³C^α/β) with the chemical shift evolutions of ¹H^α_i and ¹H^β_i for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with additional peaks located centrally between two peaks forming the peak pairs which measure the chemical shift values of ¹³C^α_i and ¹³C^β_i along ω₁(¹³C^α/β). Those additional peaks can be derived from ¹³C^α_i and ¹³C^β nuclear spin polarization. One specific embodiment (3D H^α/βC^α/βNHN) of this method is illustrated in FIG. 2F, where the applying radiofrequency pulses effects a nuclear spin polarization transfer where a radiofrequency pulse is used to create transverse ¹H^α_i and ¹H^β_i magnetization, and ¹H^α_i and ¹H^β_i magnetization is transferred to ¹³C^α_i and ¹³C^β_i, to ¹⁵N_i, and to ¹H^N_i, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3F to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3F, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pairs, and a second NMR subspectrum derived from the adding which contains the additional peaks located centrally between the two peaks forming the peak pairs.

In an alternate embodiment, the RD 3D H^α/β, C^α/β,N,HN NMR experiment can be modified to a RD 2D H^α/β,C^α/β,(N),HN NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of ¹⁵N_i does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with peak pairs where (1) the chemical shift value of ¹H^N_i is measured in a frequency domain dimension, ω₂(¹H^N), and (2) (i) the chemical shift values of ¹H^α_i and ¹H^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequency differences between the two peaks forming the peak pairs, and (ii) the chemical shift values of ¹³C^α_i, and ¹³C^β_i are measured in a frequency domain dimension, ω₁(¹³C^α/β), by the frequencies at the center of the two peaks forming the peak pairs.

The 3D H,C,H-COSY Experiment

The present invention also relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, ¹Hⁿ, and ¹³Cⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups that are linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effects a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolutions of ¹Hⁿ and ¹³Cⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^m) and t₂(¹³Cⁿ), respectively, and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₃(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H_m. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³Cⁿ and ¹Hⁿ are measured in two frequency domain dimensions, ω₂(¹³Cⁿ) and ω₃(¹Hⁿ), respectively, and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

In addition, the method of conducting a RD 3D H,C,C,H-COSY NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in t₁(¹³C^m) and t₂(¹³Cⁿ), respectively, and the chemical shift value of ¹Hⁿ in t₃(¹Hⁿ), and (2) to cosine modulate the ¹³C^m chemical shift evolution in t₁(¹³C^m) with the chemical shift evolution of ¹H_m for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D H,C,C,H-COSY NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in t₁(¹³C^m) and t₂(¹³Cⁿ) and the chemical shift value of ¹Hⁿ in t₃(¹H), and (2) to avoid cosine modulating the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with additional peaks located centrally between two peaks forming the peak pairs which measure the chemical shift value of ¹³C^m along ω₁(¹³C^m). Those additional peaks can be derived from ¹³C^m nuclear spin polarization. One specific embodiment (3D HCCH-COSY) of this method is illustrated in FIG. 2H, where the applying radiofrequency pulses effects a nuclear spin polarization transfer, where a radiofrequency pulse is used to create transverse ¹H^m magnetization, and ¹H^m magnetization is transferred to ¹³C^m, to ¹³C_n, and to ¹Hⁿ, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3H to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3H, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pairs, and a second NMR subspectrum derived from the adding which contains the additional peaks located centrally between the two peaks forming the peak pairs.

In an alternate embodiment, the RD 3D H,C,C,H-COSY NMR experiment can be modified to a RD 2D H,C,(C),H-COSY NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of ¹³Cⁿ does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with peak pairs where (1) the chemical shift value of ¹Hⁿ is measured in a frequency domain dimension, ω₂(¹Hⁿ), and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between the two peaks forming the peak pairs and the frequencies at the center of the two peaks, respectively.

The 3D H,C,C,H-TOCSY Experiment

Another aspect of the present invention relates to a method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-TOCSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, ¹Hⁿ, and ¹³Cⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups that may or may not be directly linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolutions of ¹Hⁿ and ¹³Cⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in two indirect time domain dimensions, t₁(¹³C^m) and t₂(¹³Cⁿ), and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₃(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m. Then, the NMR signals are processed to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift values of ¹³Cⁿ and ¹Hⁿ are measured in two frequency domain dimensions, ω₂(¹³Cⁿ) and ω₃(¹Hⁿ), respectively, and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 3D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

In addition, the method of conducting a RD 3D H,C,C,H-TOCSY NMR can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in t₁(¹³C^m) and t₂(¹³Cⁿ), respectively, and the chemical shift value of ¹Hⁿ in t₃(¹Hⁿ) and (2) to cosine modulate the ¹³C^m chemical shift evolution in t₁(¹³C^m) with the chemical shift evolution of ¹H_m for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 3D NMR spectrum generated by adding the sine-modulated 3D NMR spectrum and the cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting the cosine-modulated 3D NMR spectrum from the sine-modulated 3D NMR spectrum. The combined use of the sum 3D NMR spectrum and the difference 3D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 3D H,C,C,H-TOCSY NMR can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of ¹³C^m and ¹³Cⁿ in a phase sensitive manner in t₁(¹³C^m) and t₂(¹³Cⁿ) and the chemical shift value of ¹Hⁿ in t₃(¹Hⁿ), and (2) to avoid cosine modulating the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 3D NMR spectrum with additional peaks located centrally between two peaks forming the peak pairs which measure the chemical shift value of ¹³C^m along ω₁(¹³C^m). Those additional peaks can be derived from ¹³C^m nuclear spin polarization. One specific embodiment (3D HCCH-TOCSY) of this method is illustrated in FIG. 2I, where the applying radiofrequency pulses effects a nuclear spin polarization transfer where a radiofrequency pulse is used to create transverse ¹H^m magnetization, and ¹H^m magnetization is transferred to ¹³C^m, to ¹³Cⁿ, and to ¹Hⁿ, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3I to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3I, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pairs, and a second NMR subspectrum derived from the adding which contains the additional peaks located centrally between the two peaks forming the peak pairs.

In an alternate embodiment, the RD 3D H,C,C,H-TOCSY NMR experiment can be modified to a RD 2D H,C,(C),H-TOCSY NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of ¹³Cⁿ does not occur. Then, the NMR signals are processed to generate a two dimensional (2D) NMR spectrum with peak pairs where (1) the chemical shift value of ¹Hⁿ is measured in a frequency domain dimension, ω₂(¹Hⁿ), and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between the two peaks forming the peak pairs and the frequencies at the center of the two peaks, respectively.

The 2D HB,CB,(CG,CD),HD Experiment

A further aspect of the present invention relates to a method of conducting a reduced dimensionality two-dimensional (2D) HB,CB,(CG,CD),HD nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule: (1) a β-proton of an amino acid residue with an aromatic side chain, ¹H^β; (2) a β-carbon of an amino acid residue with an aromatic side chain, ¹³C^β; and (3) a δ-proton of an amino acid residue with an aromatic side chain, ¹H^δ, where the chemical shift values of ¹H^β and ¹³C^β which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^β and ¹³C^β are connected to the chemical shift evolution of ¹H^δ, under conditions effective (1) to generate NMR signals encoding the chemical shift value of ¹³C^β in a phase sensitive manner in an indirect time domain dimension, t₁(¹³C^β), and the chemical shift value of ¹H^δ in a direct time domain dimension, t₂(¹H^δ), and (2) to sine modulate the chemical shift evolution of ¹³C^β in t₁(¹³C^β) with the chemical shift evolution of ¹H^β. Then, the NMR signals are processed to generate a sine-modulated 2D NMR spectrum with an anti-phase peak pair derived from the sine modulating where (1) the chemical shift value of ¹H^δ is measured in a frequency domain dimension, ω₂(¹H^δ), and (2) the chemical shift values of ¹H^β and ¹³C^β are measured in a frequency domain dimension, ω₁(¹³C^β), by the frequency difference between the two peaks forming the anti-phase peak pair and the frequency at the center of the two peaks, respectively, where the sine-modulated 2D NMR spectrum enables detection of the chemical shift value of ¹H^β in a phase sensitive manner.

In addition, the method of conducting a RD 2D HB,CB,(CG,CD),HD NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of ¹³C^β in a phase sensitive manner in t₁(¹³C^β) and the chemical shift value of ¹H^δ in t₂(¹H^δ) and (2) to cosine modulate the ¹³C^β chemical shift evolution in t₁(¹³C^β) with the chemical shift evolution of ¹H^β for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 2D NMR spectrum with an in-phase peak pair derived from the cosine modulating, a sum 2D NMR spectrum generated by adding the sine-modulated 2D NMR spectrum and the cosine-modulated 2D NMR spectrum, and a difference 2D NMR spectrum generated by subtracting the cosine-modulated 2D NMR spectrum from the sine-modulated 2D NMR spectrum. The combined use of the sum 2D NMR spectrum and the difference 2D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

In addition, the method of conducting a RD 2D HB,CB,(CG,CD),HD NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of ¹³C^β in a phase sensitive manner in t₁(¹³C^β) and the chemical shift value of ¹H^δ in t₂(¹H^δ), and (2) to avoid cosine modulating the chemical shift evolution of ¹³C^β in t₁(¹³C^β) with the chemical shift evolution of ¹H^β for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to generate a 2D NMR spectrum with an additional peak located centrally between the two peaks forming the peak pair which measure the chemical shift value of ¹³C^β along ω₁(¹³C). That additional peak can be derived from ¹³C^β nuclear spin polarization. One specific embodiment (2D HBCB(CGCD)HD) of this method is illustrated in FIG. 2J, where the applying radiofrequency pulses effects a nuclear spin polarization transfer where a radiofrequency pulse is used to create transverse ¹H^β magnetization, and ¹H^β magnetization is transferred to ¹³C^β, to ¹³C^δ, and to ¹H^δ, where the NMR signal is detected. Another specific embodiment of this method involves applying radiofrequency pulses by (1) applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3J to generate a first NMR signal, and (2) applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3J, where phase φ₁ of the first ¹H pulse is altered by 180° to generate a second NMR signal. Then, prior to the processing, the first NMR signal and the second NMR signal are added and subtracted, whereby the NMR signals are processed to generate a first NMR subspectrum derived from the subtracting which contains the peak pair, and a second NMR subspectrum derived from the adding which contains the additional peak located centrally between the two peaks forming the peak pair.

In an alternate embodiment, the RD 2D HB,CB,(CG,CD),HD NMR experiment can be modified to a RD 3D HB,CB,(CG),CD,HD NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of a 3-carbon of an amino acid residue with an aromatic side chain, ¹³C^δ occurs under conditions effective to generate NMR signals encoding the chemical shift value of ¹³C^δ in a phase sensitive manner in an indirect time domain dimension, t₃(¹³C^δ). Then, the NMR signals are processed to generate a three dimensional (3D) NMR spectrum with a peak pair where (1) the chemical shift values of ¹H^δ and ¹³C^δ are measured in two frequency domain dimensions, ω₂(¹H^δ) and ω₃(¹³C^δ), respectively, and (2) the chemical shift values of ¹H^β and ¹³C^β are measured in a frequency domain dimension, ω₁(¹³C^β), by the frequency difference between the two peaks forming the peak pair and the frequency at the center of the two peaks, respectively.

In an alternate embodiment, the RD 2D HB,CB,(CG,CD),HD NMR experiment can be modified to a RD 3D HB,CB,CG,(CD),HD NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of a γ-carbon of an amino acid residue with an aromatic side chain, ¹³C^γ occurs under conditions effective to generate NMR signals encoding the chemical shift value of ¹³C^γ in a phase sensitive manner in an indirect time domain dimension, t₃(¹³C^γ), and said processing the NMR signals generates a three dimensional (3D) NMR spectrum with a peak pair wherein (1) the chemical shift values of ¹H^δ and ¹³C^γ are measured in two frequency domain dimensions, ω₂(¹H^δ) and ω₃(¹³C^γ), respectively, and (2) the chemical shift values of ¹H^β and ¹³C^β are measured in a frequency domain dimension, ω₁(¹³C^β), by the frequency difference between the two peaks forming said peak pair and the frequency at the center of the two peaks, respectively.

The 2D H,C,H-COSY Experiment

The present invention also relates to a method of conducting a reduced dimensionality two-dimensional (2D) H,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for ¹H^m, ¹³C^m, and ¹Hⁿ of a protein molecule where m and n indicate atom numbers of two CH, CH₂ or CH₃ groups in an amino acid residue, where the chemical shift values of ¹H^m and ¹³C^m which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner. The method involves providing a protein sample and applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer where the chemical shift evolutions of ¹H^m and ¹³C^m are connected to the chemical shift evolution of ¹Hⁿ, under conditions effective (1) to generate NMR signals encoding the chemical shift value of ¹³C^m in a phase sensitive manner in an indirect time domain dimension, t₁(¹³C^m), and the chemical shift value of ¹Hⁿ in a direct time domain dimension, t₂(¹Hⁿ), and (2) to sine modulate the chemical shift evolution of ¹³C^m in t₁(¹³C^m) with the chemical shift evolution of ¹H^m. Then, the NMR signals are processed to generate a sine-modulated 2D NMR spectrum with anti-phase peak pairs derived from the sine modulating where (1) the chemical shift value of ¹H^m is measured in a frequency domain dimension, ω₂(¹Hⁿ), and (2) the chemical shift values of ¹H^m and ¹³C^m are measured in a frequency domain dimension, ω₁(¹³C^m), by the frequency differences between each of the two peaks forming each of the anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, where the sine-modulated 2D NMR spectrum enables detection of the chemical shift value of ¹H_m in a phase sensitive manner.

In addition, the method of conducting a RD 2D H,C,H-COSY NMR experiment can involve applying radiofrequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of ¹³C^m in a phase sensitive manner in t₁(¹³C^m) and the chemical shift value of ¹Hⁿ in t₂(¹Hⁿ) and (2) to cosine modulate the ¹³C^m chemical shift evolution in t₁(¹³C^m) with the chemical shift evolution of ¹H_m for the additional NMR signals. Then, the NMR signals and the additional NMR signals are processed to further generate a cosine-modulated 2D NMR spectrum with in-phase peak pairs derived from the cosine modulating, a sum 2D NMR spectrum generated by adding the sine-modulated 2D NMR spectrum and the cosine-modulated 2D NMR spectrum and a difference 2D NMR spectrum generated by subtracting the cosine-modulated 2D NMR spectrum from the sine-modulated 2D NMR spectrum. The combined use of the sum 2D NMR spectrum and the difference 2D NMR spectrum enables placement of the two peaks forming the peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming the peak pairs.

One specific embodiment (2D ¹H-TOCSY-HCH-COSY) of this method is illustrated in FIG. 2K, where the applying radiofrequency pulses effects a nuclear spin polarization transfer where a radiofrequency pulse is used to create transverse ¹H^m magnetization, and ¹H^m polarization is transferred to ¹³C^m, to ¹H^m, and to ¹Hⁿ, where the NMR signal is detected. Although the specific embodiment illustrated in FIG. 2K shows this method applied to an amino acid residue with an aromatic side chain, this method also applies to amino acid residues with aliphatic side chains. Another specific embodiment of this method involves applying radiofrequency pulses according to the scheme shown in FIG. 3K.

FIG. 4 outlines which chemical shifts are correlated in the various NMR experiments described above.

Combinations of RD NMR Experiments

Accordingly, a suite of multidimensional RD NMR experiments enables one to devise strategies for RD NMR-based HTP resonance assignment of proteins.

Thus, another aspect of the present invention relates to a method for sequentially assigning chemical shift values of an α-proton, ¹H^α, an α-carbon, ¹³C^α, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^α and ¹³C^α which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D HA,CA,(CO),N,HN NMR experiment to measure and connect chemical shift values of the α-proton of amino acid residue i−1, ¹H^α_i−1, the α-carbon of amino acid residue i−1, ¹³C^α_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N_i and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 with the chemical shift values of ¹H^α_i and ¹³C^α_i, (ii) using the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 to identify the type of amino acid residue i−1 (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986); Grzesiek et al., J. Biomol. NMR, 3: 185-204 (1993), which are hereby incorporated by reference in their entirety), and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements (such as α-helices and β-sheets) within the polypeptide chain (Spera et al., J. Am. Chem. Soc., 113:5490-5492 (1991); Wishart et al., Biochemistry, 31:1647-1651 (1992), which are hereby incorporated by reference in their entirety).

In one embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift value of ¹³C′_i−1, are obtained by matching the chemical shift value of ¹³C^α_i measured by the RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D HA,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to (i) a RD 3D H^α/β,C^α/β,CO,HA NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i, and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of ¹³C′_i, the α-carbon of amino acid residue i+1, ¹³C^α_i+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, ¹⁵N_i+1, and the polypeptide backbone amide proton of amino acid residue i+1, ¹H^N_i+1. Then, sequential assignments are obtained by matching the chemical shift value of ¹³C′_i measured by the RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of ¹³C′_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of aliphatic protons (including α-, β-, and γ-protons) of amino acid residue i−1, ¹H^ali_i−1, aliphatic carbons (including α-, β-, and γ-carbons) of amino acid residue i−1, ¹³C^ali_i−1, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 for amino acid residues i having unique pairs of ¹⁵N_i and ¹H^N_i chemical shift values are obtained by matching the chemical shift values of ¹H^α and ¹³C^α measured by said RD 3D HNNCAHA NMR experiment and RD 3D HA,CA,(CO),N,HN NMR experiment with the chemical shift values of ¹H^α_i−1 and ¹³C^α_i−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and using the ¹H^ali_i−1 and ¹³C^ali_i−1 chemical shift values to identify the type of amino acid residue i−1.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of ¹H^ali_i and ¹³C^ali_i of amino acid residue i. Then, sequential assignments of the chemical shift values of ¹H^ali_i and ¹³C^ali_i, the chemical shift values of a γ-proton, ¹H^γ, and a γ-carbon, ¹³C^γ_i, in particular, are obtained by (i) matching the chemical shift values of ¹H^α_i and ¹³C^α_i measured using the RD 3D H,C,C,H-COSY NMR experiment or the RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of ¹H^α_i and ¹³C^α measured by the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and (ii) using the chemical shift values of ¹H^ali and ¹³C^ali, including the chemical shift values of ¹H^γ_i, and ¹³C^γ_i, to identify the type of amino acid residue i.

In yet another embodiment, this method involves, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, further subjecting the protein sample to a RD 3D H^α/βC^α/β(CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, ¹H^β_i−1, the β-carbon of amino acid residue i−1, ¹³C^β_i−1, ¹H^α_i−1, ¹³C^α_i−1, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^β and ¹³C^β are obtained by using the chemical shift values of ¹H^β_i−1 and ¹³C^β_i−1 to identify the type of amino acid residue i−1.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, be further subjected to a RD 3D H^α/β,C^α/β, CO,HA NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i. Then, sequential assignments of the chemical shift value of ¹³C′_i are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D H^α/β, C^α/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, be further subjected to a RD 3D H^α/β,C^α/β,N,HN NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i with the chemical shift values of ¹H^β_i−1, ¹³C^β_i−1, ¹H^α_i−1, and ¹³C^α_i−1 measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of ¹³C^β_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹³C^β_i and ¹³C^α_i measured by said 3D HNNCACB NMR experiment with the chemical shift values of ¹³C^β_i−1 and ¹³C^α_i−1 measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, be further subjected to a RD 2D HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of ¹H^β_i−1, ¹³C^β_i−1, and a δ-proton of amino acid residue I−1 with an aromatic side chain, ¹H^δ_i−1. Then, sequential assignments are obtained by matching (i) the chemical shift values of ¹H^β_i−1 and ¹³C^β_i−1 measured by said RD 2D HB,CB,(CG,CD),HD NMR experiment with the chemical shift values of ¹H^β and ¹³C^β measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, (ii) using the chemical shift values to identify amino acid residue i as having an aromatic side chain, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along the polypeptide chain.

In another embodiment, the protein sample could, in addition to the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, be further subjected to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons (including α-, β-, and γ-protons) of amino acid residue i, ¹H^ali_i, and aliphatic carbons (including α-, β-, and γ-carbons) of amino acid residue i, ¹³C^ali_i, of amino acid residue i. Then, sequential assignments of the chemical shift values of ¹H^ali_i and ¹³C^ali_i, the chemical shift values of a γ-proton, ¹H^γ, and a γ-carbon, ¹³C^γ, in particular, are obtained by (i) matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i, measured using the RD 3D H,C,C,H-COSY NMR experiment or the RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D HA,CA,(CO),N,HN NMR experiment, the RD 3D HNNCAHA NMR experiment, and the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and (ii) using the chemical shift values of ¹H^ali and ¹³C^ali, including the chemical shift values of ¹H^γ and ¹³C^γ, to identify the type of amino acid residue i.

Yet another aspect of the present invention relates to a method for sequentially assigning chemical shift values of a β-proton, ¹H^β, a β-carbon, ¹³C^β, an α-proton, ¹H^α, an α-carbon, ¹³C^α, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N_i, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^α/β and ¹³C^α/β which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H^α/βC^α/β(CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, ¹H^β_i−1, the β-carbon of amino acid residue i−1, ¹³C^β_i−1, the α-proton of amino acid residue i−1, ¹H^α_i−1, the α-carbon of amino acid residue i−1, ¹³C^α_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N_i and (2) a RD 3D H^α/β,C^α/β,N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, ¹H^α/β_i−1, and the chemical shift values of the α- and β-carbons of amino acid residue i−1, ¹³C^α/β_i−1, with ¹H^α/β_i and ¹³C^α/β_i, (ii) using ¹H^α/β_i−1 and ¹³C^α/β_i−1 to identify the type of amino acid residue i−1 (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986); Grzesiek et al., J. Biomol. NMR, 3: 185-204 (1993), which are hereby incorporated by reference in their entirety), (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain (Spera et al., J. Am. Chem. Soc., 113:5490-5492 (1991); Wishart et al., Biochemistry, 31:1647-1651 (1992), which are hereby incorporated by reference in their entirety).

In one embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment (i) to measure and connect chemical shift values of ¹H^α_i−1, ¹³C^α_i−1, ¹⁵N_i, and ¹H^N_i and (ii) to distinguish between NMR signals for ¹H^β/¹³C^α and ¹H^β/¹³C^β measured in the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β, N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D H^α/βC^α/β,CO,HA NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i. Then, sequential assignments of the chemical shift value of ¹³C′_i are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i−1, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift value of ¹³C′_i−1 are obtained by matching the chemical shift value of ¹³C^α_i measured by the RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and RD 3D HP,C,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to (i) a RD 3D H^α/β,C^α/β,CO,HA NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^α/β, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of ¹³C′_i, the α-carbon of amino acid residue i+1, ¹³C^α_i+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, ¹⁵N_i+1, and the polypeptide backbone amide proton of amino acid residue i+1, ¹H^N_i+1. Then, sequential assignments are obtained by matching the chemical shift value of ¹³C′_i measured by said RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of ¹³C′_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of ¹H^ali_i−1, ¹³C^ali_i−1, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 for amino acid residues i having unique pairs of ¹⁵N_i and ¹H^N_i chemical shift values are obtained by matching the chemical shift values of ¹H^β, ¹³C^β, ¹H^α, and ¹³C^α measured by the RD 3D H^α/β,C^α/β(CO)NHN NMR experiment and RD 3D H^α/β,C^α/βN,HN NMR experiment with the chemical shift values of ¹H^β_i−1,¹³C^β_i−1, ¹H^α_i−1, and ¹³C^α_i−1 measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and using the ¹H^ali_i−1 and ¹³C^ali_i−1 chemical shift values to identify the type of amino acid residue i−1.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/βC^α/β,N,HN NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of ¹³C^β_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹³C^β_i and ¹³C^α_i measured by said 3D HNNCACB NMR experiment with the chemical shift values of ¹³C^β_i and ¹³C^α_i−1 measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 2D HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, and a δ-proton of amino acid residue i with an aromatic side chain, ¹H^δ_i. Then, sequential assignments are obtained by (i) matching the chemical shift values of ¹H^β_i and ¹³C^β_i measured by said RD 2D HB,CB,(CG,CD),HD NMR experiment with the chemical shift values of ¹H^β and ¹³C^β measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, (ii) using the chemical shift values to identify amino acid residue i as having an aromatic side chain, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along the polypeptide chain (Spera et al., J. Am. Chem. Soc., 113:5490-5492 (1991); Wishart et al., Biochemistry, 31:1647-1651 (1992), which are hereby incorporated by reference in their entirety).

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/βC^α/β,N,HN NMR experiment, be further subjected to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, ¹H^ali_i, and aliphatic carbons of amino acid residue i, ¹³C^ali_i, of amino acid residue i. Then, sequential assignments of the chemical shift values of ¹H^ali_i and ¹³C^ali_i, the chemical shift values of a γ-proton, ¹H^γ_i, and a γ-carbon, ¹³C^γ_i, in particular, are obtained by (i) matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured using the RD 3D H,C,C,H-COSY NMR experiment or the RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of ¹H^β, ¹³C^β, ¹H^α, and ¹³C^α measured by the RD 3DH^α/βC^α/β(CO)NHN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, and (ii) using the chemical shift values of ¹H^ali_i and ¹³C^ali_i, including the chemical shift values of ¹H^γ_i and ¹³C^ε_i, to identify the type of amino acid residue i.

A further aspect of the present invention involves a method for sequentially assigning the chemical shift values of aliphatic protons, ¹H^ali, aliphatic carbons, ¹³C^ali, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^ali and ¹³C^ali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, ¹H^ali_i−1, the aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹⁵H^N_i and (2) a RD 3D H^α/β,C^α/β,N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, ¹H^β_i, the β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali, ¹³C^ali, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, ¹H^α/β_i−1 and the α- and β-carbons of amino acid residue i−1, ¹³C^α/β, with the chemical shift values of ¹H^α/β_i and ¹³C^α/β_i of amino acid residue i, (ii) using the chemical shift values of ¹H^ali_i−1 and ¹³C^ali₁₋₁ to identify the type of amino acid residue i−1 (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986); Grzesiek et al., J. Biomol NMR, 3: 185-204 (1993), which are hereby incorporated by reference in their entirety), and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain (Spera et al., J. Am. Chem. Soc., 113:5490-5492 (1991); Wishart et al., Biochemistry, 31:1647-1651 (1992), which are hereby incorporated by reference in their entirety).

In one embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D H^α/β,C^α/β,CO,HA NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i. Then, sequential assignments of the chemical shift value of ¹³C′_i are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹_H^N measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i−1, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift value of ¹³C′_i−1 are obtained by matching the chemical shift value of ¹³C^α_i measured by the RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to (i) a RD 3D H^α/β,C^α/β, CO,HA NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i, and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of ¹³C′_i, the α-carbon of amino acid residue i+1, ¹³C^α_i+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, ¹⁵N_i+1, and the polypeptide backbone amide proton of amino acid residue i+1, ¹H^N_i+1. Then, sequential assignments are obtained by matching the chemical shift value of ¹³C′_i, measured by the RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of ¹³C′_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D H^α/βC^α/β(CO)NHN NMR experiment (i) to measure and connect the chemical shift values of ¹H^α/β_i−1, ¹³C^α/β_i−1, ¹⁵N_i, and ¹H^N_i, and (ii) to identify NMR signals for ¹H^α/β_i−1, ¹³C^α/β_i−1, ¹⁵N_i, and ¹H^N_i in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment (i) to measure and connect chemical shift values of ¹H^α_i−1, ¹³C^α_i−1, ¹⁵N_i, and ¹H^N_i and (ii) to identify NMR signals for ¹H^α and ¹³C^α in the RD 3D HC,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D HC,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of ¹³C^β_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹³C^β_i and ¹³C^α_i measured by said 3D HNNCACB NMR experiment with the chemical shift values of ¹³C^β_i−1 and ¹³C^α_i−1 measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 2D HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, and a δ-proton of amino acid residue i with an aromatic side chain, ¹H^δ_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹H^β_i and ¹³C^β_i measured by said RD 2D HB,CB,(CG,CD)ND NMR experiment with the chemical shift values of ¹H^β and ¹³C^β measured by the RD 3D H^α/βC^α/β,N,HN NMR experiment and the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, using the chemical shift values to identify amino acid residue i as having an aromatic side chain, and mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along the polypeptide chain.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D H^α/β,C^α/β,N,HN NMR experiment, be further subjected to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, ¹H^ali_i, and aliphatic carbons of amino acid residue i, ¹³C^ali_i. Then, sequential assignments of the chemical shift values of ¹H^ali_i and ¹³C^ali_i, the chemical shift values of a γ-proton, ¹H^γ_i, and a γ-carbon, ¹³C^γ_i, in particular, are obtained by (i) matching the chemical shift values of ¹H^ali_i and ¹³C^ali_i measured using the RD 3D H,C,C,H-COSY NMR experiment or the RD 3D H,C,C,H-TOCSY NMR experiment with the chemical shift values of ¹H^ali and ¹³C^ali measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D H^α/β,C^α/β,N,HN NMR experiment, and (ii) using the chemical shift values of ¹H^ali_i and ¹³C^ali_i, including the chemical shift values of ¹H^γ_i and ¹³C^γ_i, to identify the type of amino acid residue i.

The present invention also relates to a method for sequentially assigning chemical shift values of aliphatic protons, ¹H^ali, aliphatic carbons, ¹³C^ali, a polypeptide backbone amide nitrogen, ¹⁵N, and a polypeptide backbone amide proton, ¹H^N, of a protein molecule. The method involves providing a protein sample and conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H^ali and ¹³C^ali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, including: (1) a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, ¹H^ali_i−1, the aliphatic carbons of amino acid residue i−1, ¹³C^ali_i−1, the polypeptide backbone amide nitrogen of amino acid residue i, ¹⁵N_i, and the polypeptide backbone amide proton of amino acid residue i, ¹H^N_i and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift values of ¹H^ali, ¹³C^ali, ¹⁵N, and ¹H^N are obtained by (i) matching the chemical shift values of the α-proton of amino acid residue i−1, ¹H^α_i−1 and the α-carbon of amino acid residue i−1, ¹³C^α_i−1 with the chemical shift values of ¹H^α_i and ¹³C^α_i, (ii) using the chemical shift values of ¹H^ali_i−1 and ¹³C^ali₁₋₁ to identify the type of amino acid residue i−1 (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986); Grzesiek et al., J. Biomol. NMR, 3: 185-204 (1993), which are hereby incorporated by reference in their entirety), and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using the chemical shift values to locate secondary structure elements within the polypeptide chain (Spera et al., J. Am. Chem. Soc., 113:5490-5492 (1991); Wishart et al., Biochemistry, 31:1647-1651 (1992), which are hereby incorporated by reference in their entirety).

In one embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H^α/β,C^α/β,CO,HA NMR experiment to measure and connect the chemical shift values of a β-proton of amino acid residue i, ¹H^β_i, a β-carbon of amino acid residue i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i. Then, sequential assignments of the chemical shift value of ¹³C′_i are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of ¹H^β, ¹³C^β, ¹H^α, ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, ¹³C′_i−1, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments of the chemical shift value of ¹³C′_i−1 are obtained by matching the chemical shift value of ¹³C^α_i measured by the RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of ¹³C^α, ¹⁵N, and ¹H^N measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to (i) a RD 3D H^α/β,C^α/β, CO,HA NMR experiment to measure and connect the chemical shift values of a β-proton of amino acid residue i, ¹H^β_i, a β-carbon of amino acid residue i, ¹³C^β_i, the α-proton of amino acid residue i, ¹H^α_i, the α-carbon of amino acid residue i, ¹³C^α_i, and a polypeptide backbone carbonyl carbon of amino acid residue i, ¹³C′_i, and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of ¹³C′_i, an α-carbon of amino acid residue i+1, ¹³C^α_i−1, a polypeptide backbone amide nitrogen of amino acid residue i+1, ¹⁵N_i+1, and the polypeptide backbone amide proton of amino acid residue i+1, ¹H^N_i+1. Then, sequential assignments are obtained by matching the chemical shift value of ¹³C′_i measured by the RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of ¹³C′_i, measured by the RD 3D H^α/β,C^α/β,CO,HA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H^α/βC^α/β(CO)NHN NMR experiment (i) to measure and connect the chemical shift values of the α- and β-protons of amino acid residue i−1, ¹H^α/β_i−1, the α- and β-carbons of amino acid residue i−1, ¹³C^α/β_i−1, ¹⁵N_i, and ¹H^N_i, and (ii) to distinguish NMR signals for the chemical shift values of ¹H^β_i−1, ¹³C^β_i−1, ¹H^α_i−1, and ¹³C^α_i−1 measured by the RD 3D H^α/βC^α/β(CO)NHN NMR experiment from NMR signals for the chemical shift values of ¹H^ali_i−1 and ¹³C^ali_i−1 other than ¹H^α/β_i−1 and ¹³C^α/β_i−1 measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H^α/β,C^α/β,N,HN NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by said RD 3D H^α/β,C^α/β,N,HN NMR experiment with the chemical shift values of ¹H^β_i−1, ¹³C^β_i−1, ¹H^α_i−1, and ¹³C^α_i−1 measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift values of ¹³C^β_i, ¹³C^α_i, ¹⁵N_i, and ¹H^N_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹³C^β_i and ¹³C^α_i measured by said 3D HNNCACB NMR experiment with the chemical shift values of ¹³C^β_i−1 and ¹³C^α_i−1 measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 2D HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of ¹H^β_i, ¹³C^β_i, and a δ-proton of amino acid residue i with an aromatic side chain, ¹H^δ_i. Then, sequential assignments are obtained by matching the chemical shift values of ¹H^β_i and ¹³C^β_i measured by said RD 2D HB,CB,(CG,CD),HD NMR experiment with the chemical shift values of ¹H^β and ¹³C^β measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, using the chemical shift values to identify amino acid residue i as having an aromatic side chain, and mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and by locating amino acid residues with aromatic side chains along the polypeptide chain.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, be further subjected to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, ¹H^ali_i, and aliphatic carbons of amino acid residue i, ¹³C^ali_i. Then, sequential assignments of the chemical shift values of ¹H^ali_i and ¹³C^ali_i, the chemical shift values of a γ-proton, ¹H^γ_i, and a γ-carbon, ¹³C^γ_i, in particular, are obtained by (i) matching the chemical shift values of ¹H^ali and ¹³C^ali measured using the RD 3D H,C,C,H-COSY NMR experiment or the RD 3D H,C,C,H-TOCSY NMR experiment with the chemical shift values of ¹H^β_i, ¹³C^β_i, ¹H^α_i, and ¹³C^α_i measured by the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNNCAHA NMR experiment, and (ii) using the chemical shift values of ¹H^ali_i and ¹³C^ali_i, including the chemical shift values of ¹H^γ_i, and ¹³C^γ_i, to identify the type of amino acid residue i.

Another aspect of the present invention involves a method for obtaining nearly complete assignments of chemical shift values of ¹H, ¹³C and ¹⁵N of a protein molecule (excluding only chemical shift values of ¹³C^δ and ¹⁵N^ε2 of glutamines, of ¹³C^γ and ¹⁵N^δ2 of asparagines, of ¹³C^ε3, ¹H^ε3, ¹³C^ζ2, ¹H^ζ2, ¹³C^ζ3, ¹H^ζ3, ¹³C^η2, and ¹H^η2 groups of tryptophans, of ¹³C^ε and ¹H^ε of methionines, and of labile sidechain protons that exchange rapidly with the protons of the solvent water) (Yamazaki et al., J. Am. Chem. Soc., 115:11054-11055 (1993), which is hereby incorporated by reference in its entirety), which are required for the determination of the tertiary structure of a protein in solution (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986), which is hereby incorporated by reference in its entirety). The method involves providing a protein sample and conducting four reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, where the chemical shift values of ¹H and ¹³C which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner and (1) a first experiment is selected from a RD three-dimensional (3D) H^α/βC^α/β(CO)NHN NMR experiment, a RD 3D HA,CA,(CO),N,HN NMR experiment, or a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment for obtaining sequential correlations of chemical shift values; (2) a second experiment is selected from a RD 3D HNNCAHA NMR experiment, a RD 3D H^α/βC^α/β,N,HN NMR experiment, or a RD 3D HNN<CO,CA> NMR experiment for obtaining intraresidue correlations of chemical shift values; (3) a third experiment is a RD 3D H,C,C,H-COSY NMR experiment for obtaining assignments of aliphatic and aromatic sidechain chemical shift values; and (4) a fourth experiment is a RD 2D HB,CB,(CG,CD),HD NMR experiment for obtaining assignments of aromatic sidechain chemical shift values.

In one embodiment of this method, the protein sample could be further subjected to a RD 2D H,C,H-COSY NMR experiment for obtaining assignments of aliphatic and aromatic sidechain chemical shift values.

In another embodiment of this method, the first experiment is the RD 3D H^α/βC^α/β(CO)NHN NMR experiment and the second experiment is the RD 3D HNNCAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment to distinguish between NMR signals for ¹H^α/¹³C^α and ¹H^β/¹³C^β from the RD 3D H^α/βC^α/β(CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to obtain assignments of chemical shift values of ¹H^ali and ¹³C^ali.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β,N,HN NMR experiment to obtain assignments of chemical shift values of ¹H^β and ¹³C^β.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β, CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment and a RD 3D H^α/βC^α/β,CO,HA NMR experiment to obtain assignments of chemical shift values of ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aliphatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aromatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H^α/βC^α/β(CO)NHN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to obtain assignments of chemical shift values of ¹³C^β.

In yet another embodiment of this method, the first experiment is the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the second experiment is the RD 3D HNNCAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment to identify NMR signals for ¹H^α/¹³C^α in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β,N,HN NMR experiment to obtain assignments of chemical shift values of ¹H^β and ¹³C^β.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β, CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment and a RD 3D H^α/βC^α/β,CO,HA NMR experiment to obtain assignments of chemical shift values of ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aliphatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aromatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to obtain assignments of chemical shift values of ¹³C^β.

In yet another embodiment of this method, the first experiment is the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the second experiment is the RD 3D H^α/βC^α/β,N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment to identify NMR signals for ¹H^α and ¹³C^α in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β(CO)NHN NMR experiment to identify NMR signals for ¹H^α/β and ¹³C^α/β in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HNN<CO,CA> NMR experiment and a RD 3D H^α/βC^α/β,CO,HA NMR experiment to obtain assignments of chemical shift values of ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aliphatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aromatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D H^α/βC^α/β,N,HN NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to obtain assignments of chemical shift values of ¹³C^β.

In yet another embodiment of this method, the first experiment is the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and the second experiment is the RD 3D HNN<CO,CA> NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D HA,CA,(CO),N,HN NMR experiment to identify NMR signals for ¹H^α and ¹³C^α in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β(CO)NHN NMR experiment to identify NMR signals for ¹H^α/β and ¹³C^α/β in the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H^α/βC^α/β,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, ¹³C′.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aliphatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a RD 3D H,C,C,H-TOCSY NMR experiment to obtain assignments of chemical shift values of ¹H and ¹³C of aromatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, RD 3D HNN<CO,CA> NMR experiment, RD 3D H,C,C,H-COSY NMR experiment, and RD 2D HB,CB,(CG,CD),HD NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to obtain assignments of chemical shift values of ¹³C^β.

In addition, the above-described method for obtaining assignments of chemical shift values of ¹H, ¹³C and ¹⁵N of a protein molecule can involve further subjecting the protein sample to nuclear Overhauser effect spectroscopy (NOESY) (Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York (1986), which is hereby incorporated by reference in its entirety), to NMR experiments that measure scalar coupling constants (Eberstadt et al., Angew Chem. Int. Ed. Engl., 34:1671-1695 (1995); Cordier et al., J. Am. Chem. Soc., 121:1601-1602 (1999), which are hereby incorporated by reference in their entirety), or to NMR experiments that measure residual dipolar coupling constants (Prestegard, Nature Struct. Biol., 5:517-522 (1998); Tjandra et al., Science, 278:1111-1114 (1997), which are hereby incorporated by reference in their entirety), to deduce the tertiary fold or tertiary structure of the protein molecule.

A standard set of experiments (3D H^α/βC^α/β(CO)NHN, 3D HNNCAHA, 3D HH^α/βC^α/βCOHA, 3D HNNCACB, 3D HNN<CO,CA>, 3D HCCH-COSY, 3D HCCH-TOCSY, 2D HBCB(CDCG)HD, and 2D ¹H-TOCSY-relayed HCH-COSY) can be employed for obtaining nearly complete resonance assignments of proteins including aliphatic and aromatic side chain spin systems.

For larger proteins, complementary recording of highly sensitive 3D HACA(CO)NHN promises (i) to yield spin systems which escape detection in H^α/βC^α/β(CO)NHN, and (ii) to offer the distinction of α- and β-moiety resonances by comparison with H^α/βC^α/β(CO)NHN. Furthermore, employment of 50% random fractional protein deuteration (LeMaster, Annu. Rev. Biophys. Biophys Chem., 19:43-266 (1990); Nietlispach et al., J. Am. Chem. Soc., 118:407-415 (1996); Shan et al., J. Am. Chem. Soc., 118:6570-6579 (1996); Leiting et al., Anal. Biochem., 265:351-355 (1998); Hochuli et al., J. Biomol. NMR, 17:33-42 (2000), which are hereby incorporated by reference in their entirety) in combination with the standard suite of NMR experiments (or transverse relaxation-optimized spectroscopy (TROSY) versions thereof) is attractive. The impact of deuteration for recording 4D H^α/βC^α/β(CO)NHN for proteins reorienting with correlation times up to around 20 ns (corresponding to a molecular weight around 30 kDa at ambient T) has been demonstrated (Nietlispach et al., J. Am. Chem. Soc., 118:407-415 (1996), which is hereby incorporated by reference in its entirety). Accordingly, 3D H^α/βC^α/β(CO)NHN can be expected to maintain its pivotal role for obtaining complete resonance assignments for deuterated proteins at least up to about that size. Furthermore, protein deuteration offers the advantage that HNNCACB, which can be expected to become significantly less sensitive than HNNCAHA for larger non-deuterated systems, (Szyperski et al., J. Biomol. NMR, 11:387-405 (1998), which is hereby incorporated by reference in its entirety) can be kept to recruit ¹³C^β chemical shifts for sequential assignment (Shan et al., J. Am. Chem. Soc., 118:6570-6579 (1996), which is hereby incorporated by reference in its entirety).

If solely chemical shifts are considered, the unambiguous identification of peak pairs is more involved whenever multiple peak pairs with degenerate chemical shifts in the other dimensions are present. The acquisition of the corresponding central peaks addresses this complication in a conceptually straightforward fashion. However, it is important to note that pairs of peaks generated by a chemical shift splitting have quite similar intensity. In contrast, peak pairs arising from different moieties, possible located in different amino acid residues, most often do not show similar intensity. This is because the nuclear spin relaxation times, which determine the peak intensities, vary within each residue as well as along the polypeptide chain. One may thus speak of a “nuclear spin relaxation time labeling” of peak pairs, which makes their identification an obvious task in most cases.

Using cryogenic probes can reduce NMR measurement times by about a factor of 10 or more (Flynn et al., J. Am. Chem. Soc., 122:4823-4824 (2000), which is hereby incorporated by reference in its entirety). The high sensitivity of cryogenic probes shifts even the recording of RD NMR experiments entirely into the sampling limited data acquisition regime. In view of this dramatic reduction in spectrometer time demand, minimally achievable RD NMR measurement times are of keen interest to be able to adapt the NMR measurement times to sensitivity requirements in future HTP endeavours. To further reduce the measurement time, and in view of the aforementioned “spin relaxation time labelling” of peak pairs, one may decide to also discard the use of ¹³C-steady state magnetization for central peak detection.

Although RD NMR was proposed in 1993 (Szyperski et al., J. Biomol. NMR, 3:127-132 (1993); Szyperski et al., J. Am. Chem. Soc., 115:9307-9308 (1993), which are hereby incorporated by reference in their entirety), its wide-spread use has been delayed by the more demanding spectral analysis when compared to conventional TR NMR. In particular, the necessity to extract chemical shifts from in-phase splittings suggests that strong computer support is key for employment of RD NMR on a routine basis. This can be readily addressed by using automated resonance assignment software for automated analysis of RD TR NMR data.

In conclusion, the joint employment of RD NMR spectroscopy (as well as phase-sensitively detected RD NMR spectroscopy), cryogenic probes, and automated backbone resonance assignment will allow one to determine a protein's backbone resonance assignments and secondary structure in a short time.

EXAMPLES

The following examples are provided to illustrate embodiments of the present invention but are by no means intended to limit its scope.

Example 1

Sample Preparation

NMR measurements were performed using a 1 mM solution of uniformly ¹³C/¹⁵N enriched “Z-domain” of the Staphylococcal protein A (Tashiro et al., J. Mol. Biol., 272:573-590 (1997); Lyons et al., Biochemistry, 32:7839-7845 (1993), which are hereby incorporated by reference in their entirety) dissolved in 90% D₂O/10% H₂O (20 M K—PO₄) at pH=6.5 and a 2 mM solution of ¹⁵N/¹³C doubly labeled ubiquitin in 90% H₂O/10% D₂O (50 mM K—PO₄; pH=5.8).

Example 2

NMR Spectroscopy

Multidimensional NMR experiments (FIG. 2; Table 1) were recorded for a 1 mM solution of the 8.5 kDa Z-domain protein and/or a 2 mM solution of ubiquitin at a temperature of 25° C. The spectra were assigned, and the chemical shifts obtained from RD NMR were in very good agreement with those previously determined at 30° C. using conventional triple resonance (TR) NMR spectroscopy (Tashiro et al., J. Mol. Biol., 272:573-590 (1997); Lyons et al., Biochemistry, 32:7839-7845 (1993), which are hereby incorporated by reference in their entirety).

NMR experiments were recorded at a temperature of 25° C. on a Varian Inova 600 spectrometer equipped with a new generation ¹H{¹³C,¹⁵N} triple resonance probe which exhibits a signal-to-noise ratio of 1200:1 for a standard 0.1% ethylbenzene sample.

Specific embodiments of the 11 RD NMR experiments disclosed by the present invention were implemented for the present study. FIG. 2 provides a survey of (i) the names, (ii) the magnetization transfer pathways and (iii) the peak patterns observed in the projected dimension of each of the 11 RD NMR experiments disclosed by the present invention. For simplicity, FIG. 2 shows the in-phase peak pattern from the cosine-modulated RD NMR experiments. When acquiring the sine-modulated congeners, anti-phase peak pairs were observed instead (see FIG. 1). The group comprising the first three experiments are designed to yield “sequential” connectivities via one-bond scalar couplings: 3D H^α/βC^α/β(CO)NHN (FIG. 2A), 3D HACA(CO)NHN (FIG. 2B), and 3D HC(C-TOCSY-CO)NHN (FIG. 2C). The following three experiments provide “intraresidual” connectivities via one-bond scalar couplings: 3D HNNCAHA (FIG. 2D), 3D H^α/βC^α/βCOHA (FIG. 2E), and 3D H^α/βC^α/βNNH (FIG. 2F). 3D HNN<CO,CA> (FIG. 2G) offers both intraresidual ¹H^N-¹³C^α and sequential ¹H^N-¹³C′ connectivities. Although 3D HNNCAHA (FIG. 2D), 3D H^α/βC^α/βNHN (FIG. 2F) and 3D HNN<CO,CA> (FIG. 2G) also provide sequential connectivities via two-bond ¹³C^α_i−1-¹⁵N_i scalar couplings, those are usually smaller than the one-bond couplings (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety), and obtaining complete backbone resonance assignments critically depends on experiments designed to provide sequential connectivities via one-bond couplings (FIGS. 2D-F). 3D HCCH-COSY (FIG. 2H) and 3D HCCH-TOCSY (FIG. 2I) allow one to obtain assignments for the “aliphatic” side chain spin systems, while 2D HBCB(CDCG)HD (FIG. 2J) and 2D ¹H-TOCSY-relayed HCH-COSY (FIG. 2K) provide the corresponding information for the “aromatic” spin systems.

The RD NMR experiments are grouped accordingly in Table 1, which lists for each experiment (i) the nuclei for which the chemical shifts are measured, (ii) if and how the central peaks are acquired and (iii) additional notable technical features. State-of-the art implementations (Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996); Kay, J. Am. Chem. Soc., 115:2055-2057 (1993); Grzesiek et al., J. Magn Reson., 99:201-207 (1992); Montelione et al., J. Am. Chem. Soc., 114:10974-10975 (1992); Boucher et al., J. Biomol. NMR, 2:631-637 (1992); Yamazaki et al., J. Am. Chem. Soc., 115:11054-11055 (1993); Zerbe et al., J. Biomol. NMR, 7:99-106 (1996); Grzesiek et al., J. Biomol. NMR 3:185-204 (1993), which are hereby incorporated by reference in their entirety) making use of pulsed field z-gradients for coherence selection and/or rejection, and sensitivity enhancement (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) were chosen, which allow executing these experiments with a single transient per acquired free induction decay (FID). Semi (Grzesiek et al., J. Biomol. NMR, 3:185-204 (1993), which is hereby incorporated by reference in its entirety) constant-time (Cavanagh et al., Protein NMR Spectroscopy, Academic Press, San Diego, (1996), which is hereby incorporated by reference in its entirety) chemical shift frequency-labeling modules were used throughout in the indirect dimensions in order to minimize losses arising from transverse nuclear spin relaxation. FIGS. 3A-K provide comprehensive descriptions of the RD NMR r.f. pulse sequences.

In total, nine RD TR NMR experiments were recorded for the Z-domain protein (Table 2) and eleven RD TR NMR experiments for ubiquitin (Table 3). FIGS. 5-15 show composite plots of [ω₁,ω₃]- or [ω₁,ω₂]-strips taken from the recorded phase-sensitively detected RD NMR experiments. Except for 3D HNNCAHA, 3D HNN<CO,CA> and 2D ¹H-TOCSY-relayed HCH-COSY (FIG. 1), central peaks were derived from ¹³C magnetization (FIG. 2; Table 1). Hence, two subspectra, I and II containing the peak pairs and central peaks respectively, were generated (Szyperski et al., J. Am. Chem. Soc., 118:8146-8147 (1996); Szyperski et al., J. Biomol. NMR, 11:387-405 (1998), which are hereby incorporated by reference in their entirety) for eight of the RD NMR experiments (FIG. 2).

TABLE 2
Phase-Sensitively Detected RD NMR Data Sets Recorded for “Z-domain” Protein
	3D HACA(CO)	3D	3D Hα/βCα/β	3D Hα/βCα/β	3D
	NHN	HNNCAHA	(CO)NHN	NHN	HNN<CO,CA>
	1H Resonance Frequency (MHz)
No. of Pointsa	600	600	600	600	600
collected	40, 28, 512	64, 28, 512	76, 28, 512	68, 28, 512	56, 28, 512
after LP	80, 56, 512	96, 56, 512	152, 56, 512	136, 56, 512	112, 56, 512
after zero filling	256, 64, 1024	256, 64, 1024	256, 64, 1024	256, 64, 1024	256, 64, 1024
window functionsb	sin 70/70/90	sin 70/70/90	sin 70/70/90	sin 70/70/90	sin 70/70/90
No. of Transientsc	2	2	2	2	2
Spectral Widthd	6000 (RD),	5200.2 (RD),	12001.2 (RD),	12001.2 (RD),	8000 (RD),
(ω1, ω2, ω3, ω4; Hz)	1300, 6983	1300, 6983	1300, 6983	1300, 6983	1300, 6983
tmax (ms)e	6.5, 20.77,	12.11, 20.77,	6.25, 20.77,	5.58, 20.77,	6.88, 20.77,
	73.18	73.18	73.18	73.18	73.18
Carrier Position	53.05 (3.78),	53.05 (3.78),	38.05 (3.78),	38.05 (3.78),	171.07 (53.0),
(ω1, ω2, ω3, ω4; ppm)f	119.3, 4.78	119.3, 4.78	119.3, 4.78	119.3, 4.78	119.3, 4.78
Recycle Delay (s)g	0.67	0.67	0.67	0.67	0.67
Collection Time (h)h	6.7	10.73	12.74	11.4	9.38
	3D HC(C-			2D
	TOCSY—	3D HCCH—	3D HCCH-	HBCB(CGCD)
	CO)NHN	COSY	TOCSY	HD
	1H Resonance Frequency (MHz)
	No. of Pointsa	600	600	600	600
	collected	76, 28, 512	90, 20, 12	80, 20, 512	76, 512
	after LP	152, 56, 512	180, 40, 512	160, 40, 512	152, 512
	after zero filling	256, 64, 1024	256, 64, 1024	256, 64, 1024	512, 1024
	window functionsb	sin 70/70/90	sin 70/70/90	sin 70/70/90	sin 70/90
	No. of Transientsc	2	2	2	64
	Spectral Widthd	12001.2 (RD),	12001.2 (RD),	12001.2 (RD),	12001.2 (RD),
	(ω1, ω2, ω3, ω4; Hz)	1300, 6983	3125, 6983	3125, 6983	6983
	tmax (ms)e	6.25, 20.77,	7.42, 6.08,	6.58, 6.08,	6.25, 73.18
		73.18	73.18	73.18
	Carrier Position	38.05 (3.78),	38.05 (3.78),	38.05 (3.78),	33.04(3.78),
	(ω1, ω2, ω3, ω4; ppm)f	119.3, 4.78	38.05, 4.78	38.05, 4.78	4.78
	Recycle Delay (s)g	0.67	0.67	0.77	0.72
	Collection Time (h)h	12.74	10.77	11.0	7.82
	a“No. of Points” represents the number of complex data points used to sample indirect dimensions. Before Fourier transformation, the time domain points are extended by linear prediction (LP).
	bThe “Window Function” is a mathematical function multiplied with the FID along each indirect dimension before zero-filling and Fourier transformation.
	c“No. of Transients” represents the number of FIDs acquired for each real increment.
	d“Spectral Width” is the frequency range covered in each dimension.
	e“tmax” is the maximum chemical shift evolution time.
	f“Carrier Position” refers to the frequency (in ppm) of the center point of the spectrum along each dimension.
	g“Recycle Delay” denotes the relaxation delay between acquisitions of FIDs.
	h“Collection Time” is the total measurement time.

TABLE 3
Phase-Sensitively Detected RD NMR Data Sets Recorded for Ubiquitin
	3D		3D		3D
	HACA(CO)	3D	Hα/βCα/β	3D Hα/βCα/β	HNN<CO,	3D Hα/βCα/β
	NHN	HNNCAHA	(CO)NHN	NHN	CA>	COHA
	1H Resonance Frequency (MHz)
No. of Pointsa	600	600	600	600	600	600
collected	40, 28, 512	56, 28, 512	76, 28, 512	68, 28, 512	56, 28, 512	76, 32, 512
after LP						152, 64, 512
after zero filling						256, 64, 1024
window functionsb						sin 70/70/90
No. of Transientsc	2	2	2	2	2	2
Spectral Widthd	6000 (RD),	6000 (RD),	12001.2 (RD),	12001.2 (RD),	8000 (RD),	12001(RD),
(ω1, ω2, ω3, ω4; Hz)	1337, 7018	1337, 7018	1337, 7018	1337, 7018	1337, 7018	1800, 7018
tmax (ms)e	6.5, 20.2,	9.17, 20.2,	6.25, 20.2,	5.58, 20.2,	6.88, 20.2,	6.25, 17.2,
	72.8	72.8	72.8	72.8	72.8	72.8
Carrier Position	53.04 (3.78),	53.04 (3.78),	38.05 (3.78),	38.05 (3.78),	171.07 (53.0),	38.05 (3.78),
(ω1, ω2, ω3, ω4; ppm)f	119.3, 4.78	119.3, 4.78	119.3, 4.78	119.3, 4.78	119.3, 4.78	172.4, 4.78
Recycle Delay (s)g	0.67	0.67	0.67	0.67	0.67	0.67
Collection Time (h)h	6.7	9.38	12.73	11.39	9.38	14.55
	3D HC(C-			2D	2D H-
	TOCSY—	3D HCCH—	3D HCCH-	HBCB(CGCD)	TOCSY—
	CO)NHN	COSY	TOCSY	HD	HCH—COSY
	1H Resonance Frequency (MHz)
	No. of Pointsa	600	600	600	600	600
	collected	76, 28, 512	90, 20, 512	80, 20, 512	76, 512	100, 512
	after LP				152, 512	150, 512
	after zero filling				512, 1024	512, 1024
	window functionsb				sin 70/90	sin 70/90
	No. of Transientsc	2	2	2	32	16
	Spectral Widthd	12001.2 (RD),	12001.2 (RD),	12001.2 (RD),	12001(RD),	10000(RD),
	(ω1, ω2, ω3, ω4; Hz)	1337, 7018	3125, 7018	3125, 7018	7018	7018
	tmax (ms)e	6.25, 20.2,	7.42, 6.08,	6.58, 6.08,	6.25, 72.8	9.9, 72.8
		72.8	72.8	72.8
	Carrier Position	38.05 (3.78),	38.05(3.78),	38.05 (3.78),	33.05 (3.78),	120.05 (4.78),
	(ω1, ω2, ω3, ω4; ppm)f	119.3, 4.78	38.05,4.78	38.05, 4.78	4.78	4.78
	Recycle Delay (s)g	0.67	0.67	0.77	0.72	0.77
	Collection Time (h)h	12.73	10.77	10.99	3.91	1.37
	a“No. of Points” represents the number of complex data points used to sample indirect dimensions. Before Fourier transformation, the time domain points are extended by linear prediction (LP).
	bThe “Window Function” is a mathematical function multiplied with the FID along each indirect dimension before zero-filling and Fourier transformation.
	c“No. of Transients” represents the number of FIDs acquired for each real increment.
	d“Spectral Width” is the frequency range covered in each dimension.
	e“tmax” is the maximum chemical shift evolution time.
	f“Carrier Position” refers to the frequency (in ppm) of the center point of the spectrum along each dimension.
	g“Recycle Delay” denotes the relaxation delay between acquisitions of FIDs.
	h“Collection Time” is the total measurement time.

Example 3

HTP Assignment Strategy

The comprehensive analysis of the suite of multidimensional spectra recorded for the present study (Tables 1-3) lays the foundation to devise strategies for RD NMR-based HTP resonance assignment of proteins.

For proteins in the molecular weight range up to about 20 kDa, 3D H^α/βC^α/β(CO)NHN plays a pivotal role. Firstly, the peak patterns observed along ω₁(¹³C^α/β) in subspectra I and II enable sequential resonance assignment in combination with HNNCAHA and HNNCACB, respectively, by matching intraresidue and sequential ¹H^α, ¹³C^α and ¹³C^β chemical shifts. (When considering “nuclear spin relaxation time labelling” of peak pairs, subspectrum II derived from ¹³C steady state magnetization provides largely redundant information when compared with subspectrum I. However, the observation of the central peaks allows direct matching of peak positions between subspectrum II, essentially a CBCA(CO)NHN spectrum, and HNNCACB.) Moreover, this set of chemical shifts alone provides valuable information for amino acid type identification (Zimmerman et al., J. Mol. Biol., 269:592-610 (1997); Cavanagh et al., Protein NMR Spetroscopy, Academic Press, San Diego, (1996); Grzesiek et al., J. Biomol NMR, 3:185-204 (1993), which are hereby incorporated by reference in their entirety). Complementary recording of 3D H^α/βC^α/βCOHA and 3D HNN<CO,CA> contributes polypeptide backbone ¹³C═O chemical shift measurements for establishing sequential assignments: the intraresidue correlation is obtained by ω₁(¹³C^α/β) peak pattern matching with 3D H^α/βC^α/β(CO)NHN, and the sequential correlation is inferred from ¹³C^α, ¹⁵N and ¹H^N chemical shifts in 3D HNN<CO,CA> (Szyperski et al., J. Biomol. NMR, 11:387-405 (1998), which is hereby incorporated by reference in its entirety). Notably, even for medium-sized (non-deuterated) proteins this approach is superior to the use of a low sensitivity HNNCACO-type experiment (e.g., in combination with HNNCOCA), where the magnetization transfer via rapidly relaxing ¹³C^α relies on the rather small ¹⁵N—¹³C^α one-bond scalar coupling. Secondly, comparison of ω₁(¹³C^α/β) peak patterns with 3D HCCH-COSY and TOCSY connects the C^α/β/H^α/β chemical shifts with those of the aliphatic side chain spin systems (For Z-domain, complete side chain assignments were obtained for all but six residues using 3D HCCH-COSY only.), while comparison of ω₁(¹³C^β) peaks with 2D HBCB(CDCG)HD and subsequent linking with ¹H^δ chemical shifts detected in 2D ¹H-TOCSY-relayed HCH-COSY affords assignment of the aromatic spin systems. Since for many amino acid residues the two β-protons exhibit non-degenerate chemical shifts, the connection of H^α/βC^α/β(CO)NHN and HBCB(CDCG)HD or HCCH-COSY/TOCSY may in fact often rely on comparison of three chemical shifts, i.e., δ(¹H^β2), δ(¹H^β3) and δ(¹³C^β). This consideration underscores the potential of recruiting β-proton chemical shifts for establishing sequential resonance assignments.

Although preferred embodiments have been depicted and described in detail herein, it will be apparent to those skilled in the relevant art that various modifications, additions, substitutions, and the like can be made without departing from the spirit of the invention and these are therefore considered to be within the scope of the invention as defined in the claims which follow.

Claims

1. A method of conducting a reduced dimensionality three-dimensional (3D) HA,CA,(CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) an α-proton of amino acid residue i−1, 1Hαi−1; (2) an α-carbon of amino acid residue i−1, 13Cαi−1; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15Ni; and (4) a polypeptide backbone amide proton of amino acid residue i, 1HNi, wherein the chemical shift values of 1Hαi−1 and 13Cαi−1 which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hαi−1 and 13Cαi−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15Ni and 1HNi of amino acid residue i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13Cαi−1 and 15Ni in a phase sensitive manner in two indirect time domain dimensions, t1(13Cα) and t2(15N), respectively, and the chemical shift value of 1HNi in a direct time domain dimension, t3(1HN), and (2) to sine modulate the 13Cαi−1 chemical shift evolution in t1(13Cα) with the chemical shift evolution of 1Hαi−1; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with an anti-phase peak pair derived from said sine modulating, wherein (1) the chemical shift values of 15Ni and 1HNi are measured in two frequency domain dimensions, ω2(15N) and ω3(1HN), respectively, and (2) the chemical shift values of 1Hαi−1 and 13Cαi−1 are measured in a frequency domain dimension, ω1(13Cα), by the frequency difference between the two peaks forming said anti-phase peak pair and the frequency at the center of the two peaks, respectively, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift value of 1Hαi−1 in a phase sensitive manner.

2. The method according to claim 1, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi−1 and 15Ni in a phase sensitive manner in t1(13Cα) and t2(15N), respectively, and the chemical shift value of 1HNi in t3(1HN) and (2) to cosine modulate the 13Cαi−1 chemical shift evolution in t1(13Cα) with the chemical shift evolution of 1Hαi−1 for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with an in-phase peak pair derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

3. The method according to claim 1, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 15Ni does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with a peak pair wherein (1) the chemical shift value of 1HNi is measured in a frequency domain dimension, ω2(1HN), and (2) the chemical shift values of 1Hαi−1 and 13Cαi−1 are measured in a frequency domain dimension, ω1(13Cα), by the frequency difference between the two peaks forming said peak pair and the frequency at the center of the two peaks, respectively.

4. The method according to claim 1, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13C′i−1 in a phase sensitive manner in an indirect time domain dimension, t4(13C′), and said processing the NMR signals generates a four dimensional (4D) NMR spectrum with a peak pair wherein (1) the chemical shift values of 15Ni, 1HNi and 13C′i−1 are measured in three frequency domain dimensions, ω2(15N), ω3(1HN), and ω4(13C′), respectively, and (2) the chemical shift values of 1Hαi−1 and 13Cαi−1 are measured in a frequency domain dimension, ω1(13Cα), by the frequency difference between the two peaks forming said peak pair and the frequency at the center of the two peaks, respectively.

5. The method according to claim 1, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi−1 and 15Ni in a phase sensitive manner in t1(13Cα) and t2(15N), respectively, and the chemical shift value of 1HNi in t3(1HN), and (2) to avoid sine modulating the 13Cαi−1 chemical shift evolution in t1(13Cα) with the chemical shift evolution of 1Hαi−1 for the additional NMR signals, and said processing the NMR signals and the additional NMR signals generates a 3D NMR spectrum with an additional peak located centrally between two peaks forming said peak pair which measures the chemical shift value of 13Cαi−1 along ω1(13Cα).

6. The method according to claim 5, wherein said additional peak is derived from 13Cα nuclear spin polarization.

7. The method according to claim 6, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2B, wherein a radiofrequency pulse is used to create transverse 1Hαi−1 magnetization, which is transferred to 13Cαi−1, to 15Ni, and to 1HNi, to generate the NMR signal.

8. The method according to claim 7, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3B to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3B, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pair and a second NMR subspectrum derived from said adding which contains said additional peak located centrally between the two peaks forming said peak pair.

9. A method of conducting a reduced dimensionality three-dimensional (3D) H,C,-(C-TOCSY-CO),N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having two consecutive amino acid residues, i−1 and i: (1) aliphatic protons of amino acid residue i−1, 1Halii−1; (2) aliphatic carbons of amino acid residue i−1, 13Calii−1; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15Ni; and (4) a polypeptide backbone amide proton of amino acid residue i, 1HNi, wherein the chemical shift values of 1Halii−1 and 13Calii−1 which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Halii−1 and 13Calii−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15Ni and 1HNi of amino acid residue i, under conditions effective (1) to generate a NMR signal encoding the chemical shift values of 13Calii−1 and 15Ni in a phase sensitive manner in two indirect time domain dimensions, t1(13Cali) and t2(15N), respectively, and the chemical shift value of 1HNi in a direct time domain dimension, t3(1HN), and (2) to sine modulate the chemical shift evolutions of 13Calii−1 in t1(13Cali) with the chemical shift evolutions of 1Halii−1; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift values of 15Ni and 1HNi are measured in two frequency domain dimensions, ω2(15N) and ω3(1HN), respectively, and (2) the chemical shift values of 1Halii−1 and 13Calii−1 are measured in a frequency domain dimension, ω1(13Cali), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift value of 1Halii−1 in a phase sensitive manner.

10. The method according to claim 9, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Calii−1 and 15Ni in a phase sensitive manner in t1(13Cali) and t2(15N), respectively, and the chemical shift value of 1HNi in t3(1HN) and (2) to cosine modulate the chemical shift evolutions of 13Calii−1 in t1(13Cali) with the chemical shift evolutions of 1Halii−1 for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

11. The method according to claim 9, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 15Ni does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with peak pairs wherein (1) the chemical shift value of 1HNi is measured in a frequency domain dimension, ω2(1HN), and (2) the chemical shift values of 1Halii−1 and 13Calii−1 are measured in a frequency domain dimension, ω1(13Cali), by the frequency differences between the two peaks forming said peak pairs and the frequencies at the center of the two peaks, respectively.

12. The method according to claim 9, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13C′i−1 in a phase sensitive manner in an indirect time domain dimension, t4(13C′), and said processing the NMR signals generates a four dimensional (4D) NMR spectrum with variant peak pairs wherein (1) the chemical shift values of 15Ni, 1HNi and 13C′i−1 are measured in three frequency domain dimensions, ω2(15N), ω3(1HN), and ω4(13C′), respectively, and (2) the chemical shift values of 1Halii−1 and 13Calii−1 are measured in a frequency domain dimension, ω1(13Cali), by the frequency differences between the two peaks forming said variant peak pairs and the frequencies at the center of the two peaks, respectively.

13. The method according to claim 9, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Calii−1 and 15Ni in a phase sensitive manner in t1(13Cali) and t2(15N) and the chemical shift value of 1HNi in t3(1HN), and (2) to avoid sine modulating the chemical shift evolutions of 13Calii−1 in t1(13Cali) with the chemical shift evolution of 1Hαi−1 for the additional NMR signals, and said processing the NMR signals and the additional NMR signals generates a 3D NMR spectrum with additional peaks located centrally between said peak pairs which measure the chemical shift values of 13Calii−1 along ω1(13Cali).

14. The method according to claim 13, wherein said additional peaks are derived from 13Cali nuclear spin polarization.

15. The method according to claim 14, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2C, wherein a radiofrequency pulse is used to create transverse 1Halii−1 magnetization, and 1Halii−1 magnetization is transferred to 13Calii−1, to 13Cαi−1, to 13C′i−1, to 15Ni, and to 1HNi, where the NMR signal is detected.

16. The method according to claim 15, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3C to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3C, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pairs, and a second NMR subspectrum derived from said adding which contains said additional peaks located centrally between said peak pairs.

17. A method of conducting a reduced dimensionality three-dimensional (3D) Hα/βCα/β,CO,HA nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, 1Hβi; (2) a β-carbon of amino acid residue i, 13Cβi; (3) an α-proton of amino acid residue i, 1Hαi; (4) an α-carbon of amino acid residue i, 13Cαi; and (5) a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i, wherein the chemical shift values of 1Hαi/13Cαi and 1Hβi/13Cβi which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hαi, 1Hβi, 13Cαi, and 13Cβi are connected to the chemical shift evolution of 13C′i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 13C′i in a phase sensitive manner in two indirect time domain dimensions, t1(13Cα/β) and t2(13C′), respectively, and the chemical shift value of 1Hαi in a direct time domain dimension, t3(1Hα) and (2) to sine modulate the chemical shift evolutions of 13Cαi and 13Cβi in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi, respectively; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift values of 13C′i and 1Hαi are measured in two frequency domain dimensions, ω2(13C′) and ω3(1Hα), respectively, and (2) (i) the chemical shift values of 1Hαi and 1Hβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs, and (ii) the chemical shift values of 13Cαi and 13Cβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequencies at the center of the two peaks forming said anti-phase peak pairs, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift values of 1Hαi and 1Hβi in a phase sensitive manner.

18. The method according to claim 17, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 13C′i in a phase sensitive manner in t1(13Cα/β) and t2(13C′), respectively, and the chemical shift value of 1Hαi in t3(1Hα) and (2) to cosine modulate the 13Cαi and 13Cβi chemical shift evolutions in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi for the additional NMR signals and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

19. The method according to claim 17, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 13C′i does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with peak pairs wherein (1) the chemical shift value of 1Hαi is measured in a frequency domain dimension, ω2(1Hα), and (2) (i) the chemical shift values of 1Hαi and 1Hβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequency differences between two peaks forming said peak pairs, respectively, and (ii) the chemical shift values of 13Cαi, and 13Cβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequencies at the center of the two peaks forming said peak pairs.

20. The method according to claim 17 wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 15Ni in a phase sensitive manner in t1(13Cα/β) and t2(15N) and the chemical shift value of 1Hαi in t3(1Hα), and (2) to avoid sine modulating the chemical shift evolutions of 13Cαi and 13Cβi in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi for the additional NMR signal, and said processing the NMR signals and the additional NMR signals generates a 3D NMR spectrum with additional peaks located centrally between the two peaks forming said peak pairs which measure the chemical shift values of 13Cαi and 13Cβi along ω1(13Cα/β).

21. The method according to claim 20, wherein said additional peaks are derived from 13Cα and 13Cβ nuclear spin polarization.

22. The method according to claim 21, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2E, wherein a radiofrequency pulse is used to create transverse 1Hαi and 1Hβi magnetization, and 1Hαi and 1Hβi polarization is transferred to 13Cαi and 13Cβi, to 13C′i, and back to 1Hαi, where the NMR signal is detected.

23. The method according to claim 22, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3E to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3E, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pairs, and a second NMR subspectrum derived from said adding which contains said additional peaks located centrally between the two peaks forming said peak pairs.

24. A method of conducting a reduced dimensionality three-dimensional (3D) Hα/β,Cα/β,N,HN nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule having an amino acid residue, i: (1) a β-proton of amino acid residue i, 1Hβi; (2) a β-carbon of amino acid residue i, 13Cβi; (3) an α-proton of amino acid residue i, 1Hαi; (4) an α-carbon of amino acid residue i, 13Cαi; (5) a polypeptide backbone amide nitrogen of amino acid residue i, 15Ni; and (6) a polypeptide backbone amide proton of amino acid residue i, 1HNi, wherein the chemical shift values of 1Hαi/13Cαi and 1Hβi/13Cβi which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hαi, 1Hβi, 13Cαi, and 13Cβi are connected to the chemical shift evolutions of 15Ni and 1HNi, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 15Ni in a phase sensitive manner in two indirect time domain dimensions, t1(13Cα/β) and t2(15N), respectively, and the chemical shift value of 1HNi in a direct time domain dimension, t3(1HN) and (2) to sine modulate the chemical shift evolutions of 13Cαi and 13Cβi in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi, respectively; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift values of 15Ni and 1HNi are measured in two frequency domain dimensions, ω2(15N) and ω3(1HN), respectively, and (2) (i) the chemical shift values of 1Hαi and 1Hβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs, and (ii) the chemical shift values of 13Cαi and 13Cβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequencies at the center of said two peaks forming said anti-phase peak pairs, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift values of 1Hαi and 1Hβi in a phase sensitive manner.

25. The method according to claim 24, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 15Ni in a phase sensitive manner in t1(13Cα/β) and t2(15N), respectively, and the chemical shift value of 1HNi in t3(1HN) and (2) to cosine modulate the 13Cαi and 13Cβi chemical shift evolutions in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

26. The method according to claim 24, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 15Ni does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with peak pairs wherein (1) the chemical shift value of 1HNi is measured in a frequency domain dimension, ω2(1HN), and (2) (i) the chemical shift values of 1Hαi and 1Hβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequency differences between the two peaks forming said peak pairs, and (ii) the chemical shift values of 13Cαi, and 13Cβi are measured in a frequency domain dimension, ω1(13Cα/β), by the frequencies at the center of the two peaks forming said peak pairs.

27. The method according to claim 24, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cαi, 13Cβi and 15Ni in a phase sensitive manner in t1(13Cα/β) and t2(15N) and the chemical shift value of 1HNi in t3(1HN), and (2) to avoid sine modulating the chemical shift evolutions of 13Cαi and 13Cβi in t1(13Cα/β) with the chemical shift evolutions of 1Hαi and 1Hβi for the additional NMR signals, and said processing the NMR signals and the additional NMR signals generates a 3D NMR spectrum with additional peaks located centrally between the two peaks forming said peak pairs which measure the chemical shift values of 13Cαi and 13Cβi along ω1(13Cα/β).

28. The method according to claim 27, wherein said additional peaks are derived from 13Cα and 13Cβ nuclear spin polarization.

29. The method according to claim 28, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2F, wherein a radiofrequency pulse is used to create transverse 1Hαi and 1Hβi magnetization, and 1Hαi and 1Hβi magnetization is transferred to 13Cαi and 13Cβi, to 15Ni, and to 1HNi, where the NMR signal is detected.

30. The method according to claim 29, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3F to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3F, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pairs, and a second NMR subspectrum derived from said adding which contains said additional peaks located centrally between the two peaks forming said peak pairs.

31. A method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for 1Hm, 13Cm, 1Hn, and 13Cn of a protein molecule wherein m and n indicate atom numbers of two CH, CH2 or CH3 groups that are linked by a single covalent carbon-carbon bond in an amino acid residue, wherein the chemical shift values of 1Hm and 13Cm which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hm and 13Cm are connected to the chemical shift evolutions of 1Hn and 13Cm, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in two indirect time domain dimensions, t1(13Cm) and t2(13Cn), respectively, and the chemical shift value of 1Hn in a direct time domain dimension, t3(1Hn), and (2) to sine modulate the chemical shift evolution of 13Cm in t1(13Cm) with the chemical shift evolution of 1Hm; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift values of 13Cn and 1Hn are measured in two frequency domain dimensions, ω2(13Cn) and ω3(1Hn), respectively, and (2) the chemical shift values of 1Hm and 13Cm are measured in a frequency domain dimension, ω1(13Cm), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift value of 1Hm in a phase sensitive manner.

32. The method according to claim 31, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in t1(13Cm) and t2(13Cn), respectively, and the chemical shift value of 1Hn in t3(1Hn), and (2) to cosine modulate the 13Cm chemical shift evolution in t1(13Cm) with the chemical shift evolution of 1Hm for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

33. The method according to claim 31, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 13Cn does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with peak pairs wherein (1) the chemical shift value of 1Hn is measured in a frequency domain dimension, ω2(1Hn), and (2) the chemical shift values of 1Hm and 13Cm are measured in a frequency domain dimension, ω1(13Cm), by the frequency differences between the two peaks forming said peak pairs and the frequencies at the center of the two peaks, respectively.

34. The method according to claim 31, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate an additional NMR signal encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in t1(13Cm) and t2(13Cn) and the chemical shift value of 1Hn in t3(1H), and (2) to avoid sine modulating the chemical shift evolution of 13Cm in t1(13Cm) with the chemical shift evolution of 1Hm for the additional NMR signal, and said processing the NMR signals and the additional NMR signal generates a 3D NMR spectrum with additional peaks located centrally between the two peaks forming said peak pairs which measure the chemical shift value of 13Cm along ω1(13Cm).

35. The method according to claim 34, wherein said additional peaks are derived from 13Cm nuclear spin polarization.

36. The method according to claim 35, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2H, wherein a radiofrequency pulse is used to create transverse 1Hm magnetization, and 1Hm magnetization is transferred to 13Cm, to 13Cn, and to 1Hn, where the NMR signal is detected.

37. The method according to claim 36, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3H to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3H, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pairs, and a second NMR subspectrum derived from said adding which contains said additional peaks located centrally between the two peaks forming said peak pairs.

38. A method of conducting a reduced dimensionality three-dimensional (3D) H,C,C,H-TOCSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for 1Hm, 13Cm, 1Hn, and 13Cn of a protein molecule wherein m and n indicate atom numbers of two CH, CH2 or CH3 groups that may or may not be directly linked by a single covalent carbon-carbon bond in an amino acid residue, wherein the chemical shift values of 1Hm and 13Cm which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hm and 13Cm are connected to the chemical shift evolutions of 1Hn and 13Cn, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in two indirect time domain dimensions, t1(13 Cm) and t2(13Cn), respectively, and the chemical shift value of 1Hn in a direct time domain dimension, t3(1Hn), and (2) to sine modulate the chemical shift evolution of 13Cm in t1(13Cm) with the chemical shift evolution of 1Hm; and

processing the NMR signals to generate a sine-modulated 3D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift values of 13Cn and 1Hn are measured in two frequency domain dimensions, ω2(13Cn) and ω3(1Hn), respectively, and (2) the chemical shift values of 1Hm and 13Cm are measured in a frequency domain dimension, ω1(13Cm), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, wherein said sine-modulated 3D NMR spectrum enables detection of the chemical shift value of 1Hm and in a phase sensitive manner.

39. The method according to claim 38, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in t1(13Cm) and t2(13Cn), respectively, and the chemical shift value of 1Hn in t3(1Hn) and (2) to cosine modulate the 13Cm chemical shift evolution in t1(13Cm) with the chemical shift evolution of 1Hm for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 3D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 3D NMR spectrum generated by adding said sine-modulated 3D NMR spectrum and said cosine-modulated 3D NMR spectrum, and a difference 3D NMR spectrum generated by subtracting said cosine-modulated 3D NMR spectrum from said sine-modulated 3D NMR spectrum, wherein combined use of said sum 3D NMR spectrum and said difference 3D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

40. The method according to claim 38, wherein said applying radiofrequency pulses is carried out so that the chemical shift evolution of 13Cn does not occur and said processing the NMR signals generates a two dimensional (2D) NMR spectrum with peak pairs wherein (1) the chemical shift value of 1Hn is measured in a frequency domain dimension, ω2(1Hn), and (2) the chemical shift values of 1Hm and 13Cm are measured in a frequency domain dimension, ω1(13Cm), by the frequency differences between the two peaks forming said peak pairs and the frequencies at the center of the two peaks, respectively.

41. The method according to claim 38, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift values of 13Cm and 13Cn in a phase sensitive manner in t1(13Cm) and t2(13Cn) and the chemical shift value of 1Hn in t3(1Hn), and (2) to avoid sine modulating the chemical shift evolution of 13Cm in t1(13Cm) with the chemical shift evolution of 1Hm for the additional NMR signals, and said processing the NMR signals and the additional NMR signals generates a 3D NMR spectrum with additional peaks located centrally between the two peaks forming said peak pairs which measure the chemical shift value of 13Cm along ω1(13Cm).

42. The method according to claim 41, wherein said additional peaks are derived from 13Cm nuclear spin polarization.

43. The method according to claim 42, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2I, wherein a radiofrequency pulse is used to create transverse 1Hm magnetization, and 1Hm magnetization is transferred to 13Cm, to 13Cn, and to 1Hn, where the NMR signal is detected.

44. The method according to claim 43, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3I to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3I, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pairs, and a second NMR subspectrum derived from said adding which contains said additional peaks located centrally between the two peaks forming said peak pairs.

45. A method of conducting a reduced dimensionality two-dimensional (2D) HB,CB,(CG,CD),HD nuclear magnetic resonance NMR) experiment by measuring the chemical shift values for the following nuclei of a protein molecule: (1) a β-proton of an amino acid residue with an aromatic side chain, 1Hβ; (2) a β-carbon of an amino acid residue with an aromatic side chain, 13Cβ; and (3) a δ-proton of an amino acid residue with an aromatic side chain, 1Hδ, wherein the chemical shift values of 1Hβ and 13Cβ which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hβ and 13Cβ are connected to the chemical shift evolution of 1Hδ, under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13Cβ in a phase sensitive manner in an indirect time domain dimension, t1(13Cβ), and the chemical shift value of 1Hδ in a direct time domain dimension, t2(1Hδ), and (2) to sine modulate the chemical shift evolution of 13Cβ in t1(13Cβ) with the chemical shift evolution of 1Hβ; and

processing the NMR signals to generate a sine-modulated 2D NMR spectrum with an anti-phase peak pair derived from said sine modulating wherein (1) the chemical shift value of 1Hδ is measured in a frequency domain dimension, ω2(1Hδ), and (2) the chemical shift values of 1Hβ and 13Cβ are measured in a frequency domain dimension, ω1(13Cβ), by the frequency difference between the two peaks forming said anti-phase peak pair and the frequency at the center of the two peaks, respectively, wherein said sine-modulated 2D NMR spectrum enables detection of the chemical shift value of 1Hβ in a phase sensitive manner.

46. The method according to claim 45, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of 13Cβ in a phase sensitive manner in t1(13Cβ) and the chemical shift value of 1Hδ in t2(1Hδ) and (2) to cosine modulate the 13Cβ chemical shift evolution in t1(13Cβ) with the chemical shift evolution of 1Hβ for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 2D NMR spectrum with an in-phase peak pair derived from said cosine modulating, a sum 2D NMR spectrum generated by adding said sine-modulated 2D NMR spectrum and said cosine-modulated 2D NMR spectrum, and a difference 2D NMR spectrum generated by subtracting said cosine-modulated 2D NMR spectrum from said sine-modulated 2D NMR spectrum, wherein combined use of said sum 2D NMR spectrum and said difference 2D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

47. The method according to claim 45, wherein said applying radiofrequency pulses is carried out so that:

(i) the chemical shift evolution of a δ-carbon of an amino acid residue with an aromatic side chain, 13Cδ, occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13Cδ in a phase sensitive manner in an indirect time domain dimension, t3(13Cδ), and said processing the NMR signals generates a three dimensional (3D) NMR spectrum with a peak pair wherein (1) the chemical shift values of 1Hδ and 13Cδ are measured in two frequency domain dimensions, ω2(1Hδ) and ω3(13Cδ), respectively, and (2) the chemical shift values of 1Hβ and 13Cβ are measured in a frequency domain dimension, ω1(13Cβ), by the frequency difference between the two peaks forming said peak pair and the frequency at the center of the two peaks, respectively; or

(ii) the chemical shift evolution of a γ-carbon of an amino acid residue with an aromatic side chain, 13Cγ occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13Cγ, in a phase sensitive manner in an indirect time domain dimension, t3(13Cγ), and said processing the NMR signals generates a three dimensional (3D) NMR spectrum with a peak pair wherein (1) the chemical shift values of 1Hδ and 13Cγ are measured in two frequency domain dimensions, ω2(1Hδ) and ω3(13Cγ), respectively, and (2) the chemical shift values of 1Hβ and 13Cβ are measured in a frequency domain dimension, ω1(13Cβ), by the frequency difference between the two peaks forming said peak pair and the frequency at the center of the two peaks, respectively.

48. The method according to claim 46, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of 13Cβ in a phase sensitive manner in t1(13Cβ) and the chemical shift value of 1Hδ in t2(1Hδ), and (2) to avoid sine modulating the chemical shift evolution of 13Cβ in t1(13Cβ) with the chemical shift evolution of 1Hβ for the additional NMR signals, and said processing the NMR signals and the additional NMR signals generates a 2D NMR spectrum with an additional peak located centrally between said peak pair which measure the chemical shift value of 13Cβ along ω1(13Cβ).

49. The method according to claim 48, wherein said additional peak is derived from 13Cβ nuclear spin polarization.

50. The method according to claim 49, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2J, wherein a radiofrequency pulse is used to create transverse 1Hβ magnetization, and 1Hβ magnetization is transferred to 13Cβ, to 13Cδ, and to 1Hδ, where the NMR signal is detected.

51. The method according to claim 50, wherein said applying radiofrequency pulses comprises:

applying a first set of radiofrequency pulses according to the scheme shown in FIG. 3J to generate a first NMR signal, and

applying a second set of radiofrequency pulses according to the scheme shown in FIG. 3J, wherein phase φ1 of the first 1H pulse is altered by 180° to generate a second NMR signal, said method further comprising:

adding and subtracting the first NMR signal and the second NMR signal prior to said processing, whereby said processing the NMR signals generates a first NMR subspectrum derived from said subtracting which contains said peak pair, and a second NMR subspectrum derived from said adding which contains said additional peak located centrally between the two peaks forming said peak pair.

52. A method of conducting a reduced dimensionality two-dimensional (2D) H,C,H-COSY nuclear magnetic resonance (NMR) experiment by measuring the chemical shift values for 1Hm, 13Cm, and 1Hn of a protein molecule wherein m and n indicate atom numbers of two CH, CH2 or CH3 groups in an amino acid residue, wherein the chemical shift values of 1Hm and 13Cm which are encoded in a peak pair of a 2D NMR spectrum are detected in a phase sensitive manner, said method comprising:

providing a protein sample;

applying radiofrequency pulses to the protein sample which effect a nuclear spin polarization transfer wherein the chemical shift evolutions of 1Hm and 13Cm are connected to the chemical shift evolution of 1Hn, under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13Cm in a phase sensitive manner in an indirect time domain dimension, t1(13Cm), and the chemical shift value of 1Hn in a direct time domain dimension, t2(1Hn) and (2) to sine modulate the chemical shift evolution of 13Cm in t1(13Cm) with the chemical shift evolution of 1Hm; and

processing the NMR signals to generate a sine-modulated 2D NMR spectrum with anti-phase peak pairs derived from said sine modulating wherein (1) the chemical shift value of 1Hn is measured in a frequency domain dimension, ω2(1Hn), and (2) the chemical shift values of 1Hm and 13Cm are measured in a frequency domain dimension, ω1(13Cm), by the frequency differences between each of the two peaks forming each of said anti-phase peak pairs and the frequencies at the center of the two peaks, respectively, wherein said sine-modulated 2D NMR spectrum enables detection of the chemical shift value of 1Hm in a phase sensitive manner.

53. The method according to claim 52, wherein said applying radiofrequency pulses is carried out under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of 13Cm in a phase sensitive manner in t1(13Cm) and the chemical shift value of 1Hn in t2(13Hn) and (2) to cosine modulate the 13Cm chemical shift evolution in t1(13Cm) with the chemical shift evolution of 1Hm for the additional NMR signals, and said processing the NMR signals and the additional NMR signals further comprises generating a cosine-modulated 2D NMR spectrum with in-phase peak pairs derived from said cosine modulating, a sum 2D NMR spectrum generated by adding said sine-modulated 2D NMR spectrum and said cosine-modulated 2D NMR spectrum, and a difference 2D NMR spectrum generated by subtracting said cosine-modulated 2D NMR spectrum from said sine-modulated 2D NMR spectrum, wherein combined use of said sum 2D NMR spectrum and said difference 2D NMR spectrum enables placement of the two peaks forming said peak pairs into separate spectra, thereby allowing phase-sensitive editing of the two peaks forming said peak pairs.

54. The method according to claim 52, wherein said applying radiofrequency pulses effects a nuclear spin polarization transfer according to FIG. 2K, wherein a radiofrequency pulse is used to create transverse 1Hm magnetization, and 1Hm polarization is transferred to 13Cm, to 1Hm, and to 1Hn, where the NMR signal is detected.

55. The method according to claim 54, wherein said applying radiofrequency pulses is carried out according to the scheme shown in FIG. 3K.

56. A method for sequentially assigning chemical shift values of an α-proton, 1Hα, an α-carbon, 13Cα, a polypeptide backbone amide nitrogen, 15N, and a polypeptide backbone amide proton, 1HN, of a protein molecule comprising:

providing a protein sample;

conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, wherein the chemical shift values of 1Hα and 13Cα which are encoded in a peak pair of a 3D NMR spectrum are detected in a phase sensitive manner, comprising: (1) a RD three dimensional (3D) HA,CA,(CO),N,HN NMR experiment to measure and connect chemical shift values of the α-proton of amino acid residue i−1, 1Hαi−1, the α-carbon of amino acid residue i−1, 13Cαi−1, the polypeptide backbone amide nitrogen of amino acid residue i, 15Ni, and the polypeptide backbone amide proton of amino acid residue i, 1HNi and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Hα, 13Cα, 15N, and 1HN by (i) matching the chemical shift values of 1Hαi−1 and 13Cαi−1 with the chemical shift values of 1Hαi and 13Cαi, (ii) using the chemical shift values of 1Hαi−1 and 13Cαi−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using said chemical shift values to locate secondary structure elements within the polypeptide chain.

57. The method according to claim 56 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β(CO)NUN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, 1Hβi−1, the β-carbon of amino acid residue i−1, 13Cβi−1, 1Hαi−1, 13Cαi−1, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Hβ and 13Cβ by using the chemical shift values of 1Hβi−1 and 13Cβi−1 to identify the type of amino acid residue i−1.

58. The method according to claim 57 further comprising:

subjecting the protein sample to a RD 3D Hα/β,Cα/β,CO,HA NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, 1Hβi, the β-carbon of amino acid residue i, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i; and

obtaining sequential assignments of the chemical shift value of 13C′i by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D Hα/β,Cα/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of 1Hβ, 13Cβ, 1Hα, 13Cα, 15N, and 1HN measured by said RD 3D HA,CA,(CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, and RD 3D Hα/βCα/β(CO)NHN NMR experiment.

59. The method according to claim 57 further comprising:

subjecting the protein sample to a RD 3D Hα/β,Cα/β,N,HN NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi with the chemical shift values of 1Hβi−1, 13Cβi−1, 1Hαi−1, and 13Cαi−1 measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment.

60. The method according to claim 57 further comprising:

subjecting the protein sample to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13Cβi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 13Cβi and 13Cαi measure by said 3D HNNCACB NMR experiment with the chemical shift values of 13Cβi−1 and 13Cαi−1 measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment.

61. The method according to claim 57 further comprising:

subjecting the protein sample to a RD two-dimensional (2D) HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of 1Hβi−1, 13Cβi−1, and a δ-proton of amino acid residue i−1 with an aromatic side chain, 1Hδi−1; and

obtaining sequential assignments by (i) matching the chemical shift values of 1Hβi−1 and 13Cβi−1 measured by said RD 2D HB, CB, (CG,CD), HD NMR experiment with the chemical shift values of 1Hβ and 13Cβ measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment, (ii) using said chemical shift values to identify amino acid residue i as having an aromatic side chain, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along said polypeptide chain.

62. The method according to claim 57 further comprising:

subjecting the protein sample to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, 1Halii, and aliphatic carbons of amino acid residue i, 13Calii; and

obtaining sequential assignments of the chemical shift values of 1Halii and 13Calii, by (i) matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured using said RD 3D H,C,C,H-COSY NMR experiment or RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of 1Hβ, 13Cβ, 1Hαi, and 13Cαi measured by said RD 3D HA,CA,(CO),N,HN NMR experiment, RD 3D HNNCAHA NMR experiment, and RD 3D Hα/βCα/β(CO)NHN NMR experiment and (ii) using the chemical shift values of 1Halii and 13Calii, to identify the type of amino acid residue i.

63. The method according to claim 56 further comprising:

subjecting the protein sample to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift value of 13C′i−1 by matching the chemical shift value of 13Cαi measured by said RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of 13Cα, 15N, and 1HN measured by said RD 3D HA,CA,(CO),N,HN NMR experiment and RD 3D HNNCAHA NMR experiment.

64. The method according to claim 56 further comprising:

subjecting the protein sample to (i) a RD 3D Hα/βCα/β,CO,HA NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, 1Hβi, the β-carbon of amino acid residue i, 13Cβi, the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of 13C′i, the α-carbon of amino acid residue i+1, 13Cαi+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, 15Ni+1, and the polypeptide backbone amide proton of amino acid residue i+1, 1HNi+1; and

obtaining sequential assignments by matching the chemical shift value of 13C′i measured by said RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of 13C′i measured by said RD 3D Hα/βCα/β,CO,HA NMR experiment.

65. The method according to claim 56, further comprising:

subjecting the protein sample to a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i−1, 1Halii−1, aliphatic carbons of amino acid residue i−1, 13Calii−1, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Halii−1 and 13Calii−1 for amino acid residues i having unique pairs of 15Ni and 1HNi chemical shift values by matching the chemical shift values of 1Hα and 13Cα measured by said RD 3D HNNCAHA NMR experiment and RD 3D HA,CA,(CO),N,HN NMR experiment with the chemical shift values of 1Hαi−1 and 13Cαi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and using the 1Halii−1 and 13Calii−1 chemical shift values to identify the type of amino acid residue i−1.

66. The method according to claim 56 further comprising:

subjecting the protein sample to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, 1Halii, and aliphatic carbons of amino acid residue i, 13Calii; and

obtaining sequential assignments of the chemical shift values of 1Halii and 13Calii by (i) matching the chemical shift values of 1Hαi and 13Cαi measured using said RD 3D H,C,C,H-COSY NMR experiment or RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of 1Hα and 13Cα measured by said RD 3D HA,CA,(CO),N,HN NMR experiment and RD 3D HNNCAHA NMR experiment and (ii) using the chemical shift values of 1Halii and 13Calii, to identify the type of amino acid residue i.

67. A method for sequentially assigning chemical shift values of a β-proton, 1Hβ, a β-carbon, 13Cβ, an α-proton, 1Hα, an α-carbon, 13Cα, a polypeptide backbone amide nitrogen, 15N, and a polypeptide backbone amide proton, 1HN, of a protein molecule comprising:

providing a protein sample;

conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, wherein the chemical shift values of 1Hα/β and 13Cα/β which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, comprising: (1) a RD three-dimensional (3D) Hα/βCα/β(CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, 1Hβ1−i, the β-carbon of amino acid residue i−1, 13Cβi−1, the α-proton of amino acid residue i−1, 1Hαi−1, the α-carbon of amino acid residue i−1, 13Cαi−1, the polypeptide backbone amide nitrogen of amino acid residue i, 15Ni, and the polypeptide backbone amide proton of amino acid residue i, 1HNi and (2) a RD 3D Hα/β,Cα/β,N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, 1Hβi, the β-carbon of amino acid residue i, 13Cβi, the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Hβ, 13Cβ, 1Hα, 13Cα, 15N, and 1HN by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1Hα/βi−1, and the α- and β-carbons of amino acid residue i−1, 13Cα/βi−1, with the chemical shift values of 1Hα/βi and 13Cα/βi, (ii) using the chemical shift values of 1Hα/βi−1 and 13Cα/βi, to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using said chemical shift values to locate secondary structure elements within the polypeptide chain.

68. The method according to claim 67 further comprising:

subjecting the protein sample to a RD 3D HA,CA,(CO),N,HN NMR experiment (i) to measure and connect chemical shift values of 1Hαi−1, 13Cαi−1, 15Ni, and 1HNi and (ii) to distinguish between NMR signals for 1Hα/13Cα and 1Hβ/13Cβ measured in said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/β,Cα/βN,HN NMR experiment.

69. The method according to claim 67 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β,CO,HA NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i; and

obtaining sequential assignments of the chemical shift value of 13C′i by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D Hα/β,Cα/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of 1Hβ, 13Cβ, 1Hα, 13Cα, 15N, and 1HN measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/β,Cα/β,N,HN NMR experiment.

70. The method according to claim 67 further comprising:

subjecting the protein sample to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, 13C′i−1, 13Cαi, and 1HNi; and

obtaining sequential assignments of the chemical shift value of 13C′i−1 by matching the chemical shift value of 13Cαi measured by said RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of 13Cα, 15N, and 1HN measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/β,Cα/β,N,HN NMR experiment.

71. The method according to claim 67 further comprising:

subjecting the protein sample to (i) a RD 3D Hα/βCα/β,CO,HA NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of 13C′i, the α-carbon of amino acid residue i+1, 13Cαi+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, 15Ni+1, and the polypeptide backbone amide proton of amino acid residue i+1, 1HNi+1; and

obtaining sequential assignments by matching the chemical shift value of 13C′i measured by said RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of 13C′i measured by said RD 3D Hα/β,Cα/β,CO,HA NMR experiment.

72. The method according to claim 67 further comprising:

subjecting the protein sample to a RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of 1Halii−1, 13Calii−1, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Halii−1 and 13Calii−1 for amino acid residues i having unique pairs of 15Ni and 1HNi chemical shift values by matching the chemical shift values of 1Hβ, 13Cβ, 1Hα, and 13Cα measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/β,Cα/β,N,HN NMR experiment with the chemical shift values of 1Hβi−1, 13Cβi−1, 1Hαi−1, and 13Cαi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and using the 1Halii−1 and 13Calii−1 chemical shift values to identify the type of amino acid residue i−1.

73. The method according to claim 67 further comprising:

subjecting the protein sample to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13Cβi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 13Cβi and 13Cαi measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13Cβi−1 and 13Cαi−1 measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment.

74. The method according to claim 67 further comprising:

subjecting the protein sample to a RD two-dimensional (2D) HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, and a δ-proton of amino acid residue i with an aromatic side chain, 1Hδi; and

obtaining sequential assignments by (i) matching the chemical shift values of 1Hβi and 13Cβi measured by said RD 2D HC,CB, (CG, CD), HDNMR experiment with the chemical shift values of 1Hβ and 13Cβ measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment, (ii) using said chemical shift values to identify amino acid residue i as having an aromatic side chain, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along said polypeptide chain.

75. The method according to claim 67, further comprising:

subjecting the protein sample to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, 1Hali i and aliphatic carbons of amino acid residue i, 13Cali i; and

obtaining sequential assignments of the chemical shift values of 1Halii and 13Calii by (i) matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured using said RD 3D H,C,C,H-COSY NMR experiment or RD 3D H,C,C,H-TOCSY RD NMR experiment with the chemical shift values of 1Hβ, 13Cβ, 1Hα, and 13Cα measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment, and (ii) using the chemical shift values of 1Halii and 13Calii, to identify the type of amino acid residue i.

76. A method for sequentially assigning the chemical shift values of aliphatic protons, 1Hali, aliphatic carbons, 13Cali, a polypeptide backbone amide nitrogen, 15N, and a polypeptide backbone amide proton, 1HN, of a protein molecule comprising:

providing a protein sample;

conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, wherein the chemical shift values of 1Hali and 13Cali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, comprising: (1) a RD three-dimensional (3D) H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, 1Halii−1, the aliphatic carbons of amino acid residue i−1, 13Calii−1, the polypeptide backbone amide nitrogen of amino acid residue i, 15Ni, and the polypeptide backbone amide proton of amino acid residue i, 1HNi and (2) a RD 3D Hα/βCα/β,N,HN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i, 1Hβi, the β-carbon of amino acid residue i, 13Cβi, the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Hali, 13Cali, 15N, and 1HN by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1Hα/βi−1 and the α- and β-carbons of amino acid residue i−1, 13Cα/βi−1 with the chemical shift values of 1Hα/βi and 13Cα/βi of amino acid residue i, (ii) using the chemical shift values of 1Halii−i and 13Calii−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using said chemical shift values to locate secondary structure elements within the polypeptide chain.

77. The method according to claim 76 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β, CO,HA NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i; and

obtaining sequential assignments of the chemical shift value of 13C′i by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D Hα/βCα/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of 1Hβ, 13Cβ, 1Hα, 13Cα, 15N, and 1HN measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment.

78. The method according to claim 76 further comprising:

subjecting the protein sample to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift value of 13C′i−1 by matching the chemical shift value of 13Cαi measured by said RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of 13Cα, 15N, and 1HN measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment.

79. The method according to claim 76 further comprising:

subjecting the protein sample to (i) a RD 3D Hα/βCα/β,CO,HA NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of 13C′i, the α-carbon of amino acid residue i+1, 13Cαi+1, the polypeptide backbone amide nitrogen of amino acid residue i+1, 15Ni+1, and the polypeptide backbone amide proton of amino acid residue i+1, 1HNi+1; and

obtaining sequential assignments by matching the chemical shift value of 13C′i measured by said RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of 13C′i measured by said RD 3D Hα/βCα/β,CO,HA NMR experiment.

80. The method according to claim 76 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β(CO)NHN NMR experiment (i) to measure and connect the chemical shift values of 1Hα/βi−1, 13Cα/βi−1, 15Ni, and 1HNi, and (ii) to identify NMR signals for 1Hα/βi−1, 13Cα/βi−1, 15Ni, and 1HNi in said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

81. The method according to claim 76 further comprising:

subjecting the protein sample to a RD 3D HA,CA,(CO),N,HN NMR experiment (i) to measure and connect chemical shift values of 1Hαi−1, 13Cαi−1, 15Ni, and 1HNi and (ii) to identify NMR signals for 1Hα and 13Cα in said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment.

82. The method according to claim 76 further comprising:

subjecting the protein sample to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13Cβi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 13Cβi and 13Cαi measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13Cβi−1 and 13Cαi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

83. The method according to claim 76 further comprising:

subjecting the protein sample to a RD two-dimensional (2D) HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, and a δ-proton of amino acid residue i with an aromatic side chain, 1Hδi; and

obtaining sequential assignments by matching the chemical shift values of 1Hβi and 13Cβi measured by said RD 2D HB,CB, (CG, CD), HD NMR experiment with the chemical shift values of 1Hβ and 13Cβ measured by said RD 3D Hα/βCα/β,N,HN NMR experiment and RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, using said chemical shift values to identify amino acid residue i as having an aromatic side chain, and mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along said polypeptide chain.

84. The method according to claim 76 further comprising:

subjecting the protein sample to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, 1Halii and aliphatic carbons of amino acid residue i, 13Calii; and

obtaining sequential assignments of the chemical shift values of 1Halii and 13Calii by (i) matching the chemical shift values of 1Halii and 13Calii measured using said RD 3D H,C,C,H-COSY NMR experiment or RD 3D H,C,C,H-TOCSY NMR experiment with the chemical shift values of 1Hali and 13Cali measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D Hα/βCα/β,N,HN NMR experiment, and (ii) using the chemical shift values of 1Halii and 13Calii, to identify the type of amino acid residue i.

85. A method for sequentially assigning chemical shift values of aliphatic protons, 1Hali, aliphatic carbons, 13Cali, a polypeptide backbone amide nitrogen, 15N, and a polypeptide backbone amide proton, 1HN, of a protein molecule comprising:

providing a protein sample;

conducting a set of reduced dimensionality (RD) nuclear magnetic resonance (NMR) experiments on the protein sample, wherein the chemical shift values of 1Hali and 13Cali which are encoded in peak pairs of a 3D NMR spectrum are detected in a phase sensitive manner, comprising: (1) a RD three-dimensional (3D) H,C,(C-TOCSY-CO),N,HN NMR experiment to measure and connect the chemical shift values of the aliphatic protons of amino acid residue i−1, 1Halii−1, the aliphatic carbons of amino acid residue i−1, 13Calii−1, the polypeptide backbone amide nitrogen of amino acid residue i, 15Ni, and the polypeptide backbone amide proton of amino acid residue i, 1HNi and (2) a RD 3D HNNCAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift values of 1Hali, 13Cali, 15N, and 1HN by (i) matching the chemical shift values of the α-proton of amino acid residue i−1, 1Hαi−1, and the α-carbon of amino acid residue i−1, 13Cαi−1, with the chemical shift values of 1Hαi and 13Cαi, (ii) using the chemical shift values of 1Halii−1 and 13Calii−1 to identify the type of amino acid residue i−1, and (iii) mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and using said chemical shift values to locate secondary structure elements within the polypeptide chain.

86. The method according to claim 85 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β, CO,HA NMR experiment to measure and connect the chemical shift values of a β-proton of amino acid residue i, 1Hβi, a β-carbon of amino acid residue i, 13Cβi, 1Hαi, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i; and

obtaining sequential assignments of the chemical shift value of 13C′i by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D Hα/βCα/β,CO,HA NMR experiment with the sequentially assigned chemical shift values of 1Hβ, 13Cβ, 1Hα, 13Cβ, 15N, and 1HN measured by said RD 3D H C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D HNNCAHA NMR experiment.

87. The method according to claim 85 further comprising:

subjecting the protein sample to a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13C′i−1, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments of the chemical shift value of 13C′i−1 by matching the chemical shift value of 13Cαi measured by said RD 3D HNN<CO,CA> NMR experiment with the sequentially assigned chemical shift values of 13Cα, 15N, and 1HN measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D HNNCAHA NMR experiment.

88. The method according to claim 85 further comprising:

subjecting the protein sample to (i) a RD 3D Hα/βCα/β,CO,HA NMR experiment to measure and connect the chemical shift values of a β-proton of amino acid residue i, 1Hβi, a β-carbon of amino acid residue i, 13Cβi, the α-proton of amino acid residue i, 1Hαi, the α-carbon of amino acid residue i, 13Cαi, and a polypeptide backbone carbonyl carbon of amino acid residue i, 13C′i and (ii) a RD 3D HNN<CO,CA> NMR experiment to measure and connect the chemical shift values of 13C′i, an α-carbon of amino acid residue i+1, 13Cαi+1, a polypeptide backbone amide nitrogen of amino acid residue i+1, 15Ni+1, and a polypeptide backbone amide proton of amino acid residue i+1, 1HNi+1; and

obtaining sequential assignments by matching the chemical shift value of 13C′i measured by said RD 3D HNN<CO,CA> NMR experiment with the chemical shift value of 13C′i measured by said RD 3D Hα/β,Cα/β,CO,HA NMR experiment.

89. The method according to claim 85 further comprising:

subjecting the protein sample to a RD 3D Hα/βCα/β(CO)NUN NMR experiment (i) to measure and connect the chemical shift values of the α- and β-protons of amino acid residue i−1, 1Hα/βi−1, α- and β-carbons of amino acid residue i−1, 13Cα/βi−1, 15Ni, and 1HNi, and (ii) to distinguish NMR signals for the chemical shift values of 1Hβi−1, 13Cβi−1, 1Hαi−1, and 13Cαi−1 measured by said RD 3D Hα/βCα/β(CO)NHN NMR experiment from NMR signals for the chemical shift values of 1Halii−1 and 13Calii−1 other than 1Hα/βi−1 and 13Cα/βi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

90. The method according to claim 85 further comprising:

subjecting the protein sample to a RD 3D Hα/β,Cα/β,N,HN NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, 1Hαi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D Hα/βCα/β,N,HN NMR experiment with the chemical shift values of 1Hβi−1, 13Cβi−1, 1Hαi−1, and 13Cαi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

91. The method according to claim 85 further comprising:

subjecting the protein sample to a 3D HNNCACB NMR experiment to measure and connect the chemical shift values of 13Cβi, 13Cαi, 15Ni, and 1HNi; and

obtaining sequential assignments by matching the chemical shift values of 13Cβi and 13Cαi measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13Cβi−1 and 13Cαi−1 measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment.

92. The method according to claim 85 further comprising:

subjecting the protein sample to a RD two-dimensional (2D) HB,CB,(CG,CD),HD NMR experiment to measure and connect the chemical shift values of 1Hβi, 13Cβi, and a δ-proton of amino acid residue i with an aromatic side chain, 1Hδi; and

obtaining sequential assignments by matching the chemical shift values of 1Hβi and 13Cβi measured by said RD 2D HB, CB,(CG, CD), HD NMR experiment with the chemical shift values of 1Hβ and 13Cβ measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment, using said chemical shift values to identify amino acid residue i as having an aromatic side chain, and mapping sets of sequentially connected chemical shift values to the amino acid sequence of the polypeptide chain and locating amino acid residues with aromatic side chains along said polypeptide chain.

93. The method according to claim 85 further comprising:

subjecting the protein sample to a RD 3D H,C,C,H-COSY NMR experiment or a RD 3D H,C,C,H-TOCSY NMR experiment to measure and connect the chemical shift values of aliphatic protons of amino acid residue i, 1Halii and aliphatic carbons of amino acid residue i, 13Calii; and

obtaining sequential assignments of the chemical shift values of 1Halii and 13Calii by (i) matching the chemical shift values of 1Hali and 13Cali measured using said RD 3D H,C,C,H-COSY NMR experiment or RD 3D H,C,C,H-TOCSY NMR experiment with the chemical shift values of 1Hβi, 13Cβi, 1Hαi, and 13Cαi measured by said RD 3D H,C,(C-TOCSY-CO),N,HN NMR experiment and RD 3D HNNCAHA NMR experiment, and (ii) using the chemical shift values of 1Halii and 13Calii, to identify the type of amino acid residue i.