The importance of being ordered: Improving NMR structures using residual dipolar couplings

Comptes Rendus - Biologies

Volumn 325, Issue 9, 2002, Pages 957-966

  Gronenborn, A M ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Alignment; Anisotropy; Liquid crystal; NMR; Orientational constraints; Protein structure determination; Residual dipolar couplings

Indexed keywords

PHOSPHOLIPID; PROTEIN; SURFACTANT;

ANISOTROPY;

ACCURACY; ANISOTROPY; ARTICLE; CALCULATION; COLLOID; CONTROLLED STUDY; GEL; GENOMICS; LIQUID CRYSTAL; MAGNETIC FIELD; METHODOLOGY; MOLECULE; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PH; SAMPLE; STRUCTURE ANALYSIS; TEMPERATURE; TIME; VIRUS;

EID: 0036760089     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1631-0691(02)01512-3     Document Type: Article

References (46)

1. K. Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York, 1986.
2. G.M. Clore, A.M. Gronenborn, Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy, CRC Crit. Rev. Biochem. Mol. Biol. 24 (1989) 479-564.
3. N. Tjandra, A. Bax, Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium [erratum in Science (1997) 278, 1697], Science 278 (1997) (1997) 1111-1114.
4. 1H couplings in proteins, J. Magn. Reson. Ser. B 112 (1996) 245-252.
5. 15N-enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling, J. Am. Chem. Soc. 118 (1996) 6264-6272.
6. J.H. Prestegard, New techniques in structural NMR - anisotropic interactions, Nat. Struct. Biol. 5 (Suppl) (1998) 517-522.
7. A. Bax, G. Kontaxis, N. Tjandra, Dipolar couplings in macromolecular structure determination, Methods Enzymol. 339 (2001) 127-174.
8. C.R. Sanders II, J.P. Schwonek, Characterization of magnetically orientable bilayers in mixtures of dihexanoylphosphatidylcholine and dimyristoylphosphatidylcholine by solid-state NMR, Biochemistry 31 (1992) 8898-9905.
9. C.R. Sanders II, G.C. Landis, Reconstitution of membrane proteins into lipid-rich bilayered mixed micelles for NMR studies, Biochemistry 34 (1995) 4030-4040.
10. M-P. Nieh, C.J. Glinka, S. Krueger, R.S. Prosser, J. Katsaras, SANS study on the effect of lanthanide ions and charged lipids on the morphology of phospholipid mixtures, Biophys. J. 82 (2002) 2487-2498.
11. J.A. Losonczi, J.H. Prestegard, Improved dilute bicelle solutions for high-resolution NMR of biological macromolecules, J. Biomol. NMR 12 (1998) 447-451.
12. H. Wang, M. Eberstadt, E.T. Olejniczak, R.P. Meadows, S.W. Fesik, A liquid crystalline medium for measuring residual dipolar couplings over a wide range of temperatures, J. Biomol. NMR 12 (1998) 443-446.
13. M. Ottiger, A. Bax, Bicelle-based liquid crystals for NMR-measurement of dipolar couplings at acidic and basic pH values, J. Biomol. NMR 13 (1999) 187-191.
14. H. Nakamura, K. Okano, Pretransitional phenomena in the isotropic phase of a lyotropic liquid crystal of bacterial virus fd, Phys. Rev. Lett. 50 (1983) 186-189.
15. S. Fraden, G. Maret, D.L.D. Caspar, R.B. Meyer, Isotropic-nematic phase transition and angular correlations in isotropic suspensions of tobacco mosaic virus, Phys. Rev. Lett. 63 (1989) 2068-2071.
16. G.M. Clore, M.R. Starich, A.M. Gronenborn, Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses, J. Am. Chem. Soc. 120 (1998) 10571-10572.
17. M.R. Hansen, L. Mueller, A. Pardi, Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions, Nat. Struct. Biol. 5 (1998) 1065-1074.
18. L.G. Barrientos, J.M. Louis, A.M. Gronenborn, Characterization of the cholisteric phase of filamentous bacteriophage fd for molecular alignment, J. Magn. Reson. 148 (2001) 159-162.
19. R.S. Prosser, J.A. Losonczi, I.V. Shiyanovskaya, Use of a novel aqueous liquid crystalline medium for high-resolution NMR of macromolecules in solution, J. Am. Chem. Soc. 120 (1998) 11010-11011.
20. L.G. Barrientos, C. Dolan, A.M. Gronenborn, Characterization of surfactant liquid crystal phases suitable for molecular alignment and measurement of dipolar couplings, J. Biomol. NMR 16 (2000) 329-337.
21. L.G. Barrientos, K. Gawrisch, N. Cheng, A.C. Steven, A.M. Gronenborn, Structural Characterization of the dilute aqueous surfactant solution of cetylpyridinium bromide/hexanol/sodium bromide, Langmuir 18 (2002) 3773-3779.
22. M. Rückert, G. Otting, Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments, J. Am. Chem. Soc. 122 (2000) 7793-7797.
23. B.W. Koenig, J.S. Hu, M. Ottiger, S. Bose, R.W. Hendler, A. Bax, NMR measurement of dipolar couplings in proteins aligned by transient binding to purple membrane fragments, J. Am. Chem. Soc. 121 (1999) 1385-1386.
24. H.J. Sass, F. Cordier, A. Hoffmann, M. Rogowski, A. Cousin, J.G. Omichinski, H. Lowen, S. Grzesiek, Purple membrane induced alignment of biological macromolecules in the magnetic field, J. Am. Chem. Soc. 121 (1999) 2047-2055.
25. K. Fleming, D. Gray, S. Prasannan, S. Matthews, Cellulose cystallites: a new and robust liquid crystalline medium for the measurement of residual dipolar couplings, J. Am. Chem. Soc. 122 (2000) 5224-5225.
26. R. Tycko, F.J. Blanco, Y. Ishii, Alignment of biopolymers in strained gels: a new way to create detectable dipole-dipole couplings in high resolution biomolecular NMR, J. Am. Chem. Soc. 122 (2000) 9340-9341.
27. H.J. Sass, G. Musco, S.J. Stahl, P.T. Wingfield, S. Grzesiek, Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes, J. Biomol. NMR 18 (2000) 303-309.
28. D. Shortle, M.S. Ackerman, Persistence of native-like topology in a denatured protein in 8 M urea, Science 293 (2001) 487-489.
29. 13C couplings in the structure determination of magnetically oriented macromolecules in solution, Nat. Struct. Biol. 4 (1997) 732-738.
30. G.M. Clore, A.M. Gronenborn, N. Tjandra, Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude, J. Magn. Reson. 131 (1998) 159-162.
31. G. Lipari, A. Szabo, Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. I. Theory and range of validity, J. Am. Chem. Soc. 104 (1982) 4546-4559.
32. G.M. Clore, A.M. Gronenborn, A. Bax, A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information, J. Magn. Reson. 133 (1998) 216-221.
33. PQ and R for sets of dipolar coupling data, J. Magn. Reson. 149 (2001) 271-275.
34. J.A. Losonczi, M. Andrec, M.W. Fischer, J.H. Prestegard, Order matrix analysis of residual dipolar couplings using singular value decomposition, J. Magn. Reson. 138 (1999) 334-342.
35. G.M. Clore, A.M. Gronenborn, New methods of structure refinement for macromolecular structure determination by NMR, Proc. Natl Acad. Sci. USA 95 (1998) 5891-5898.
36. J. Kuszewski, A.M. Gronenborn, G.M. Clore, Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases, Protein Sci. 5 (1996) 1067-1080.
37. D.S. Garrett, Y.J. Seok, A. Peterkofsky, A.M. Gronenborn, G.M. Clore, Solution structure of the 40 000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr, Nat. Struct. Biol. 6 (1999) 166-173.
38. Y.I. Wolf, N.V Grishin, E.V. Koonin, Estimating the number of protein folds and families from complete genome data, J. Mol. Biol. 299 (2000) 897-905.
39. M. Zweckstetter, A. Bax, Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR, J. Am. Chem. Soc. 122 (2000) 3791-3792.
40. P. Bayer, L. Varani, G. Varani, Refinement of the structure of protein-RNA complexes by residual coupling analysis, J. Biomol. NMR 14 (1999) 149-155.
41. M.W.F. Fischer, J.A. Losonczi, J.L. Weaver, J.H. Prestegard, Domain orientation and dynamics in multidomain proteins from residual dipolar couplings, Biochemistry 38 (1999) 9013-9022.
42. N.R. Skrynnikov, N.K. Goto, D. Yang, W.Y. Choy, J.R. Tolman, G.A. Mueller, L.E. Kay, Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with β-cyclodextrin, J. Mol. Biol. 295 (2000) 1265-1273.
43. J.J. Chou, S. Li, A. Bax, Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings, J. Biomol. NMR 18 (2000) 217-227.
44. L.G. Barrientos, J.M. Louis, I. Botos, T. Mori, Z. Han, B.R. O'Keefe, M.R. Boyd, A. Wlodawer, A.M. Gronenborn, The domain-swapped dimer of Cyanovirin-N is in a metastable folded state. Reconciliation of X-ray and NMR structures, Structure 10 (2002) 673-686.
45. A. Annila, H. Aittio, E. Thulin, T. Drakenberg, Recognition of protein folds via dipolar couplings, J. Biomol. NMR 14 (1999) 223-230.
46. F. Delaglio, G. Kontaxis, A. Bax, Protein structure determination using molecular fragment replacement and NMR dipolar couplings, J. Am. Chem. Soc. 122 (2000) 2142-2143.