Measurement of One and Two Bond N-C Couplings in Large Proteins by TROSY-based J-modulation Experiments

Overview

Journal J Magn Reson

Publisher Elsevier

Date 2009 Jul 8

PMID 19581113

Citations 19

Authors

Yizhou Liu

James H Prestegard

Affiliations

Soon will be listed here.

Abstract

Residual dipolar couplings (RDCs) between NC' and NC(alpha) atoms in polypeptide backbones of proteins contain information on the orientation of bond vectors that is complementary to that contained in NH RDCs. The (1)J(NC)(alpha) and (2)J(NC)(alpha) scalar couplings between these atoms also display a Karplus relation with the backbone torsion angles and report on secondary structure. However, these N-C couplings tend to be small and they are frequently unresolvable in frequency domain spectra having the broad lines characteristic of large proteins. Here a TROSY-based J-modulated approach for the measurement of small (15)N-(13)C couplings in large proteins is described. The cross-correlation interference effects inherent in TROSY methods improve resolution and signal to noise ratios for large proteins, and the use of J-modulation to encode couplings eliminates the need to remove frequency distortions from overlapping peaks during data analysis. The utility of the method is demonstrated by measurement of (1)J(NC'), (1)J(NC)(alpha) , and (2)J(NC)(alpha) scalar couplings and (1)D(NC') and D(NC)(alpha) residual dipolar couplings for the myristoylated yeast ARF1.GTPgammas protein bound to small lipid bicelles, a system with an effective molecule weight of approximately 70kDa.

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References

Tolman J, Flanagan J, Kennedy M, Prestegard J . Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc Natl Acad Sci U S A. 1995; 92(20):9279-83. PMC: 40968. DOI: 10.1073/pnas.92.20.9279. View

Mueller G, Choy W, Yang D, Forman-Kay J, Venters R, Kay L . Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein. J Mol Biol. 2000; 300(1):197-212. DOI: 10.1006/jmbi.2000.3842. View

Wienk H, Martinez M, Yalloway G, Schmidt J, Perez C, Ruterjans H . Simultaneous measurement of protein one-bond and two-bond nitrogen-carbon coupling constants using an internally referenced quantitative J-correlated [(15)N,(1)H]-TROSY-HNC experiment. J Biomol NMR. 2003; 25(2):133-45. DOI: 10.1023/a:1022233103990. View

Cierpicki T, Bushweller J . Charged gels as orienting media for measurement of residual dipolar couplings in soluble and integral membrane proteins. J Am Chem Soc. 2004; 126(49):16259-66. DOI: 10.1021/ja046054g. View

Yang D, Kay L . Improved 1HN-detected triple resonance TROSY-based experiments. J Biomol NMR. 2010; 13(1):3-10. DOI: 10.1023/A:1008329230975. View

Ding K, Gronenborn A . Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. J Am Chem Soc. 2004; 126(20):6232-3. DOI: 10.1021/ja049049l. View

Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A . NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995; 6(3):277-93. DOI: 10.1007/BF00197809. View

Nietlispach D . Suppression of anti-TROSY lines in a sensitivity enhanced gradient selection TROSY scheme. J Biomol NMR. 2005; 31(2):161-6. DOI: 10.1007/s10858-004-8195-7. View

Pardi A, Billeter M, Wuthrich K . Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure. J Mol Biol. 1984; 180(3):741-51. DOI: 10.1016/0022-2836(84)90035-4. View

10.

Billeter M, Neri D, Otting G, Qian Y, Wuthrich K . Precise vicinal coupling constants 3JHN alpha in proteins from nonlinear fits of J-modulated [15N,1H]-COSY experiments. J Biomol NMR. 1992; 2(3):257-74. DOI: 10.1007/BF01875320. View

11.

Tjandra N, Bax A . Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 1997; 278(5340):1111-4. DOI: 10.1126/science.278.5340.1111. View

12.

Tolman J, Prestegard J . Measurement of amide 15N-1H one-bond couplings in proteins using accordion heteronuclear-shift-correlation experiments. J Magn Reson B. 1996; 112(3):269-74. DOI: 10.1006/jmrb.1996.0141. View

13.

Liu Y, Prestegard J . Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment. J Magn Reson. 2008; 193(1):23-31. PMC: 2542487. DOI: 10.1016/j.jmr.2008.03.013. View

14.

DSouza-Schorey C, Chavrier P . ARF proteins: roles in membrane traffic and beyond. Nat Rev Mol Cell Biol. 2006; 7(5):347-58. DOI: 10.1038/nrm1910. View

15.

Ottiger M, Delaglio F, Bax A . Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson. 1998; 131(2):373-8. DOI: 10.1006/jmre.1998.1361. View

16.

Bax A, Vuister G, Grzesiek S, Delaglio F, Wang A, Tschudin R . Measurement of homo- and heteronuclear J couplings from quantitative J correlation. Methods Enzymol. 1994; 239:79-105. DOI: 10.1016/s0076-6879(94)39004-5. View

17.

McFeeters R, Fowler C, Gaponenko V, Byrd R . Efficient and precise measurement of H(alpha)-C(alpha), C(alpha)-C', C(alpha)-C(beta) and H(N)-N residual dipolar couplings from 2D H(N)-N correlation spectra. J Biomol NMR. 2005; 31(1):35-47. DOI: 10.1007/s10858-004-6057-y. View

18.

Bax A . Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci. 2002; 12(1):1-16. PMC: 2312400. DOI: 10.1110/ps.0233303. View

19.

Prestegard J, Bougault C, Kishore A . Residual dipolar couplings in structure determination of biomolecules. Chem Rev. 2004; 104(8):3519-40. DOI: 10.1021/cr030419i. View

20.

Liu Y, Kahn R, Prestegard J . Structure and membrane interaction of myristoylated ARF1. Structure. 2009; 17(1):79-87. PMC: 2659477. DOI: 10.1016/j.str.2008.10.020. View