Phase sensitively-detected reduced dimensionality nuclear magnetic resonance spectroscopy for rapid chemical shift assignment and secondary structure determination of proteins

The present invention 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.

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.

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 1 H- 1 H 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 13 C 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 high-throughput (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 13 C, 15 N, 1 H-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. Mann. 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 1 H 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 13 C, 15 N, 1 H-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.

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, 1 H α i−1 ; (2) an α-carbon of amino acid residue i−1, 13 C α i−1 ; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (4) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H α i−1 and 13 C 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 1 H α i−1 and 13 C α i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15 N i and 1 H N i of amino acid residue i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i−1 and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the 13 C α i−1 chemical shift evolution in t 1 ( 13 C α ) with the chemical shift evolution of 1 H 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 15 N i and 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) the chemical shift values of 1 H α i−1 , and 13 C α i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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, 1 H ali i−1 ; (2) aliphatic carbons of amino acid residue i−1, 13 C ali i−1 ; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (4) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H ali i−1 and 13 C 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 1 H ali i−1 and 13 C ali i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15 N i and 1 H N i of amino acid residue i, under conditions effective (1) to generate a NMR signal encoding the chemical shifts of 13 C ali i−1 and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C ali ) and t 2 ( 15 N), respectively, and the chemical shift of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the chemical shift evolutions of 13 C ali i−1 in t 1 ( 13 C ali ) with the chemical shift evolutions of 1 H 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 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) the chemical shift values of 1 H ali i−1 and 13 C ali i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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, 1 H β i ; (2) a β-carbon of amino acid residue i, 13 C β i ; (3) an α-proton of amino acid residue i, 1 H α i ; (4) an α-carbon of amino acid residue i, 13 C α i ; and (5) a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i , where the chemical shift values of 1 H α i / 13 C α i and 1 H β i / 13 C 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 1 H α i , 1 H β i , 13 C α i , and 13 C β i are connected to the chemical shift evolution of 13 C′ i , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i , 13 C β i and 13 C′ i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α/β ) and t 2 ( 13 C′), respectively, and the chemical shift value of 1 H α i in a direct time domain dimension, t 3 ( 1 H α ), and (2) to sine modulate the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C′ i and 1 H α i are measured in two frequency domain dimensions, ω 2 ( 13 C′) and ω 3 ( 1 H α ), respectively, and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 13 C α i and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H α i and 1 H 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, 1 H β i ; (2) a β-carbon of amino acid residue i, 13 C β i ; (3) an α-proton of amino acid residue i, 1 H α i ; (4) an α-carbon of amino acid residue i, 13 C α i ; (5) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (6) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H α i / 13 C α i and 1 H β i / 13 C 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 1 H α i , 1 H β i , 13 C α i , and 13 C β i are connected to the chemical shift evolutions of 15 N i and 1 H N i , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i , 13 C β i and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α/β ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 15 N i and 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 13 C α i and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H α i and 1 H 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 1 H m , 13 C m , 1 H n , and 13 C n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 groups that are linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolutions of 1 H n and 13 C n , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C m and 13 C n in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C m ) and t 2 ( 13 C n ), respectively, and the chemical shift value of 1 H n in a direct time domain dimension, t 3 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C n and 1 H n are measured in two frequency domain dimensions, ω 2 ( 13 C n ) and ω 3 ( 1 H n ), respectively, and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 1 H m , 13 C m , 1 H n , and 13 C n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 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 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolutions of 1 H n and 13 C n , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C m and 13 C n in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C m ) and t 2 ( 13 C n ), and the chemical shift value of 1 H n in a direct time domain dimension, t 3 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C n and 1 H n are measured in two frequency domain dimensions, ω 2 ( 13 C n ) and ω 3 ( 1 H n ), respectively, and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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, 1 H β ; (2) a β-carbon of an amino acid residue with an aromatic side chain, 13 C β ; and (3) a δ-proton of an amino acid residue with an aromatic side chain, 1 H δ , where the chemical shift values of 1 H β and 13 C 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 1 H β and 13 C β are connected to the chemical shift evolution of 1 H δ , under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13 C β in a phase sensitive manner in an indirect time domain dimension, t 1 ( 13 C β ), and the chemical shift value of 1 H δ in a direct time domain dimension, t 2 ( 1 H δ ), and (2) to sine modulate the chemical shift evolution of 13 C β in t 1 ( 13 C β ) with the chemical shift evolution of 1 H 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 1 H δ is measured in a frequency domain dimension, ω 2 ( 1 H δ ), and (2) the chemical shift values of 1 H β and 13 C β are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 1 H m , 13 C m , and 1 H n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 groups in an amino acid residue, where the chemical shift values of 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolution of 1 H n , under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13 C m in a phase sensitive manner in an indirect time domain dimension, t 1 ( 13 C m ), and the chemical shift value of 1 H n in a direct time domain dimension, t 2 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 1 H n is measured in a frequency domain dimension, ω 2 ( 1 H n ), and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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, 1 H α , an α-carbon, 13 C α , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H α and 13 C 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, 1 H α i−1 , the α-carbon of amino acid residue i−1, 13 C α i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H N i and (2) a RD 3D HNN CAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H α , 13 C α , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of 1 H α i−1 and 13 C α i−1 with the chemical shift values of 1 H α i and 13 C α i , (ii) using the chemical shift values of 1 H α i−1 and 13 C 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, 1 H β , a β-carbon, 13 C β , an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H α/β and 13 C 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/β C α/β (CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, 1 H β i−1 , the β-carbon of amino acid residue i−1, 13 C β i−1 , the α-proton of amino acid residue i−1, 1 H α i−1 , the α-carbon of amino acid residue i−1, 13 C α i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H β , 13 C β , 1 H α , 13 C α , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1 H α/β i−1 , and the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , with the chemical shift values of 1 H α/β i and 13 C α/β i , (ii) using the chemical shift values of 1 H α/β i−1 and 13 C 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, 1 H ali , aliphatic carbons, 13 C ali , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H ali and 13 C 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, 1 H ali i−1 , the aliphatic carbons of amino acid residue i−1, 13 C ali i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali , 13 C ali , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1 H α/β i−1 , and the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , with the chemical shift values of 1 H α/β i and 13 C α/β i of amino acid residue i, (ii) using the chemical shift values of 1 H ali i−1 and 13 C 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, 1 H ali , aliphatic carbons, 13 C ali , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H ali and 13 C 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, 1 H ali i−1 , the aliphatic carbons of amino acid residue i−1, 13 C ali i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H N i and (2) a RD 3D HNN CAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali , 13 C ali , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of the α-proton of amino acid residue i−1, 1 H α i−1 , and the α-carbon of amino acid residue i−1, 13 C α i−1 , with the chemical shift values of 1 H α i and 13 C α i , (ii) using the chemical shift values of 1 H ali i−1 and 13 C 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 1 H, 13 C and 15 N 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 1 H and 13 C 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/β C 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 HNN CAHA 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.

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 ω 1 ( 13 C) (bottom) for the cosine-modulated RD NMR experiments implemented for the present invention (the 3D H α/β C α/β (CO)NHN experiment, the 3D HACA (CO)NHN experiment, the 3D HC (C-TOCSY-CO)NHN experiment, the 3D HNN CAHA experiment, the 3D H α/β C α/β COHA experiment, the 3D H α/β C α/β NHN experiment, the 3D HNN< CO , CA > experiment, the 3D HC CH-COSY experiment, the 3D HC CH-TOCSY experiment, the 2D HBCB (CGCD)HD experiment, and the 2D 1 H-TOCSY-relayed- HC H-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 ω 1 , and the nuclei which are detected in quadrature in t 1 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 13 C 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 t 2 and detected on the boxed protons. Except for FIG. 2G , the in-phase splittings 2ΔΩ( 1 H) are equal to 2κ·δΩ( 1 H)[γ( 1 H)/γ( 13 C)], where κ, δΩ( 1 H) and γ(X) denote the scaling factor applied for 1 H chemical shift evolution (set to 1.0 for the present study), the chemical shift difference with respect to the apparent 1 H carrier position, and the gyromagnetic ratio of nucleus X, respectively. In FIG. 2G , the in-phase splittings 2ΔΩ( 13 C α ) are equal to 2κ.δΩ( 13 C α ), where κ and δΩ( 13 C α ) are the scaling factor applied for 13 C α chemical shift evolution 13 (set to 0.5 for the present study) and the chemical shift difference with respect to the apparent 13 C α carrier position, respectively.

FIG. 3A illustrates the experimental scheme for the 3D H α/β C 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, φ 1 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high-power 90° pulse lengths were: 5.9 μs for 1 H, 15.4 μs for 13 C, and 38 μs for 15 N. Pulses on 13 C prior to t 1 ( 13 C) are applied at high power, and 13 C decoupling during t 1 ( 1 H) is achieved using a (90 x -180 y -90 x ) composite pulse. Subsequently, the 90° and 180° pulse lengths applied for 13 C α/β are adjusted to 47.5 μs and 42.5 μs, respectively, to minimize perturbation of 13 CO spins. The width of the 90° pulse applied on 13 CO 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 13 CO during t 1 and τ 4 . 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 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple 15 N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of 13 C α during 15 N evolution period (r.f.=1.0 kHz). The 1 H r.f. carrier is placed at 0 ppm before the start of the semi constant time 1 H chemical shift evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. Initially, the 13 C and 15 N r.f. carriers are set to 43 ppm and 120.9 ppm, respectively. The 13 C carrier is set to 56 ppm during the second τ 4 /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: τ 1 =800 μs, τ 2 =3.1 ms, τ 3 =3.6 ms, τ 4 =7.2 ms, τ 5 =4.4 ms, τ 6 =24.8 ms, τ 7 =24.8 ms, τ 8 =5.5 ms, τ 9 =4.6 ms, τ 10 =1.0 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ 2 =x, x, −x, −x; φ 3 =x, −x; φ 4 =x, −x; φ 5 =x; φ6=x, x, −x, −x; φ 7 =x; φ 8 (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 G 6 is inverted in concert with a 180° shift of φ 7 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 5 , 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 13 C steady state magnetization, a second data set with φ 1 =−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, φ 1 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for 1 H and 15.4 μs for 13 C, and 38 μs for 15 N. Pulses on 13 C prior to t 1 ( 13 C) are applied at high power, and 13 C decoupling during t 1 ( 1 H) is achieved using a (90 x -180 y -90 x ) composite pulse. Subsequently, the 90° and 180° pulse lengths of 13 C α are adjusted to 51.5 μs and 46 μs, respectively, to minimize perturbation of the 13 CO spins. The width of the 90° pulses applied to 13 CO 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 13 CO during t 1 . 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 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple 15 N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of 13 C α during the 15 N chemical shift evolution period (r.f.=1.0 kHz). The 1 H r.f. carrier is placed at 0 ppm before the start of the semi constant time 1 H evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. The 13 C α and 15 N 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: τ 1 =1.6 ms, τ 2 =3.6 ms, τ 3 =4.4 ms, τ 4 =τ 5 =24.8 ms, τ 6 =5.5 ms, τ 7 =4.6 ms, τ 8 =1 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =60 μs, Δt 1 b =35.4 μs, Δt 1 c =−24.6 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ 2 =x, x, −x, −x; φ 3 =x, −x; φ 4 =x; φ 5 =x, x, −x, −x; φ 6 =x; φ 7 (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 φ 6 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 4 , 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 13 C steady state magnetization, a second data set with φ 1 =−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, φ 1 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for 1 H and 15.5 μs for 13 C, and 38 μs for 15 N. Pulses on 13 C prior to t 1 ( 13 C) are applied at high power, and 13 C decoupling during t 1 ( 1 H) is achieved using a (90 x -180 y -90 x ) composite pulse. Subsequently, the 90° and 180° pulse lengths applied for 13 C are adjusted to 47.0 μs and 42.5 μs, respectively, to minimize perturbation of 13 CO spins. The width of the 90° pulses applied to 13 CO 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 13 CO during t 1 and τ 4 period. WALTZ16 is employed to decouple 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple 15 N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of 13 C α during the 15 N chemical shift evolution period (r.f.=1.0 kHz). The 1 H r.f. carrier is placed at 0 ppm before the start of the semi constant time 1 H evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. The 13 C and 15 N r.f. carriers are set to 43 ppm and 120.9 ppm, respectively. The lengths of the 13 C 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. 13 C 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: τ 1 =950 μs, τ 2 =3.1 ms, τ 3 =3.6 ms, τ 4 =7.2 ms, τ 5 =4.45 ms, τ 6 =24.8 ms, τ 7 =24.8 ms, τ 8 =5.5 ms, τ 9 =4.8 ms, τ 10 =1 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ 2 =x, −x; φ 3 =x, x, −x, −x; φ 4 =x, −x; ω 5 =x, x, −x, −x; φ 6 =x, x, −x, −x; φ 7 =x; φ 8 =4x, 4(−x); φ 9 =x; φ 10 (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 φ 9 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 7 , 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 13 C steady state magnetization, a second data set with φ 1 =−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 HNN CAHA 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, φ 8 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The 90° pulse lengths were: 5.8 μs for 1 H and 21.6 μs for 13 C α , and 38 μs for 15 N, where the 90° pulse width for 13 C α is adjusted to generate a null of excitation in the center of the CO chemical shift range. The selective 90° 1 H 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 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple of 15 N (r.f.=1.78 kHz) during acquisition. SEDUCE is used for decoupling of 13 CO (max. r.f.=3.0 kHz). WURST-2 is used for simultaneous band selective decoupling of 13 CO and 13 C β during τ 4 and the 1 H and 13 C chemical shift evolution during t 1 . 3.0 kHz sweeps at 176 ppm and 30 ppm, respectively, are used for decoupling of 13 CO and 13 C β (except for Ser, Thr, Ala). A sweep of 600 Hz is used at 14 ppm to decouple 13 C β of Ala. The 1 H r.f. carrier is placed at the position of the solvent line at 4.78 ppm for the first three 1 H pulses and the first WALTZ period, then switched to 0 ppm during the first delay τ 4 /2, and subsequently switched back to the water line at 4.78 ppm during t 1 c . The 13 C α and 15 N 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: τ 1 =4.6 ms, τ 2 =5.5 ms, τ 3 =24 ms, τ 4 =2.0 ms, τ 5 =500 μs labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.065 ms, t 1 b (0) 49 μs, t 1 a (0)=984 μs, Δt 1 a =65 μs, Δt 1 b =49 μs, Δt 1 c =−16 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.76. Note that the acquisition starts with the second complex point in t 1 , while the first one is obtained by linear prediction. This ensures that a zero first-order phase correction is achieved along ω 1 . Phase cycling: φ 1 =x, −x; φ 2 =x, x, −x, −x; φ 3 =x, −x, −x, x; φ 4 =x; φ 5 =4(x), 4(−x); φ 6 =x; φ 7 (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 φ 6 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 4 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/β C α/β COHA 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, φ 1 =y. The scaling factor κ for the 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.9 μs for 1 H, 15.4 μs for 13 C, and 38.2 μs for 15 N. The 90° and 180° pulse lengths of 13 C α/β were adjusted to 47.4 μs and 42.4 μs, respectively, to minimize perturbation of 13 CO spins. A 200 μs 180° pulse with SEDUCE profile is used to selectively invert 13 CO magnetization prior to the start of t 1 . The 90° and 180° pulses employed for excitation of 13 CO and subsequent magnetization transfer back to 13 C 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 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers, and for decoupling of 15 N (r.f.=1.78 kHz) during acquisition. GARP is used for decoupling of 13 C α (r.f.=2.5 kHz). The 1 H r.f. carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time 1 H evolution period and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. Initially, the 13 C and 15 N 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: τ 1 =800 μs, τ 2 =2.8 ms, τ 3 =3.6 ms, τ 4 =6.5 ms, τ 5 =1.8 ms, τ 6 =1 ms, τ 7 =2.8 ms, τ 8 =3.6 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ x =x, −x; φ 3 =x, −x, x, −x; φ 4 =x; φ 5 (receiver)=x, −x. Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 4 , 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 13 C steady state magnetization, a second data set with φ 1 =−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/β C 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, φ 1 =y. The scaling factor κ for the 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.9 μs for 1 H and 15.4 μs for 13 C, and 38 μs for 15 N. Pulses on 13 C prior to t 1 ( 13 C) are applied at high power, and 13 C decoupling during t 1 ( 1 H) is achieved using a (90 x -180 y -90 x ) composite pulse. Subsequently, the 90° and 180° pulse lengths of 13 C α/β are adjusted to 49 μs and 43.8 μs to minimize perturbation of 13 CO spins. SEDUCE 180° pulses of 200 μs pulse length are used to decouple 13 CO. WALTZ16 is employed to decouple 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers, as well as to decouple 15 N (r.f.=1.78 kHz). The 1 H carrier is placed at the position of the solvent line at 0 ppm during the first semi constant time 1 H evolution period, and then switched to the water line 4.78 ppm after the second 90° 1 H pulse. The 13 C and 15 N 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: τ 1 =800 μs, τ 2 =2.8 ms, τ 3 =3.3 ms, τ 4 =7.2 ms, τ 5 =24 ms, τ 6 =5.4 ms, τ 7 =4.8 ms, τ 8 =1 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ 2 =x; φ 3 =x, −x; φ 4 =x, x, −x, −x; φ 5 =x; φ 6 (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 φ 5 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 3 , respectively, according to States-TPPI. For acquisition of central peaks derived from 13 C steady state magnetization, a second data set with φ 1 =−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 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, φ 3 =y. The scaling factor κ for 13 C α chemical shift evolution during t 2 is set to 0.5. The high power 90° pulse lengths were: 5.8 μs for 1 H and 38.5 μs for 15 N. The 90° and 180° pulse lengths of 13 C α were adjusted 54 μs and 48.8 μs to minimize perturbation of 13 Co spins. The length of the 90° pulses applied on 13 CO 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 1 H 90° pulse used for flip-back of water magnetization is applied for 1.8 ms with the SEDUCE-i profile. WALTZ16 is employed to decouple 1 H (r.f. field strength=9.2 kHz) during the heteronuclear magnetization transfers as well as to decouple 15 N during acquisition (r.f.=1.78 kHz). The SEDUCE sequence is used for decoupling of 13 C′ during 15 N evolution period (r.f. 0.9 kHz). The 13 C α and 15 N 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: τ 1 =4.6 ms, τ 2 =5.5 ms, τ 3 =τ 4 =28 ms, τ 5 =1 ms. Phase cycling: φ 1 =x, x, −x, −x; φ 2 =x, −x, φ 3 =x; φ 4 =x; φ 5 =4(x), 4(−x); φ 6 =x; φ 7 (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 φ 6 . Quadrature detection in t 1 ( 13 C) and t 2 ( 15 N) is accomplished by altering the phases φ 2 and φ 4 , 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 13 C α carrier position to 82.65 ppm, i.e., downfield to all 13 C α resonances, φ 3 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 ω 1 ( 13 CO) were obtained by linear prediction. This ensures that a zero first-order phase correction is achieved along ω 1 (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 HC CH-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, φ 1 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for 1 H and 15.4 μs for 13 C, and 38 μs for 15 N. The lengths of the 1 H 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 13 CO during t 1 and t 2 (r.f. field strength=1 kHz). WURST is used for decoupling of 13 C during acquisition. The 1 H carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time 1 H evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. The 13 C and 15 N 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: τ 1 =1.6 ms, τ 2 =850 μs, τ 3 =2.65 ms, τ 4 =3.5 ms, τ 5 =7 ms, τ 6 =1.6 ms, τ 7 =3.2 ms. Phase cycling: φ 1 =x; φ 2 =x, −x; φ 3 =x, −x; φ 4 =x; φ 5 (receiver)=x, −x. Quadrature detection in t 1 ( 13 C) and t 2 ( 13 C) is accomplished by altering the phases φ 1 and φ 3 , 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 13 C steady state magnetization, a second data set with φ 1 =−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 HC CH-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, φ 1 =y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for 1 H and 15.4 μs for 13 C, and 38 μs for 15 N. 13 C decoupling during t 1 ( 1 H) is achieved using a (90 x -180 y -90 x ) composite pulse. The lengths of the 1 H 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 13 CO during t 1 and t 2 (r.f. field strength=1 kHz), and GARP is employed for decoupling of 13 C during acquisition (r.f.=2.5 kHz). The 1 H r.f. carrier is placed at the position of the solvent line at 0 ppm before the start of the first semi constant time 1 H evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. The 13 C α and 15 N r.f. carriers are set to 38 ppm and 120.9 ppm, respectively. The length of 13 C spin-lock purge pulses denoted SL x are of 2 ms duration. 13 C 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: τ 1 =850 μs, τ 2 =3.2 ms. 1 H-frequency labeling in t 1 is achieved in a semi constant-time fashion with t 1 a (0)==1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. 13 C-frequency labeling in t 2 is achieved in a semi constant-time fashion with t 2 a (0)=1120 μs, t 2 b (0)=62.5 μs, t 2 c (0)=995 μs, Δt 2 b =125 μs, Δt 2 c =−35 μs. These delays ensure that a 90° first-order phase correction is obtained along ω 2 ( 13 C). The fractional increases of the semi constant-time period in t 1 equals to λ=1+Δt 2 c /Δt 2 a =0.58, and in t 2 equals to λ=1+Δt 2 c /Δt 2 a =0.78. Phase cycling: φ 1=x; φ 2 =x, −x; φ 3 =x; φ 4 =2(x), 2(−x); φ 5 (receiver)=x,−x. Quadrature detection in t 1 ( 13 C) and t 2 ( 13 C) is accomplished by altering the phases φ 2 and φ 3 , 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 13 C steady state magnetization, a second data set with φ 1 =−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, 4)=y. The scaling factor κ for 1 H chemical shift evolution during t 1 is set to 1.0. The high power 90° pulse lengths were: 5.8 μs for 1 H and 15.4 μs for 13 C. The first 180° pulse on 13 C prior to t 1 ( 13 C) is applied at high power. Subsequently, the 90° pulse lengths of 13 C β is adjusted to 66 μs. The 180° 13 C β and 13 C aro pulses are of gaussian-3 shape and 375 μs duration. WALTZ16 is used for decoupling of 1 H (r.f. field strength=4.5 kHz) during the magnetization transfer from 13 C α to 13 C aro , and GARP is employed to decouple 13 C aro (r.f.=2.5 kHz) during acquisition. The 1 H r.f. carrier is placed at 0 ppm before the start of the semi constant time 1 H evolution period, and then switched to the water line at 4.78 ppm after the second 90° 1 H pulse. The 13 C r.f. carrier is set to 38 ppm during ω 1 ( 13 C β ) and then switched to 131 ppm before the first 90° pulse on 13 C aro (pulse labeled with φ 4 ). 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: τ 1 =1.8 ms, τ 2 =8.8 ms, τ 3 =71 μs, τ 4 =5.4 ms, τ 5 =4.2 ms, τ 6 =710 μs, τ 7 =2.5 ms. 1 H-frequency labeling is achieved in a semi constant-time fashion with t 1 a (0)=1.7 ms, t 1 b (0)=1 μs, t 1 c (0)=1.701 ms, Δt 1 a =33.3 μs, Δt 1 b =19.3 μs, Δt 1 c =−14 μs. Hence, the fractional increase of the semi constant-time period with t 1 equals to λ=1+Δt 1 c /Δt 1 a =0.58. Phase cycling: φ 1 =x; φ 2 =x; φ 3 =x, y, −x, −y; φ 4 =4(x), 4(−x); φ 5 (receiver)=x, −x, x, −x, −x, x, −x, x. Quadrature detection in t 1 ( 13 C) is accomplished by altering the phases φ 2 respectively, according to States-TPPI. For acquisition of central peaks derived from 13 C steady state magnetization, a second data set with φ 1 =−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 1 H-TOCSY-relayed- HC H-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, φ 6 =y. The high-power 90° pulse lengths were: 5.9 μs for 1 H and 15.4 μs for 13 C. The 1 H r.f. carrier is placed at the position of the solvent line at 4.78 ppm, and the 13 C carrier is set to 131 ppm. GARP is used for 13 C decoupling during acquisition (r.f. field strength=2.5 kHz), and 1 H 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: τ 1 =3.0 ms, τ 2 =15.38 ms. Phase cycling: φ 1 =x, −x; φ 2 =x, x, y, y, −x, −x, −y, −y; φ 3 =4(x), 4(y), 4(−x), 4(−y); φ 4 =x, x, −x, −x; φ 5 (receiver)=x, −x, x, −x, −x, x, −x, x. Quadrature detection in t 1 ( 13 C) is accomplished by altering the phase φ 1 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 [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H 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(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C α ; 1 H α )=6.5 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H N )=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 15 N chemical shift (113.8 ppm) of Asp 50 along φ 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS).

FIG. 6 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H N )]-strips taken from 3D HNN CAHA spectrum obtained for Z-domain protein with a total measurement time of 10.7 hours. The 3D NMR data were acquired with 64(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C α ; 1 H α )=12.1 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H 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 13 C 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 15 N chemical shift (117.4 ppm) of Leu 35 along ω 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to DSS.

FIG. 7 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H N )]-strips taken from 3D H α/β C 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(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C α/β ; 1 H α/β )=6.25 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H N )=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 15 N chemical shift (117.4 ppm) of Leu 35 along ω 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to DSS.

FIG. 8 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H N )]-strips taken from 3D H α/β C α/β NHN spectrum obtained for Z-domain protein with a total measurement time of 11.4 hours. The 3D NMR data were acquired with 68(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C α/β ; 1 H α/β )=5.6 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H N )=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 15 N chemical shift (117.4 ppm) of Leu 35 along ω 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to DSS.

FIG. 9 shows a composite plot of [ω 1 ( 13 C′/ 13 C α ),ω 3 ( 1 H 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(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C′; 13 C α )=6.9 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H N )=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 15 N chemical shift (170.0 ppm) of Phe 43 along ω 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to DSS.

FIG. 10 shows a composite plot of [ω 1 ( 13 C/ 1 H), ω 3 ( 1 H 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(t 1 )×28(t 2 )×512(t 3 ) complex points and t 1max ( 13 C; 1 H)=6.3 ms, t 2max ( 15 N)=20.8 ms, and t 3max ( 1 H N )=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 15 N chemical shift (118.8 ppm) of Phe 18 along ω 2 ( 15 N) and centered about the corresponding amide proton shifts detected along ω 3 ( 1 H N ). 1 H, 13 C, and 15 N chemical shifts are in ppm relative to DSS.

FIG. 11 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H β )]-strips taken from 3D HC CH-COSY spectrum obtained for Z-domain protein with a total measurement time of 10.8 hours. The 3D NMR data were acquired with 90(t 1 )×20(t 2 )×512(t 3 ) complex points and t 1max ( 13 C; 1 H)=7.4 ms, t 2max ( 13 C)=6.1 ms, and t 3max ( 1 H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 13 C β chemical shift (37.8 ppm) of Asn 19 along ω 2 ( 13 C) and centered about the corresponding proton ( 1 H β ) shifts detected along ω 3 ( 1 H). 1 H and 13 C chemical shifts are in ppm relative to DSS.

FIG. 12 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H β )]-strips taken from 3D HC CH-TOCSY spectrum obtained for Z-domain protein with a total measurement time of 11.0 hours. The 3D NMR data were acquired with 80(t 1 )×20(t 2 )×512(t 3 ) complex points and t 1max ( 13 C; 1 H)=6.6 ms, t 2max ( 13 C)=6.1 ms, and t 3max ( 1 H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 13 C β chemical shift (37.8 ppm) of Asn 36 along ω 2 ( 13 C) and centered about the corresponding proton ( 1 H β ) shifts detected along ω 3 ( 1 H). 1 H and 13 C chemical shifts are in ppm relative to DSS.

FIG. 13 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H 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(t 1 )×512(t 2 ) complex points and t 1max ( 13 C; 1 H)=6.3 ms and t 2max ( 1 H)=73.2 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from steady state 13 C 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 ( 1 H δ ) shifts of Phe 18 detected along ω 2 ( 1 H). 1 H and 13 C chemical shifts are in ppm relative to DSS.

FIG. 14 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H α )]-strips taken from 3D H α/β C α/β COHA spectrum obtained for ubiquitin protein with a total measurement time of 12.7 hours. The 3D NMR data were acquired with 76(t 1 )×32(t 2 )×512(t 3 ) complex points and t 1max ( 13 C α/β ; 1 H α/β )=6.3 ms, t 2max ( 13 C′)=ms, and t 3max ( 1 H α )=72.8 ms. Data acquisition and processing were performed as shown in FIG. 1 . The central peaks were acquired from the steady state 13 C 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 13 C′ chemical shift (175.2 ppm) of Pro 19 along ω 2 ( 13 C′) and centered about the corresponding proton shifts detected along ω 3 ( 1 H α ). 1 H and 13 C chemical shifts are in ppm relative to DSS.

FIG. 15 shows a composite plot of [ω 1 ( 13 C/ 1 H),ω 3 ( 1 H)]-strips taken from 2D H-TOCSY- HC H-COSY spectrum obtained for ubiquitin protein with a total measurement time of 1.4 hours. The 2D NMR data were acquired with 100(t 1 )×512(t 2 ) complex points and t 1max ( 13 C; 1 H)=9.9 ms and t 2max ( 1 H)=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 ω 1 ( 1 H). 1 H and 13 C chemical shifts are in ppm relative to DSS.

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/β C 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 HNN CAHA ( FIG. 2D ), 3D H α/β C α/β COHA ( FIG. 2E ), and 3D H α/β C α/β NHN ( FIG. 2F ). 3D HNN< CO , CA > ( FIG. 2G ) offers both intraresidual 1 H N - 13 C α and sequential 1 H N - 13 C′ connectivities. Although 3D HNN CAHA ( FIG. 2D ), 3D H α/β C α/β NHN ( FIG. 2F ) and 3D HNN< CO , CA > ( FIG. 2G ) also provide sequential connectivities via two-bond 13 C α i−1 - 15 N 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 HC CH-COSY ( FIG. 2H ) and 3D HC CH-TOCSY ( FIG. 2I ) allow one to obtain assignments for the “aliphatic” side chain spin systems, while 2D HBCB (CDCG)HD ( FIG. 2J ) and 2D 1 H-TOCSY-relayed HC H-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.

The 3D H,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, 1 H α i−1 ; (2) an α-carbon of amino acid residue i−1, 13 C α i−1 ; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (4) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H α i−1 and 13 C 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 1 H α i−1 and 13 C α i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15 N i and 1 H N i of amino acid residue i, under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i−1 and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the 13 C α i'1 chemical shift evolution in t 1 ( 13 C α ) with the chemical shift evolution of 1 H 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 15 N i and 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) the chemical shift values of 1 H α i−1 and 13 C α i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 13 C α i−1 and 15 N i in a phase sensitive manner in t 1 ( 13 C α ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in t 3 ( 1 H N ) and (2) to cosine modulate the 13 C α i−1 chemical shift evolution in t 1 ( 13 C α ) with the chemical shift evolution of 1 H 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 13 C α i−1 and 15 N i in a phase sensitive manner in t 1 ( 13 C α ) and t 2 ( 15 N) and the chemical shift value of 1 H N i in t 3 ( 1 H N ), and (2) to avoid sine modulating the 13 C α i−1 chemical shift evolution in t 1 ( 13 C α ) with the chemical shift evolution of 1 H 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 13 C α i−1 along ω 1 ( 13 C α ). That additional peak can be derived from 13 C 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 1 H α i−1 magnetization, which is transferred to 13 C α i−1 , to 15 N i , and to 1 H 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 φ 1 of the first 1 H 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 RD 2D HA , CA ,(CO,N),HN NMR experiment which involves applying radiofrequency pulses so that the chemical shift evolution of 15 N 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 1 H N i is measured in a frequency domain dimension, ω 2 ( 1 H N ), and (2) the chemical shift values of 1 H α i−1 and 13 C α i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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, 13 C′ i−1 , occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13 C′ i−1 in a phase sensitive manner in an indirect time domain dimension, t 4 ( 13 C′). 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 15 N i , 1 H N i and 13 C′ i−1 are measured in three frequency domain dimensions, ω 2 ( 15 N), ω 3 ( 1 H N ), and ω 4 ( 13 C′), respectively, and (2) the chemical shift values of 1 H α i−1 and 13 C α i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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, 1 H ali i−1 ; (2) aliphatic carbons of amino acid residue i−1, 13 C ali i−1 ; (3) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (4) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H ali i−1 and 13 C 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 1 H ali i−1 and 13 C ali i−1 of amino acid residue i−1 are connected to the chemical shift evolutions of 15 N i and 1 H N i of amino acid residue i, under conditions effective (1) to generate a NMR signal encoding the chemical shifts of 13 C ali i−1 and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C ali ) and t 2 ( 15 N), respectively, and the chemical shift of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the chemical shift evolutions of 13 C ali i−1 in t 1 ( 13 C ali ) with the chemical shift evolutions of 1 H ali i . 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 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) the chemical shift values of 1 H ali i−1 and 13 C ali i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 13 C ali i−1 and 15 N i in a phase sensitive manner in t 1 ( 13 C ali ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in t 3 ( 1 H N ) and (2) to cosine modulate the chemical shift evolutions of 13 C ali i−1 in t 1 ( 13 C ali ) with the chemical shift evolutions of 1 H 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 13 C ali i−1 and 15 N i in a phase sensitive manner in t 1 ( 13 C ali ) and t 2 ( 15 N) and the chemical shift value of 1 H N i in t 3 ( 1 H N ), and (2) to avoid sine modulating the chemical shift evolutions of 13 C ali i−1 in t 1 ( 13 C ali ) with the chemical shift evolution of 1 H 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 13 C ali i−1 along ω 1 ( 13 C ali ). Those additional peaks can be derived from 13 C 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 1 H ali i−1 magnetization, and 1 H ali i−1 magnetization is transferred to 13 C ali i−1 , to 13 C α i−1 , to 13 C′ i−1 , to 15 N i , and to 1 H 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 φ 1 of the first 1 H 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 15 N 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 1 H N i is measured in a frequency domain dimension, ω 2 ( 1 H N ), and (2) the chemical shift values of 1 H ali i−1 and 13 C ali i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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 radio-frequency pulses so that the chemical shift evolution of a polypeptide backbone carbonyl carbon of amino acid residue i−1, 13 C′ i−1 , occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13 C′ i−1 in a phase sensitive manner in an indirect time domain dimension, t 4 ( 13 C′). 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 15 N i , 1 H N i and 13 C′ i−1 are measured in three frequency domain dimensions, ω 2 ( 15 N), ω 3 ( 1 H N ), and ω 4 ( 13 C′), respectively, and (2) the chemical shift values of 1 H ali i−1 and 13 C ali i−1 are measured in a frequency domain dimension, ω 1 ( 13 C 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, 1 H β i ; (2) a β-carbon of amino acid residue i, 13 C β i ; (3) an α-proton of amino acid residue i, 1 H α i ; (4) an α-carbon of amino acid residue i, 13 C α i ; and (5) a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i , where the chemical shift values of 1 H α i / 13 C α i and 1 H β i / 13 C 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 1 H α i , 1 H β i , 13 C α i , and 13 C β i are connected to the chemical shift evolution of 13 C′ i , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i , 13 C β i and 13 C′ i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α/β ) and t 2 ( 13 C′), respectively, and the chemical shift value of 1 H α i in a direct time domain dimension, t 3 ( 1 H α ), and (2) to sine modulate the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C′ i and 1 H α i are measured in two frequency domain dimensions, ω 2 ( 13 C′) and ω 3 ( 1 H α ), respectively, and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 13 C α i and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H α i and 1 H 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 13 C α i , 13 C β i and 13 C′ i in a phase sensitive manner in t 1 ( 13 C α/β ) and t 2 ( 13 C′), respectively, and the chemical shift value of 1 H α i in t 3 ( 1 H α ) and (2) to cosine modulate the 13 C α i and 13 C β i chemical shift evolutions in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C α i , 13 C β i and 15 N i in a phase sensitive manner in t 1 ( 13 C α/β ) and t 2 ( 15 N) and the chemical shift value of 1 H α i in t 3 ( 1 H α ), and (2) to avoid cosine modulating the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C α i and 13 C β i along ω 1 ( 13 C α/β ). Those additional peaks can be derived from 13 C α and 13 C β nuclear spin polarization. One specific embodiment (3D H α/β C α/β COHA) 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 1 H α i and 1 H β i magnetization, and 1 H α i and 1 H β i polarization is transferred to 13 C α i and 13 C β i , to 13 C′ i , and back to 1 H 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 φ 1 of the first 1 H 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 13 C′ 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 1 H α i is measured in a frequency domain dimension, ω 2 ( 1 H α ), and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C α/β ), by the frequency differences between two peaks forming the peak pairs, respectively, and (ii) the chemical shift values of 13 C α i , and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C 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, 1 H β i ; (2) a β-carbon of amino acid residue i, 13 C β i ; (3) an α-proton of amino acid residue i, 1 H α i ; (4) an α-carbon of amino acid residue i, 13 C α i ; (5) a polypeptide backbone amide nitrogen of amino acid residue i, 15 N i ; and (6) a polypeptide backbone amide proton of amino acid residue i, 1 H N i , where the chemical shift values of 1 H α i / 13 C α i and 1 H β i / 13 C 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 1 H α i , 1 H β i , 13 C α i , and 13 C β i are connected to the chemical shift evolutions of 15 N i and 1 H N i , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C α i , 13 C β i and 15 N i in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C α/β ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in a direct time domain dimension, t 3 ( 1 H N ), and (2) to sine modulate the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 15 N i and 1 H N i are measured in two frequency domain dimensions, ω 2 ( 15 N) and ω 3 ( 1 H N ), respectively, and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 13 C α i and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H α i and 1 H 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 13 C α i , 13 C β i and 15 N i in a phase sensitive manner in t 1 ( 13 C α/β ) and t 2 ( 15 N), respectively, and the chemical shift value of 1 H N i in t 3 ( 1 H N ) and (2) to cosine modulate the 13 C α i and 13 C β i chemical shift evolutions in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C α i , 13 C β i and 15 N i in a phase sensitive manner in t 1 ( 13 C α/β ) and t 2 ( 15 N) and the chemical shift value of 1 H N i in t 3 ( 1 H N ), and (2) to avoid cosine modulating the chemical shift evolutions of 13 C α i and 13 C β i in t 1 ( 13 C α/β ) with the chemical shift evolutions of 1 H α i and 1 H 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 13 C α i and 13 C β i along ω 1 ( 13 C α/β ). Those additional peaks can be derived from 13 C α and 13 C β nuclear spin polarization. One specific embodiment (3D H α/β C α/β NHN) 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 1 H α i and 1 H β i magnetization, and 1 H α i and 1 H β i magnetization is transferred to 13 C α i and 13 C β i , to 15 N i , and to 1 H 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 φ 1 of the first 1 H 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 15 N 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 1 H N i is measured in a frequency domain dimension, ω 2 ( 1 H N ), and (2) (i) the chemical shift values of 1 H α i and 1 H β i are measured in a frequency domain dimension, ω 1 ( 13 C α/β ), by the frequency differences between the two peaks forming the peak pairs, and (ii) the chemical shift values of 13 C α i , and 13 C β i are measured in a frequency domain dimension, ω 1 ( 13 C α/β ), by the frequencies at the center of the two peaks forming the peak pairs.

The 3D H , C ,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 1 H m , 13 C m , 1 H n , and 13 C n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 groups that are linked by a single covalent carbon-carbon bond in an amino acid residue, where the chemical shift values of 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolutions of 1 H n and 13 C n , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C m and 13 C m in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C m ) and t 2 ( 13 C n ), respectively, and the chemical shift value of 1 H n in a direct time domain dimension, t 3 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C n and 1 H n are measured in two frequency domain dimensions, ω 2 ( 13 C n ) and ω 3 ( 1 H n ), respectively, and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 13 C m and 13 C n in a phase sensitive manner in t 1 ( 13 C m ) and t 2 ( 13 C n ), respectively, and the chemical shift value of 1 H n in t 3 ( 1 H n ), and (2) to cosine modulate the 13 C m chemical shift evolution in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C m and 13 C n in a phase sensitive manner in t 1 ( 13 C m ) and t 2 ( 13 C n ) and the chemical shift value of 1 H n in t 3 ( 1 H), and (2) to avoid cosine modulating the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C m along ω 1 ( 13 C m ). Those additional peaks can be derived from 13 C m nuclear spin polarization. One specific embodiment (3D HC CH-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 1 H m magnetization, and 1 H m magnetization is transferred to 13 C m , to 13 C n , and to 1 H n , 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 φ 1 of the first 1 H 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 13 C n 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 1 H n is measured in a frequency domain dimension, ω 2 ( 1 H n ), and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H m , 13 C m , 1 H n , and 13 C n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 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 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolutions of 1 H n and 13 C n , under conditions effective (1) to generate NMR signals encoding the chemical shift values of 13 C m and 13 C n in a phase sensitive manner in two indirect time domain dimensions, t 1 ( 13 C m ) and t 2 ( 13 C n ), and the chemical shift value of 1 H n in a direct time domain dimension, t 3 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in ω 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C n and 1 H n are measured in two frequency domain dimensions, ω 2 ( 13 C n ) and ω 3 ( 1 H n ), respectively, and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 13 C m and 13 C n in a phase sensitive manner in t 1 ( 13 C m ) and t 2 ( 13 C n ), respectively, and the chemical shift value of 1 H n in t 3 ( 1 H n ) and (2) to cosine modulate the 13 C m chemical shift evolution in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C m and 13 C n in a phase sensitive manner in t 1 ( 13 C m ) and t 2 ( 13 C n ) and the chemical shift value of 1 H n in t 3 ( 1 H n ), and (2) to avoid cosine modulating the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 13 C m along ω 1 ( 13 C m ). Those additional peaks can be derived from 13 C m nuclear spin polarization. One specific embodiment (3D HC CH-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 1 H m magnetization, and 1 H m magnetization is transferred to 13 C m , to 13 C n , and to 1 H n , 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 φ 1 of the first 1 H 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 13 C n 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 1 H n is measured in a frequency domain dimension, ω 2 ( 1 H n ), and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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, 1 H β ; (2) a β-carbon of an amino acid residue with an aromatic side chain, 13 C β ; and (3) a δ-proton of an amino acid residue with an aromatic side chain, 1 H δ , where the chemical shift values of 1 H β and 13 C 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 1 H β and 13 C β are connected to the chemical shift evolution of 1 H δ , under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13 C β in a phase sensitive manner in an indirect time domain dimension, t 1 ( 13 C β ), and the chemical shift value of 1 H δ in a direct time domain dimension, t 2 ( 1 H δ ), and (2) to sine modulate the chemical shift evolution of 13 C β in t 1 ( 13 C β ) with the chemical shift evolution of 1 H 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 1 H δ is measured in a frequency domain dimension, ω 2 ( 1 H δ ), and (2) the chemical shift values of 1 H β and 13 C β are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 radio-frequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of 13 C β in a phase sensitive manner in t 1 ( 13 C β ) and the chemical shift value of 1 H δ in t 2 ( 1 H δ ) and (2) to cosine modulate the 13 C β chemical shift evolution in t 1 ( 13 C β ) with the chemical shift evolution of 1 H 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 radio-frequency pulses under conditions effective (1) to generate additional NMR signals encoding the chemical shift value of 13 C β in a phase sensitive manner in t 1 ( 13 C β ) and the chemical shift value of 1 H δ in t 2 ( 1 H δ ), and (2) to avoid cosine modulating the chemical shift evolution of 13 C β in t 1 ( 13 C β ) with the chemical shift evolution of 1 H 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 13 C β along ω 1 ( 13 C). That additional peak can be derived from 13 C 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 1 H β magnetization, and 1 H β magnetization is transferred to 13 C β , to 13 C δ , and to 1 H 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 φ 1 of the first 1 H 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 δ-carbon of an amino acid residue with an aromatic side chain, 13 C δ occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13 C δ in a phase sensitive manner in an indirect time domain dimension, t 3 ( 13 C 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 1 H δ and 13 C δ are measured in two frequency domain dimensions, ω 2 ( 1 H δ ) and ω 3 ( 13 C δ ), respectively, and (2) the chemical shift values of 1 H β and 13 C β are measured in a frequency domain dimension, ω 1 ( 13 C 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, 13 C γ occurs under conditions effective to generate NMR signals encoding the chemical shift value of 13 C δ in a phase sensitive manner in an indirect time domain dimension, t 3 ( 13 C 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 1 H δ and 13 C γ are measured in two frequency domain dimensions, ω 2 ( 1 H δ ) and ω 3 ( 13 C γ ), respectively, and (2) the chemical shift values of 1 H β and 13 C β are measured in a frequency domain dimension, ω 1 ( 13 C 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 ,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 1 H m , 13 C m , and 1 H n of a protein molecule where m and n indicate atom numbers of two CH, CH 2 or CH 3 groups in an amino acid residue, where the chemical shift values of 1 H m and 13 C 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 1 H m and 13 C m are connected to the chemical shift evolution of 1 H n , under conditions effective (1) to generate NMR signals encoding the chemical shift value of 13 C m in a phase sensitive manner in an indirect time domain dimension, t 1 ( 13 C m ), and the chemical shift value of 1 H n in a direct time domain dimension, t 2 ( 1 H n ), and (2) to sine modulate the chemical shift evolution of 13 C m in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 1 H m is measured in a frequency domain dimension, ω 2 ( 1 H n ), and (2) the chemical shift values of 1 H m and 13 C m are measured in a frequency domain dimension, ω 1 ( 13 C 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 1 H 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 13 C m in a phase sensitive manner in t 1 ( 13 C m ) and the chemical shift value of 1 H n in t 2 ( 1 H n ) and (2) to cosine modulate the 13 C m chemical shift evolution in t 1 ( 13 C m ) with the chemical shift evolution of 1 H 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 1 H-TOCSY- HC H-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 1 H m magnetization, and 1 H m polarization is transferred to 13 C m , to 1 H m , and to 1 H n , 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, 1 H α , an α-carbon, 13 C α , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H α and 13 C 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, 1 H α i−1 , the α-carbon of amino acid residue i−1, 13 C α i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H N i and (2) a RD 3D HNN CAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H α , 13 C α , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of 1 H α i−1 and 13 C α i−1 with the chemical shift values of 1 H α i and 13 C α i , (ii) using the chemical shift values of 1 H α i−1 and 13 C 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 HNN CAHA 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, 13 C′ i−1 , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift value of 13 C′ i−1 , are obtained by matching the chemical shift value of 13 C α i measured by the RD 3D HNN< CO , CA > NMR experiment with the sequentially assigned chemical shift values of 13 C α , 15 N, and 1 H N measured by the RD 3D HA , CA ,(CO),N,HN NMR experiment and the RD 3D HNN CAHA 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 HNN CAHA 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i , and (ii) a RD 3D HNN< CO , CA > NMR experiment to measure and connect the chemical shift values of 13 C′ i , the α-carbon of amino acid residue i+1, 13 C α i+1 , the polypeptide backbone amide nitrogen of amino acid residue i+1, 15 N i+1 , and the polypeptide backbone amide proton of amino acid residue i+1, 1 H N i+1 . Then, sequential assignments are obtained by matching the chemical shift value of 13 C′ i measured by the RD 3D HNN< CO , CA > NMR experiment with the chemical shift value of 13 C′ 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 HA , CA ,(CO),N,HN NMR experiment and the RD 3D HNN CAHA 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, 1 H ali i−1 , aliphatic carbons (including α-, β-, and γ-carbons) of amino acid residue i−1, 13 C ali i−1 , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali i−1 and 13 C ali i−1 for amino acid residues i having unique pairs of 15 N i and 1 H N i chemical shift values are obtained by matching the chemical shift values of 1 H α and 13 C α measured by said RD 3D HNN CAHA NMR experiment and RD 3D HA , CA ,(CO),N,HN NMR experiment with the chemical shift values of 1 H α i−1 and 13 C α i−1 measured by said RD 3D H , C ,(C-TOCSY-CO),N,HN NMR experiment and using the H ali i−1 and 13 C 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 HNN CAHA 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 1 H ali i and 13 C ali i of amino acid residue i. Then, sequential assignments of the chemical shift values of 1 H ali i and 13 C ali i , the chemical shift values of a γ-proton, 1 H γ i , and a γ-carbon, 13 C γ i , in particular, are obtained by (i) matching the chemical shift values of 1 H α i and 13 C 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 1 H α i and 13 C β i measured by the RD 3D HA , CA ,(CO),N,HN NMR experiment, the RD 3D HNN CAHA NMR experiment, and the RD 3D H α/β C α/β (CO)NHN NMR experiment and (ii) using the chemical shift values of 1 H ali and 13 C ali , including the chemical shift values of 1 H γ i and 13 C 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 HNN CAHA NMR experiment, further subjecting the protein sample to a RD 3D H α/β C α/β (CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, 1 H β i− , the β-carbon of amino acid residue i−1, 13 C β i−1 , 1 H α i−1 , 13 C α i−1 , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H β and 13 C β are obtained by using the chemical shift values of 1 H β i−1 and 13 C 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 HNN CAHA NMR experiment, and the RD 3D H α/β C 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i . Then, sequential assignments of the chemical shift value of 13 C′ i are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β , 13 C β , 1 H α , 13 C α , 15 N, and 1 H N measured by the RD 3D HA , CA ,(CO),N,HN NMR experiment, the RD 3D HNN CAHA NMR experiment, and the RD 3D H α/β C 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 HNN CAHA NMR experiment, and the RD 3D H α/β C 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 1 H β i , 13 C β i , 1 H α i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C α i with the chemical shift values of 1 H β i−1 , 13 C β i−1 , 1 H α i−1 , and 13 C α i−1 measured by the RD 3D H α/β C 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 HNN CAHA NMR experiment, and the RD 3D H α/β C α/β (CO)NHN NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13 C β i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 13 C β i and 13 C α i measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13 C β i−1 and 13 C α i−1 measured by the RD 3D H α/β C 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 HNN CAHA NMR experiment, and the RD 3D H α/β C 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 1 H β i−1 , 13 C β i−1 , and a δ-proton of amino acid residue I−1 with an aromatic side chain, 1 H δ i−1 . Then, sequential assignments are obtained by matching (i) the chemical shift values of 1 H β i−1 and 13 C β i−1 measured by said RD 2D HB , CB ,(CG,CD),HD NMR experiment with the chemical shift values of 1 H β and 13 C β measured by the RD 3D H α/β C 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 HNN CAHA NMR experiment, and the RD 3D H α/β C 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 δ-protons) of amino acid residue i, 1 H α i , and aliphatic carbons (including α-, β-, and δ-carbons) of amino acid residue i, 13 C ali i , of amino acid residue i. Then, sequential assignments of the chemical shift values of 1 H ali i and 13 C ali i , the chemical shift values of a γ-proton, 1 H γ , and a γ-carbon, 13 C γ , in particular, are obtained by (i) matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β i , 13 C β i , 1 H α i , and 13 C α i measured by the RD 3D HA , CA ,(CO),N,HN NMR experiment, the RD 3D HNN CAHA NMR experiment, and the RD 3D H α/β C α/β (CO)NHN NMR experiment and (ii) using the chemical shift values of 1 H ali and 13 C ali , including the chemical shift values of 1 H δ and 13 C 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, 1 H β , a β-carbon, 13 C β , an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H α/β and 13 C 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/β C α/β (CO)NHN NMR experiment to measure and connect the chemical shift values of the β-proton of amino acid residue i−1, 1 H β i−1 , the β-carbon of amino acid residue i−1, 13 C β i−1 , the α-proton of amino acid residue i−1, 1 H α i−1 , the α-carbon of amino acid residue i−1, 13 C α i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H β i , the β-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H β , 13 C β , 1 H α , 13 C α , 15 N, and 1H N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1 H α/β i−1 , and the chemical shift values of the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , with 1 H α/β i and 13 C α/β i , (ii) using 1 H α/β i−1 and 13 C 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/β C 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 1 H α i−1 , 13 C α i−1 , 15 N i , and 1 H N i and (ii) to distinguish between NMR signals for 1 H α / 13 C α and 1 H β / 13 C β measured in the RD 3D H α/β C 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/β C 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/β , C α/β ,CO,HA NMR experiment to measure and connect the chemical shift values of 1 H β i , 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i . Then, sequential assignments of the chemical shift value of 13 C′ i are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β , 13 C β , 1 H α , 13 C α , 15 N, and 1 H N measured by the RD 3D H α/β C 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/β C 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, 13 C′ i−1 , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift value of 13 C′ i−1 are obtained by matching the chemical shift value of 13 C α i measured by the RD 3D HNN< CO , CA > NMR experiment with the sequentially assigned chemical shift values of 13 C α , 15 N, and 1 H N measured by the RD 3D H α/β C α/β (CO)NHN NMR experiment and 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/β C 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 1 H β i , 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i and (ii) a RD 3D HNN< CO , CA > NMR experiment to measure and connect the chemical shift values of 13 C′ i , the α-carbon of amino acid residue i+1, 13 C α i−1 , the polypeptide backbone amide nitrogen of amino acid residue i+1, 15 N i+1 , and the polypeptide backbone amide proton of amino acid residue i+1, 1 H N i+1 . Then, sequential assignments are obtained by matching the chemical shift value of 13 C′ i measured by said RD 3D HNN< CO , CA > NMR experiment with the chemical shift value of 13 C′ 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/β C 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 1 H ali i−1 , 13 C ali i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali i−1 and 13 C ali i−1 , for amino acid residues i having unique pairs of 15 N i and 1 H N i chemical shift values are obtained by matching the chemical shift values of 1 H β , 13 C β , 1 H α , and 13 C α measured by the RD 3D H α/β C α/β (CO)NHN NMR experiment and RD 3D H α/β , C α/β ,N,HN NMR experiment with the chemical shift values of 1 H β i−1 , 13 C β i−1 , 1 H α i−1 , and 13 C α i−1 measured by the RD 3D H , C ,(C-TOCSY-CO),N,HN NMR experiment and using the 1 H ali i−1 and 13 C 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/β C 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 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13 C β i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 13 C β i and 13 C α i measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13 C β i−1 and 13 C α i−1 measured by the RD 3D H α/β C α/β (CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C 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 1 H β i , 13 C β i , and a δ-proton of amino acid residue i with an aromatic side chain, 1 H δ i . Then, sequential assignments are obtained by (i) matching the chemical shift values of 1 H β i and 13 C β i measured by said RD 2D HB , CB (CG,CD),HD NMR experiment with the chemical shift values of 1 H β and 13 C β measured by the RD 3D H α/β C 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/β C 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,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, 1 H ali , and aliphatic carbons of amino acid residue i, 13 C ali i , of amino acid residue i. Then, sequential assignments of the chemical shift values of 1 H α i and 13 C ali i , the chemical shift values of a γ-proton, 1 H γ i , and a γ-carbon, 13 C γ i , in particular, are obtained by (i) matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β , 13 C β , 1 H α , and 13 C α measured by the RD 3D H α/β C 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 1 H ali i and 13 C ali i , including the chemical shift values of H γ i and 13 C γ 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, 1 H ali , aliphatic carbons, 13 C ali , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H ali and 13 C 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, 1 H ali −1 , the aliphatic carbons of amino acid residue i−1, 13 C ali i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H 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, 1 H β i , the β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali , 13 C ali , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of the α- and β-protons of amino acid residue i−1, 1 H α/β i−1 and the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 with the chemical shift values of H α/β i and 13 C α/β i of amino acid residue i, (ii) using the chemical shift values of 1 H ali i−1 and 13 C ali 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 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 H 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 1 H β i , 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i . Then, sequential assignments of the chemical shift value of 13 C′ i are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β , 13 C β , 1 H α , 13 C α , 15 N, 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, 13 C′ i−1 , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift value of 13 C′ i−1 are obtained by matching the chemical shift value of 13 C α i measured by the RD 3D HNN< CO , CA > NMR experiment with the sequentially assigned chemical shift values of 13 C α , 15 N, 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 (i) a RD 3D H α/β , C α/β ,CO,HA NMR experiment to measure and connect the chemical shift values of 1 H β i , 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i , and (ii) a RD 3D HNN< CO , CA > NMR experiment to measure and connect the chemical shift values of 13 C′ i , the α-carbon of amino acid residue i+1, 13 C α i+1 , the polypeptide backbone amide nitrogen of amino acid residue i+1, 15 N i+1 , and the polypeptide backbone amide proton of amino acid residue i+1, 1 H N i+1 . Then, sequential assignments are obtained by matching the chemical shift value of 13 C′ i measured by the RD 3D HNN< CO , CA > NMR experiment with the chemical shift value of 13 C′ 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/β C α/β (CO)NHN NMR experiment (i) to measure and connect the chemical shift values of 1 H α/β i-1 , 13 C α/β i-1 , 15 N i , and 1 H N i , and (ii) to identify NMR signals for 1 H α/β i-1 , 13 C α/β i-1 , 15 N i , and 1 H 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 1 H α i-1 , 13 C α i-1 , 15 N i , and 1 H N i and (ii) to identify NMR signals for 1 H α and 13 C α in 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 3D HNNCACB NMR experiment to measure and connect the chemical shift value of 13 C β i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 13 C β i and 13 C α i measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13 C β i−1 and 13 C 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 1 H β i , 13 C β i , and a δ-proton of amino acid residue i with an aromatic side chain, 1 H δ i . Then, sequential assignments are obtained by matching the chemical shift values of 1 H β i and 13 C β i measured by said RD 2D HB , CB ,(CG,CD)ND NMR experiment with the chemical shift values of 1 H β and 13 C β measured by the RD 3D H α/β , C 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, 1 H ali , and aliphatic carbons of amino acid residue i, 13 C ali i . Then, sequential assignments of the chemical shift values of 1 H ali i and 13 C ali , the chemical shift values of a γ-proton, 1 H δ i , and a γ-carbon, 13 C γ i , in particular, are obtained by (i) matching the chemical shift values of 1 H ali i and 13 C 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 1 H ali and 13 C 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 H ali i and 13 C ali i , including the chemical shift values of 1 H γ i and 13 C 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, 1 H ali , aliphatic carbons, 13 C ali , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H 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 1 H ali and 13 C 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, 1 H ali i−1 , the aliphatic carbons of amino acid residue i−1, 13 C ali i−1 , the polypeptide backbone amide nitrogen of amino acid residue i, 15 N i , and the polypeptide backbone amide proton of amino acid residue i, 1 H N i and (2) a RD 3D HNN CAHA NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift values of 1 H ali , 13 C ali , 15 N, and 1 H N are obtained by (i) matching the chemical shift values of the α-proton of amino acid residue i−1, 1 H α i−1 and the α-carbon of amino acid residue i−1, 13 C α i−1 with the chemical shift values of 1 H α i and 13 C α i , (ii) using the chemical shift values of 1 H ali i−1 and 13 C ali 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 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 HNN CAHA 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, 1 H β i , a β-carbon of amino acid residue i, 13 C β i , 1 H α i , 13 C α i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i . Then, sequential assignments of the chemical shift value of 13 C′ i are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C 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 1 H β , 13 C β , 1 H α , 13 C α , 15 N, and 1 H N measured by the RD 3D H , C ,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNN CAHA 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 HNN CAHA 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, 13 C′ i−1, 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments of the chemical shift value of 13 C′ i−1 are obtained by matching the chemical shift value of 13 C α i measured by the RD 3D HNN< CO , CA > NMR experiment with the sequentially assigned chemical shift values of 13 C α , 15 N, and 1 H N measured by the RD 3D H , C ,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNN CAHA 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 HNN CAHA 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, 1 H β i , a β-carbon of amino acid residue i, 13 C β i , the α-proton of amino acid residue i, 1 H α i , the α-carbon of amino acid residue i, 13 C β i , and a polypeptide backbone carbonyl carbon of amino acid residue i, 13 C′ i , and (ii) a RD 3D HNN< CO , CA > NMR experiment to measure and connect the chemical shift values of 13 C′ i , an α-carbon of amino acid residue i+1, 13 C α i+1 , a polypeptide backbone amide nitrogen of amino acid residue i+1, 15 N i+1 , and the polypeptide backbone amide proton of amino acid residue i+1, 1 H N i+1 . Then, sequential assignments are obtained by matching the chemical shift value of 13 C′ i measured by the RD 3D HNN< CO , CA > NMR experiment with the chemical shift value of 13 C′ 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 HNN CAHA NMR experiment, be further subjected to a RD 3D H α/β C 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, 1 H α/β i−1 , the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , 15 N i , and 1 H N i , and (ii) to distinguish NMR signals for the chemical shift values of 1 H β i−1 , 13 C β i−1 , 1 H α i−1 , and 13 C α i−1 measured by the RD 3D H α/β C α/β (CO)NHN NMR experiment from NMR signals for the chemical shift values of 1 H ali i−1 and 13 C ali i−1 other than 1 H a/β i−1 and 13 C 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 HNN CAHA 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 1 H β i , 13 C β i , 1 H α i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 1 H β i , 13 C β i , 1 H α i , and 13 C α i measured by said RD 3D H α/β , C β/α ,N,HN NMR experiment with the chemical shift values of 1 H β i−1 , 13 C β i−1 , 1 H α i−1 , and 13 C 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 HNN CAHA NMR experiment, be further subjected to a 3D HNNCACB NMR experiment to measure and connect the chemical shift values of 13 C β i , 13 C α i , 15 N i , and 1 H N i . Then, sequential assignments are obtained by matching the chemical shift values of 13 C β i and 13 C α i measured by said 3D HNNCACB NMR experiment with the chemical shift values of 13 C β i−1 and 13 C 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 HNN CAHA 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 1 H β i , 13 C β i , and a δ-proton of amino acid residue i with an aromatic side chain, 1 H δ i . Then, sequential assignments are obtained by matching the chemical shift values of 1 H β i and 13 C β i measured by said RD 2D HB , CB ,(CG,CD),HD NMR experiment with the chemical shift values of 1 H β and 13 C 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 HNN CAHA 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, 1 H ali i , and aliphatic carbons of amino acid residue i, 13 C ali i . Then, sequential assignments of the chemical shift values of 1 H ali i and 13 C ali i , the chemical shift values of a γ-proton, 1 H γ i , and a γ-carbon, 13 C γ i , in particular, are obtained by (i) matching the chemical shift values of 1 H ali and 13 C 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 1 H β i , 13 C β i , 1 H α i , and 13 C α i measured by the RD 3D H , C ,(C-TOCSY-CO),N,HN NMR experiment and the RD 3D HNN CAHA NMR experiment, and (ii) using the chemical shift values of 1 H ali i and 13 C ali i , including the chemical shift values of 1 H γ i and 13 C 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 1 H, 13 C and 15 N of a protein molecule (excluding only chemical shift values of 13 C δ and 15 N ε2 of glutamines, of 13 C γ and 15 N δ2 of asparagines, of 13 C ε3 , 1 H ε3 , 13 C ζ2 , 1 H ζ2 , 13 C ζ3 , 1 H ζ3 , 13 C η2 , and 1 H η2 groups of tryptophans, of 13 C ε and 1 H 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 1 H and 13 C 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/β C 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 HNN CAHA 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 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/β C α/β (CO)NHN NMR experiment and the second experiment is the RD 3D HNN CAHA NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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 1 H α / 13 C α and 1 H β/ 13 C β from the RD 3D H α/β C α/β (CO)NHN NMR experiment.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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 1 H ali and 13 C ali .

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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/β , C α/β ,N,HN NMR experiment to obtain assignments of chemical shift values of 1 H β and 13 C β .

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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, 13 C′.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, 13 C′.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of 13 C′.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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 1 H and 13 C of aliphatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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 1 H and 13 C of aromatic sidechains.

In another embodiment, the protein sample could, in addition to the RD 3D H α/β C α/β (CO)NHN NMR experiment, RD 3D HNN CAHA 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 13 C 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 CAHA 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 CAHA 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 1 H α / 13 C 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 CAHA 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/β , C α/β ,N,HN NMR experiment to obtain assignments of chemical shift values of 1 H β and 13 C 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 HNN CAHA 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, 13 C′.

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 CAHA 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, 13 C′.

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 CAHA 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of 13 C′.

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 CAHA 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 1 H and 13 C 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 CAHA 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 1 H and 13 C 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 CAHA 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 13 C 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/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, RD 3D H α/β , C 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 1 H α and 13 C 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/β , C 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/β C α/β (CO)NHN NMR experiment to identify NMR signals for 1 H α/β and 13 C 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/β , C 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, 13 C′.

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/β , C 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, 13 C′.

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/β , C 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of 13 C′.

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/β , C 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 1 H and 13 C 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/β , C 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 1 H and 13 C 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/β , C 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 13 C 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 1 H α and 13 C 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/β C α/β (CO)NHN NMR experiment to identify NMR signals for 1 H α/β and 13 C 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/β , C α/β ,CO,HA NMR experiment to obtain assignments of chemical shift values of polypeptide backbone carbonyl carbons, 13 C′.

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 1 H and 13 C 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 1 H and 13 C 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 13 C β .

In addition, the above-described method for obtaining assignments of chemical shift values of 1 H, 13 C and 15 N 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/β C α/β (CO)NHN, 3D HNN CAHA , 3D H α/β C α/β COHA, 3D HNNCACB, 3D HNN< CO , CA >, 3D HC CH-COSY, 3D HC CH-TOCSY, 2D HBCB (CDCG)HD, and 2D 1 H-TOCSY-relayed HC H-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/β C α/β (CO)NHN, and (ii) to offer the distinction of α- and β-moiety resonances by comparison with H α/β C α/β (CO)NHN. Furthermore, employment of 50% random fractional protein deuteration (LeMaster, Annu. Rev. Biophys. Bionhys. 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/β C 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/β C 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 HNN CAHA 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 13 C 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 13 C-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.

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