An overview of recent developments in the interpretation and prediction of fast internal protein dynamics

European Biophysics Journal

Volumn 36, Issue 8, 2007, Pages 985-993

  Nodet, Gabrielle ^a   Abergel, Daniel ^a  

^a ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

NMR; Order parameter; Protein dynamics; Relaxation

Indexed keywords

ATOM; CONCEPTUAL FRAMEWORK; CORRELATION FUNCTION; ELECTRON SPIN RESONANCE; ENTROPY; LEISURE; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARAMETER; PROTEIN DYNAMIC; PROTEIN FOLDING; PROTEIN STRUCTURE; RADIOFREQUENCY RADIATION; REVIEW; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEINS;

EID: 35748939712     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-007-0167-x     Document Type: Review

References (94)

1. Abergel D, Bodenhausen G (2004) A simple model for NMR relaxation in the presence of internal motions with dynamical coupling. J Chem Phys 121:761
2. Abergel D, Bodenhausen G (2005) Predicting internal protein dynamics from structures using coupled networks of hindered rotators. J Chem Phys 123:204901
3. Abragam A (1961) Principles of nuclear magnetism. Clarendon Press, Oxford
4. 9k. J Am Chem Soc 115:9832-9833
5. 15N NMR relaxation of globular proteins using hydrodynamic calculations with hydroNMR. J Biomol NMR 23:139-150
6. 15N relaxation. J Am Chem Soc 120:4538-4539
7. Bremi T, Brüschweiler R (1997) Locally anisotropic internal polypeptide backbone dynamics by NMR relaxation. J Am Chem Soc 119:6672-6673
8. Bremi T, Brüschweiler R, Ernst R (1997) A protocol for the interpretation of side-chain dynamics based on NMR relaxation: Application to phenylalanines in antamanide. J Am Chem Soc 119:4272
9. Brink D, Satchler G (1968) Angular momentum. Clarendon Press, Oxford
10. Brüschweiler R, Liao X, Wright P (1995) Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science 268:886-889
11. Brüschweiler R, Case DA (1994) Collective NMR relaxation model applied to protein dynamics. Phys Rev Lett 72:940-943
12. 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme. Biochemistry 34:4041-4055
13. N CSA-dipolar cross-correlation relaxation. J Am Chem Soc 122:5105-5113
14. Case D (2002) Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res 35:325-331
15. Cavanagh J, Fairbrother WJ, Palmer AG, Skelton NJ (1996) Protein NMR spectroscopy. Academic, New York
16. Chandrashekar I, Clore GM, Szabo A, Gronenborn A, Brooks B (1992) A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. correlation with nuclear magnetic resonance spectroscopy and crystallography. J Mol Biol 226:239-250
17. 13C NMR relaxation data. J Am Chem Soc 120:5301-5311
18. Clore GM, Driscoll PC, Wingfield P, Gronenborn AM (1990a) Analysis of the backbone dynamics of interleukine-1 beta using two-dimensional inverse detected heteronuclear nitrogen-15-proton NMR spectroscopy. Biochemistry 29:7387-7401
19. Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM (1990b) Deviations from the simple two-parameter model-free approach of the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112:4989-4991
20. Coffey WT, Kalmykov YP, Waldron JT (1996) The Langevin equation. World Scientific, Singapore
21. 15N NMR relaxation. Progr NMR Spectrosc 31:63-105
22. de la Torre JG, Bloomfield V (1981) Hydrodynamic properties of complex, rigid, biological macromolecules-theory and applications. Quart Rev Biophys 14:81-139
23. de la Torre JG, Huertas ML, Carrasco B (2000a) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78:719-730
24. de la Torre JG, Huertas ML, Carrasco B (2000b) HydroNMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J Magn Reson 147:138-146
25. Delarue M, Duclert-Savatier N, Miclet E, Haouz A, Giganti D, Ouazzani J, Lopes P, Nilges M, Stoven V (2007) Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from trypanosoma brucei. J Mol Biol 366:868-881
26. Dhulesia A, Abergel D, Bodenhausen G (2007) Networks of coupled rotators: Relationship between structures and internal dynamics in metal-binding proteins. application to apo- and holo-calbindin. J Am Chem Soc 129:4998-5006
27. Dosset P, Marion D, Blackledge M (2000) Tensor2. Copyright 1999, Institut de Biologie Structurale JP EBEL CEA-CNRS, Laboratoire de Resonance Magnetique nucleaire, Grenoble
28. Edholm O, Blomberg C (1979) Decay of angular-correlation functions by multiple rotational potential diffusion in polymer-chains, with applications to NMR relaxation in paraffin chains of lipid bilayers. Chem Phys 42:449
29. Favro LD (1960) Theory of the rotational brownian motion of a free rigid body. Phys Rev 119:53
30. Fischer M, Majumdar A, Zuiderweg E (1998) Protein NMR relaxation: theory, applications and outlook. Prog Nucl Magn Reson 33:207-272
31. Fushman D, Ohlenschläger O, Rüterjans H (1994) Determination of the backbone mobility of ribonuclease t1 and its 2′ GMP complex using molecular dynamics simulations and NMR relaxation data. J Biomol Struct Dyn 4:61-78
32. Fushman D, Xu R, Cowburn D (1999) Direct determination of changes of interdomain orientation on ligation: use of the orientational dependence of 15N NMR relaxation in abl sh(32). Biochemistry 38:10225-10230
33. Goldman M (1984) Interference effects in the relaxation of a pair of unlike spin-1/2 nuclei. J Magn Reson 60:437-452
34. Goodman JL, Pagel MD, Stone MJ (2000) Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters. J Mol Biol 295:963-978
35. Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci 99:1275-1279
36. Halle B, Wennerström H (1981) J Chem Phys 75:1928-1943
37. Huntress WT (1968) Effects of anisotropic molecular rotational diffusion on nuclear magnetic relaxation in liquids. J Chem Phys 48:3524-3533
38. Idiyatullin D, Daragan V, Mayo K (2004) A simple method to measure (ch2)-C-13 heteronuclear dipolar cross-correlation spectral densities. J Magn Reson 171:4-9
39. Igumenova TI, Frederick KK, Wand AJ (2006) Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 106:1672-1699
40. Jarymowicz VA, Stone M (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 106:1624-1671
41. Kateb F, Abergel D, Blouquit Y, Duchambon P, Craescu C, Bodenhausen G (2006) Slow backbone dynamics of the C-terminal fragment of human centrin 2 in complex with a target peptide probed by cross-correlated relaxation in multiple-quantum NMR spectroscopy. Biochemistry 45:15011-15019
42. Kloiber K, Konrat R (2000) Differential multiple-quantum relaxation arising from cross-correlated time-modulation of isotropic chemical shifts. J Biomol NMR 18:33
43. Kördel J, Teleman O (1992) Backbone dynamics of calbindin d9k: comparison of molecular dynamics simulations and notrogen-15 NMR relaxation measurements. J Am Chem Soc 114:4934-4936
44. Korzhnev D, Billeter M, Arseniev A, Orekhov V (2001) NMR studies of brownian tumbling and internal motions in proteins. Prog NMR Spectrosc 38:197-266
45. Kroenke CD, Loria JP, Lee LK, Rance M, Palmer AG (1998) Longitudinal and transverse 1H-15N dipolar/15N chemical shift anisotropy relaxation interference: Unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules. J Am Chem Soc 120:7905-7915
46. α nuclear spin relaxation. J Biomol NMR 9:287-298
47. Lenin F, Bremi T, Brutcher B, Ernst R (1997) Anisotropic intramolecular back-bone dynamics of ubiquitin characterized by NMR relaxation and md computer simulation. J Am Chem Soc 120:9870-9879
48. Levitt MH (2001) Spin dynamics: basics of nuclear magnetic resonance. Wiley, Chichester
49. Lipari G, Szabo A (1982a) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546
50. Lipari G, Szabo A (1982b) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J Am Chem Soc 104:4559
51. London R, Avitabile J (1978) Calculated carbon-13 NMR relaxation parameters for a restricted internal diffusionmodel. application to methionine relaxation in dihydrofolate reductase. J Am Chem Soc 100:7159-7165
52. Mandel AM, Akke M, Palmer III AG (1995) Backbone dynamics of escherichia coli ribonuclease hi: correlations with structure and function in an active enzyme. J Mol Biol 246:144-163
53. Meirovitch E, Polimeno A, Freed JH (2006) Methyl dynamics in proteins from NMR slowly relaxing local structure spin relaxation analysis: a new perspective. J Phys Chem B 110:20615-20628
54. Millet O, Loria JP, Kroenke CD, Pons M, Palmer AG (2000) The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J Am Chem Soc 122:2867-2877
55. 2H-enriched proteins in solution. J Am Chem Soc 124:6439-6448
56. Ming D, Brschweiler R (2004) Prediction of methyl side-chain dynamics in proteins. J Biomol NMR 29:363-368
57. Ming D, Brschweiler R (2006) Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation. Biophys J 90:3382-3388
58. Palmer AG (2001) Annu Rev Biophys Biomol Struct 30:129
59. Palmer AG, Case D (1992) Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J Am Chem Soc 114:9059-9067
60. Palmer AG, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth Enzymol 339:204-238
61. N vectors in proteins via dipole-dipole cross-correlation. J Biomol NMR 13:375-380
62. Pelupessy P, Chiarparin E, Ghose R, Bodenhausen G (1999b) Simultaneous detection of y and f angles in proteins from measurements of cross-correlated relaxation effects. J Biomol NMR 14:277-280
63. Pelupessy P, Ravindranathan S, Bodenhausen G (2003) Correlated motions of successive amide N-H bonds in proteins. J Biomol NMR 25:265-280
64. Perazzolo C, Wist J, Loth K, Poggi L, Homans S, Bodenhausen G (2005) Effects of protein-pheromone complexation on correlated chemical shift modulations. J Biomol NMR 33:233-242
65. Perrin F (1934) Journal de Physique du Radium 5:497-511
66. Perrin F (1936) Journal de Physique du Radium 7:1-11
67. Philippopoulos M, Mandel AM, Palmer AG III, Lim C (1997) Accuracy and precision of NMR relaxation experiments and md simulations for characterizing protein dynamics. Proteins Struct Funct Bioinformatics 28:481-493
68. Polimeno A, Freed J (1993) Adv Chem Phys 83:89-163
69. Polimeno A, Freed J (1995) Slow motional ESR in complex fluids-the slowly relaxing local-structure model of solvent cage effects. J Phys Chem 99:10995-11006
70. Prompers J, Brschweiler R (2002) General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and md simulation. J Am Chem Soc 124:4522-4534
71. Redfield AG (1965) Adv Magn Reson 1:1-32
72. Reif B, Diener A, Hennig M, Maurer M, Griesinger C (2000) Cross-correlated relaxation for the measurement of angles between tensorial interactions. J Magn Reson 143:45-68
73. Reif B, Hennig M, Griesinger C (1997) Direct measurement of angles between bond vectors in high-resolution NMR. Science 276:1230
74. Ryabov YE, Geraghty C, Varshney A, Fushman D (2006) An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation. Journal of the American Chemical Society 128:15432-15444
75. Schmidt JM, Brüschweiler R, Ernst RR, Dunbrack RL, Joseph D, Karplus M (1993) Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the charmm force field. J Am Chem Soc 115:8747-8756
76. Schurr JM, Babcock HP, Fujimoto BS (1994) A test of the model-free formulas-effects of anisotropic rotational diffusion and dimerization. J Magn Reson 105 B:211-224
77. Schwalbe H, Carlomagno T, Hennig M, Junker J, Reif B, Richter C, Griesinger C (1997) Methods Enzymol 338:35-81
78. Skrynnikov NR, Millet O, Kay LE (2002) Deuterium spin probes of side-chain dynamics in proteins 2 spectral density mapping and identification of nanosecond time-scale side-chain motions. J Am Chem Soc 124:6449-6460
79. Tirion M (1997) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905
80. Torchia D, Szabo A (1982) Spin-lattice relaxation in solids. J Magn Reson 49:107-121
81. Tugarinov V, Liang Z, Shapiro YE, Freed JH, Meirovitch E (2001) A structural mode-coupling approach to 15N NMR relaxation in proteins. J Am Chem Soc 123:3055-3063
82. Tugarinov V, Shapiro YE, Liang Z, Freed JH, Meirovitch E (2002) A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling 15N NMR relaxation. J Mol Biol 315:155
83. Tugarinov V, Shapiro YE, Liang Z, Freed JH, Meirovitch E (2003) Mode coupling srls versus mode-decoupled model-free N-H bond dynamics: mode-mixing and renormalization. J Phys Chem B 107:9898-9904
84. Wand J (2001a) Science 293:U1
85. Wand J (2001b) Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat Struct Biol 8:926-931
86. Werbelow L, Grant D (1975) The dipolar orientational correlation function. J Magn Reson 21:369
87. Wist J, Perazzolo C, Bodenhausen G (2005) Slow motions in nondeuterated proteins: concerted chemical shift modulations of backbone nuclei. Appl Magn Reson 29:251-259
88. Wittebort R, Szabo A (1978) Theory of NMR relaxation in macromolecules: restricted diffusion and jump models for multiple internal rotations in amino acid side chains. J Chem Phys 69:1722-1736
89. Wittebort R, Szabo A (1985) Influence of vibrational motion on solid state line shapes and NMR relaxation. J Chem Phys 82:4753-4761
90. Woessner DE (1962) Spin relaxation processes in a two-proton system undergoing anisotropic reorientation. J Chem Phys 36:1-4
91. Yang D, Kay LE (1996) Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol 263:369-382
92. Yang D, Mittermaier A, Mok YK, Kay LE (1998) A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk. J Mol Biol 276:939-954
93. Zhang L, Brüschweiler R (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc 276:12654-12655
94. Zidek L, Novotny MV, Stone MJ (1999) Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nat Struct Biol 6:1118-1121