Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α/β protein: A unified picture of high probability, fast atomic motions in proteins

Journal of Molecular Biology

Volumn 355, Issue 5, 2006, Pages 879-886

  Clore, G Marius ^a   Schwieters, Charles D ^b  

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

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Crystallographic B factors; Multiple alignment media; Protein dynamics; Relaxation order parameters; Residual dipolar couplings

Indexed keywords

IMMUNOGLOBULIN; PROTEIN; PROTEIN G;

ANISOTROPY; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION; ROOM TEMPERATURE; SIGNAL TRANSDUCTION; STREPTOCOCCUS; VALIDATION PROCESS;

STREPTOCOCCUS;

EID: 29444446536     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.042     Document Type: Article

References (44)

1. L.E. Kay Protein dynamics from NMR Nature Struct. Biol. 5 1998 S513 S517
2. M.W.F. Fisher, A. Majumdar, and E.R.P. Zuiderweg Protein NMR relaxation: theory, applications and outlook Prog. Nucl. Magn. Reson. Spectrosc. 33 1998 207 272
3. R. Ishima, and D.A. Torchia Protein dynamics from NMR Nature Struct. Biol. 7 2000 740 743
4. A.J. Wand Dynamic activation of protein function: a view emerging from NMR spectroscopy Nature Struct. Biol. 8 2001 926 931
5. A.G. Palmer III NMR probes of molecular dynamics: overview and comparison with other techniques Annu. Rev. Biophys. Biomol. Struct. 30 2001 129 155
6. D. Ringe, and G.A. Petsko Study of protein dynamics by X-ray diffraction Methods Enzymol. 131 1986 389 433
7. T. Thüne, and J. Badger Thermal diffuse X-ray scattering and its contribution to understanding protein dynamics Prog. Biophys. Mol. Biol. 63 1995 251 276
8. M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nature Struct. Biol. 9 2002 646 652
9. J. Drenth Principles of Protein X-ray Crystallography 1994 Springer New York
10. G. Lipari, and 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
11. A.G. Palmer, M.J. Grey, and C. Wang Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular weight systems Methods Enzymol. 384 2005 430 465
12. J.R. Tolman, J.M. Al-Hashimi, L.E. Kay, and J.H. Prestegard Structural and dynamic analysis of residual dipolar coupling data for proteins J. Am. Chem. Soc. 123 2001 1416 1424
13. J.R. Tolman A novel approach to the retrieval of structural and dynamic information from residual dipolar coupling using several oriented media in biomolecular NMR J. Am. Chem. Soc. 124 2002 12020 12030
14. K.B. Briggman, and J.R. Tolman De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy J. Am. Chem. Soc. 125 2003 10164 10165
15. J. Meiler, J.J. Promper, W. Peti, C. Griesinger, and R. Brüschweiler Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins J. Am. Chem. Soc. 123 2001 6098 6107
16. W. Peti, J. Meiler, R. Brüschweiler, and C. Griesinger Model-free analysis of protein backbone motion from residual dipolar couplings J. Am. Chem. Soc. 124 2002 5822 6833
17. J.C. Hus, W. Peti, C. Griesinger, and R. Brüschweiler Self-consistency analysis of dipolar couplings in multiple alignments of ubiquitin J. Am. Chem. Soc. 125 2003 5596 5597
18. J. Meiler, W. Peti, and C. Griesinger Dipolar couplings in multiple alignments suggest alpha helical motion in ubiquitin J. Am. Chem. Soc. 125 2003 8072 8073
19. P. Bernado, and M. Blackledge Anisotropic small amplitude peptide plane dynamics in proteins from residual dipolar couplings J. Am. Chem. Soc. 126 2004 4907 4920
20. P. Bernado, and M. Blackledge Local dynamic amplitudes on the protein backbone from dipolar couplings: toward the elucidation of slower motions in biomolecules J. Am. Chem. Soc. 126 2004 7760 7761
21. G. Bouvignies, P. Bernado, and M. Blackledge Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise J. Magn. Reson. 173 2005 328 338
22. G.M. Clore, and C.D. Schwieters How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation J. Am. Chem. Soc. 126 2004 2923 2938
23. G.M. Clore, and C.D. Schwieters Amplitudes of protein backbone dynamics and correlated motions in a small α/β protein: correspondence of dipolar coupling and heteronuclear relaxation measurements Biochemistry 43 2005 10678 10691
24. A. Bax, G. Kontaxis, and N. Tjandra Dipolar couplings in macromolecular structure determination Methods Enzymol. 339 2001 127 174
25. D.T. Braddock, M. Cai, J.L. Baber, Y. Huang, and G.M. Clore Rapid identification of medium- to large-scale interdomain motion in modular proteins using dipolar couplings J. Am. Chem. Soc. 123 2001 8634 8635
26. D.T. Braddock, J.M. Louis, J.L. Baber, D. Levens, and G.M. Clore Structure and dynamics of KH domains from FBP bound to single-stranded DNA Nature 415 2002 1051 1056
27. M.W. Fischer, J.A. Losonczi, J.L. Weaver, and J.H. Prestegard Domain orientation and dynamics in multidomain proteins from residual dipolar couplings Biochemistry 38 1999 9013 9022
28. J.R. Tolman, J.M. Flanagan, M.A. Kennedy, and J.H. Prestegard NMR evidence for slow collective motions in cyanometmyoglobin Nature Struct. Biol. 4 1997 292 297
29. P. Pfeiffer, D. Fushman, and D. Cowburn Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the βARK1 PH domain J. Am. Chem. Soc. 123 2001 3021 3036
30. E.R. Henry, and A. Szabo Influence of vibrational motion on solid state line shapes and NMR relaxation J. Chem. Phys. 82 1985 4753 4761
31. α effective bond lengths in a protein by NMR in a dilute liquid crystalline phase J. Am. Chem. Soc. 120 1998 12334 12341
32. R.B. Best, and M. Vendruscolo Determination of protein structures consistent with NMR order parameters J. Am. Chem. Soc. 126 2004 8090 8091
33. K. Larsen-Lindorff, R.B. Best, M.A. DePristo, C.M. Dobson, and M. Vendruscolo Simultaneous determination of protein structure and dynamics Nature 433 2005 128 132
34. A.M. Bonvin, and A.T. Brünger Conformational variability of solution nuclear magnetic resonance structures J. Mol. Biol. 250 1995 80 93
35. A.M. Bonvin, and A.T. Brünger Do NOE distances contain enough information to access the relative populations of multi-conformer structures J. Biomol. NMR 7 1996 72 76
36. A.M. Gronenborn, D.R. Filpula, N.Z. Essig, A. Achari, M. Whitlow, P.T. Wingfield, and G.M. Clore A novel highly stable fold of the immunoglobulin binding domain of Streptococcal protein G Science 253 1991 657 661
37. T.S. Ulmer, B.E. Ramirez, F. Delaglio, and A. Bax Evaluation of backbone protein positions and dynamics in a small protein by liquid crystal NMR spectroscopy J. Am. Chem. Soc. 125 2003 9179 9191
38. J.P. Derrick, and D.B. Wigley The third IgG-binding domain from streptococcal protein G: an analysis by X-ray crystallography of the structure alone and in a complex with Fab J. Mol. Biol. 243 1994 906 918
39. J.B. Hall, and D. Fushman Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G J. Biomol. NMR 27 2003 261 275
40. C.D. Schwieters, J. Kuszewski, N. Tjandra, and G.M. Clore The Xplor-NIH NMR molecular structure determination package J. Magn. Reson. 160 2003 66 74
41. J. Kuszewski, A.M. Gronenborn, and G.M. Clore Inproving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration J. Am. Chem. Soc. 121 1999 2337 2338
42. G.M. Clore, and J. Kuszweski χ1 rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force J. Am. Chem. Soc. 124 2002 2866 2867
43. R.S. Lipsitz, Y. Sharma, B.R. Brooks, and N. Tjandra Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry J. Am. Chem. Soc. 124 2002 10261 10266
44. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291