Method of using G-matrix fourier transformation nuclear magnetic resonance (GFT NMR) spectroscopy for rapid chemical shift assignment and secondary structure determination of proteins
View Patent ↗The present invention presents a new approach to rapidly obtaining precise high-dimensional NMR spectral information, named “GFT NMR spectroscopy”, which is based on the phase sensitive joint sampling of the indirect dimensions spanning a subspace of a conventional NMR experiment. The phase-sensitive joint sampling of several indirect dimensions of a high-dimensional NMR experiment leads to largely reduced minimum measurement times when compared to FT NMR. This allows one to avoid the “sampling limited” data collection regime. Concomitantly, the analysis of the resulting checmical shift multiplets, which are edited by the G-matrix transformation, yields increased precision for the measurement of the chemical shifts. Additionally, methods of conducting specific GFT NMR experiments as well as methods of conducting a combination of GFT NMR experiments for rapidly obtaining precise chemical shift assignment and determining the structure of proteins or other molecules are disclosed.
1. A method for sequentially assigning chemical shift values of an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (5,2)D [ HACACON HN] GFT NMR experiment to measure and connect the chemical shift values of the α-proton of amino acid residue i−1, 1 H αi−1 , the α-carbon of amino acid residue i−1, 13 C α i−1 , the polypeptide backbone carbonyl carbon of amino acid residue i−1, 13 C′ 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 (5,2)D [ HACA , CON HN] GFT NMR experiment to measure and connect the chemical shift values of 1 H α i−1 , 13 C α i−1 , 13 C′ 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 ; and
obtaining sequential assignments of the chemical shift values of 1 H α , 13 C α , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,2)D [ HACACON HN] GFT NMR experiment with the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,2)D [ HACA , CON HN] GFT NMR experiment, (ii) using the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ 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.
2. A method for sequentially assigning chemical shift values of an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (5,3)D [ HACACO NHN] GFT NMR experiment to measure and connect the 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 carbonyl carbon of amino acid residue i−1, 13 C′ 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 (5,3)D [ HACA , CO NHN] GFT NMR experiment to measure and connect the chemical shift values of 1 H α i−1 , 13 C α i−1 , 13 C′ 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 ; and
obtaining sequential assignments of the chemical shift values of 1 H α , 13 C α , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,3)D [ HACACO NHN] GFT NMR experiment with the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,3)D [ HACA , CO NHN] GFT NMR experiment, (ii) using the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ 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.
3. A method for sequentially assigning chemical shift values of α- and β-carbons, 13 C α/β , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (4,3)D [ CBCACO NHN] GFT NMR experiment to measure and connect the chemical shift values of the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , the polypeptide backbone carbonyl carbon of amino acid residue i−1, 13 C′ 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 (4,3)D [ CBCA , CO NHN] GFT NMR experiment to measure and connect the chemical shift values of 13 C α/β i−1 , 13 C′ 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 ; and
obtaining sequential assignments of the chemical shift values of 13 C α/β , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 13 C α/β i−1 and 13 C′ i−1 measured by said (4,3)D [ CBCACO NHN] GFT NMR experiment with the chemical shift values of 13 C α/β i−1 and 13 C′ i−1 measured by said (4,3)D [ CBCA , CO NHN] GFT NMR experiment, (ii) using the chemical shift values of 13 C α/β i−1 and 13 C′ 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.
4. A method for sequentially assigning chemical shift values of α- and β-carbons, 13 C α/β , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (4,3)D [HNN CACBCA ] GFT NMR experiment to measure and connect the chemical shift values of the α- and β-carbons of amino acid residue i−1, 13 C α/β 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−1, 15 N i−1 , and the polypeptide backbone amide proton of amino acid residue i−1, 1 H N i−1 and (2) a GFT NMR experiment selected from the group consisting of a (4,3)D [HNN(CO) CACBCA ] GFT NMR experiment, a (4,3)D [ CBCACA (CO)NHN] GFT NMR experiment, and a (5,3)D [ HBHACBCACA (CO)NHN] GFT NMR experiment to measure and connect the chemical shift values of 13 C α/β 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
obtaining sequential assignments of the chemical shift values of 13 C α/β , 15 N, and 1 H N by (i) matching the chemical shift values of 13 C α/β i−1 measured by said GFT NMR experiment selected from the group consisting of a (4,3)D [HNN(CO) CACBCA ] GFT NMR experiment, a (4,3)D [ CBCACA (CO)NHN] GFT NMR experiment, and a (5,3)D [ HBHACBCACA (CO)NHN] GFT NMR experiment with the chemical shift values of 13 C α/β i−1 measured by said (4,3)D [HNN CACBCA ] GFT NMR experiment, (ii) using the chemical shift values of 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.
5. A method for sequentially assigning chemical shift values of an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule to determine protein comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (5,2)D [ HACACO NHN] GFT NMR experiment to measure and connect the 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 carbonyl carbon of amino acid residue i−1, 13 C′ 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 (5,2)D [ HACA , CO NHN] GFT NMR experiment to measure and connect the chemical shift values of 1 H α i−1 , 13 C α i−1 , 13 C′ 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 ;
obtaining sequential assignments of the chemical shift values of 1 H α , 13 C α , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,2)D [ HACACO NHN] GFT NMR experiment with the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,2)D [ HACA , CO NHN] GFT NMR experiment, (ii) using the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ 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
determining the tertiary structure of the protein molecule by subjecting the protein sample to (i) nuclear Overhauser enhancement spectroscopy (NOESY), (ii) NMR experiments that measure scalar coupling constants, or (iii) NMR experiments that measure residual dipolar coupling constants.
6. The method according to claim 5 , wherein the protein sample is subjected to nuclear Overhauser enhancement spectroscopy (NOESY) to deduce the tertiary structure of the protein molecule.
7. The method according to claim 5 , wherein the protein sample is subjected to NMR experiments that measure scalar coupling constants to deduce the tertiary structure of the protein molecule.
8. The method according to claim 5 , wherein the protein sample is subjected to NMR experiments that measure residual dipolar coupling constants to deduce the tertiary structure of the protein molecule.
9. A method for sequentially assigning chemical shift values of an α-proton, 1 H α , an α-carbon, 13 C α , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule to determine protein comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (5,3)D [ HACACO NHN] GFT NMR experiment to measure and connect the 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 carbonyl carbon of amino acid residue i−1, 13 C′ 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 (5,3)D [ HACA , CO NHN] GFT NMR experiment to measure and connect the chemical shift values of 1 H α i−1 , 13 C α i−1 , 13 C′ 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 ;
obtaining sequential assignments of the chemical shift values of 1 H α , 13 C α , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,3)D [ HACACO NHN] GFT NMR experiment with the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ i−1 measured by said (5,2)D [ HACA , CO NHN] GFT NMR experiment, (ii) using the chemical shift values of 1 H α i−1 , 13 C α i−1 , and 13 C′ 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
determining the tertiary structure of the protein molecule by subjecting the protein sample to (i) nuclear Overhauser enhancement spectroscopy (NOESY), (ii) NMR experiments that measure scalar coupling constants, or (iii) NMR experiments that measure residual dipolar coupling constants.
10. The method according to claim 9 , wherein the protein sample is subjected to nuclear Overhauser enhancement spectroscopy (NOESY) to deduce the tertiary structure of the protein molecule.
11. The method according to claim 9 , wherein the protein sample is subjected to NMR experiments that measure scalar coupling constants to deduce the tertiary structure of the protein molecule.
12. The method according to claim 9 , wherein the protein sample is subjected to NMR experiments that measure residual dipolar coupling constants to deduce the tertiary structure of the protein molecule.
13. A method for sequentially assigning chemical shift values of α- and β-carbons, 13 C α/β , a polypeptide backbone carbonyl carbon, 13 C′, a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule to determine protein structure comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (4,3)D [ CBCACO NHN] GFT NMR experiment to measure and connect the chemical shift values of the α- and β-carbons of amino acid residue i−1, 13 C α/β i−1 , the polypeptide backbone carbonyl carbon of amino acid residue i−1, 13 C′ 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 (4,3)D [ CBCA , CO NHN] GFT NMR experiment to measure and connect the chemical shift values of 13 C α/β i−1 , 13 C′ 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 ;
obtaining sequential assignments of the chemical shift values of 13 C α/β , 13 C′, 15 N, and 1 H N by (i) matching the chemical shift values of 13 C α/β i−1 and 13 C′ i−1 measured by said (4,3)D [ CBCACO NHN] GFT NMR experiment with the chemical shift values of 13 C α/β i−1 and 13 C′ i−1 measured by said (4,3)D [ CBCA , CO NHN] GFT NMR experiment, (ii) using the chemical shift values of 13 C α/β i−1 and 13 C′ 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
determining the tertiary structure of the protein molecule by subjecting the protein sample to (i) nuclear Overhauser enhancement spectroscopy (NOESY), (ii) NMR experiments that measure scalar coupling constants, or (iii) NMR experiments that measure residual dipolar coupling constants.
14. The method according to claim 13 , wherein the protein sample is subjected to nuclear Overhauser enhancement spectrosc6opy (NOESY) to deduce the tertiary structure of the protein molecule.
15. The method according to claim 13 , wherein the protein sample is subjected to NMR experiments that measure scalar coupling constants to deduce the tertiary structure of the protein molecule.
16. The method according to claim 13 , wherein the protein sample is subjected to NMR experiments that measure residual dipolar coupling constants to deduce the tertiary structure of the protein molecule.
17. A method for sequentially assigning chemical shift values of α- and β-carbons, 13 C α/β , a polypeptide backbone amide nitrogen, 15 N, and a polypeptide backbone amide proton, 1 H N , of a protein molecule to determine protein structure comprising:
providing a protein sample;
conducting a set of G matrix Fourier transformation (GFT) nuclear magnetic resonance (NMR) experiments on the protein sample comprising: (1) a (4,3)D [HNN CACBCA ] GFT NMR experiment to measure and connect the chemical shift values of the α- and β-carbons of amino acid residue i−1, 13 C α/β 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−1, 15 N i−1 , and the polypeptide backbone amide proton of amino acid residue i−1, 1 H N i−1 and (2) a GFT NMR experiment selected from the group consisting of a (4,3)D [HNN(CO) CACBCA ] GFT NMR experiment, a (4,3)D [ CBCACA (CO)NHN] GFT NMR experiment, and a (5,3)D [ HBHACBCACA (CO)NHN] GFT NMR experiment to measure and connect the chemical shift values of 13 C α/β 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 ;
obtaining sequential assignments of the chemical shift values of 13 C α/β , 15 N, and 1 H N by (i) matching the chemical shift values of 13 C α/β i−1 measured by said GFT NMR experiment selected from the group consisting of a (4,3)D [HNN(CO) CACBCA ] GFT NMR experiment, a (4,3)D [ CBCACA (CO)NHN] GFT NMR experiment, and a (5,3)D [ HBHACBCACA (CO)NHN] GFT NMR experiment with the chemical shift values of 13 C α/β i−1 measured by said (4,3)D [HNN CACBCA ] GFT NMR experiment, (ii) using the chemical shift values of 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.
determining the tertiary structure of the protein molecule by subjecting the protein sample to (i) nuclear Overhauser enhancement spectroscopy (NOESY), (ii) NMR experiments that measure scalar coupling constants, or (iii) NMR experiments that measure residual dipolar coupling constants.
18. The method according to claim 17 , wherein the protein sample is subjected to nuclear Overhauser enhancement spectrosc6opy (NOESY) to deduce the tertiary structure of the protein molecule.
19. The method according to claim 17 , wherein the protein sample is subjected to NMR experiments that measure scalar coupling constants to deduce the tertiary structure of the protein molecule.
20. The method according to claim 17 , wherein the protein sample is subjected to NMR experiments that measure residual dipolar coupling constants to deduce the tertiary structure of the protein molecule.