Application of the random coil index to studying protein flexibility

Journal of Biomolecular NMR

Volumn 40, Issue 1, 2008, Pages 31-48

  Berjanskii, Mark V ^a   Wishart, David S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Chemical shift; Flexibility; NMR; Order parameters; Protein

Indexed keywords

ARTICLE; AUTOMATION; CARBON NUCLEAR MAGNETIC RESONANCE; COMPUTER PROGRAM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; RANDOM COIL INDEX; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS;

ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOFTWARE;

EID: 37848999781     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-007-9208-0     Document Type: Article

References (83)

1. Baber JL, Levens D, Libutti D et al (2000) Chemical shift mapped DNA-binding sites and 15N relaxation analysis of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K. Biochemistry 39:6022-6032
2. Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970-14971
3. Berjanskii M, Wishart DS (2006) NMR: Prediction of protein flexibility. Nature Protocols 1:683-688
4. Berjanskii MV, Riley MI, Xie A et al (2000) NMR structure of the N-terminal J domain of polyomavirus T antigens: Implications for DnaJ-like domains and for T antigen mutations. J Biol Chem 275:36094-36103
5. Berjanskii M, Riley M, Van Doren SR (2002) Hsc70-interacting HPD loop of the J domain of polyomavirus T antigens fluctuates in ps to ns and micros to ms. J Mol Biol 321:503-516
6. Braun D, Wider G, Wuthrich K (1994) Sequence-corrected N-15 random coil chemical-shifts. J Am Chem Soc 116:8466-8469
7. Bundi A, Wuthrich K (1979) H-1-NMR parameters of the common amino-acid residues measured in aqueous-solutions of the linear tetrapeptides H-GLY-GLY-X-L-ALA-OH. Biopolymers 18:285-297
8. Bundi A, Grathwohl C, Hochmann J et al (1975) Proton NMR of protected tetrapeptides TFA-GLY-GLY-L-X-L-ALA-OCH3, where X stands for one of 20 common amino-acids. JMagn Reson 18:191-198
9. Carugo O, Argos P (1999) Reliability of atomic displacement parameters in protein crystal structures. Acta Crystallogr D Biol Crystallogr 55(Pt 2):473-478
10. Case DA (1998) The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 8:624-630
11. Case DA (2002) Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res 35:325-331
12. Chang SL, Tjandra N (2001) Analysis of NMR relaxation data of biomolecules with slow domain motions using wobble-in-a-cone approximation. J Am Chem Soc 123:11484-11485
13. Chen J, Brooks CL 3rd, Wright PE (2004) Model-free analysis of protein dynamics: Assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 29:243-257
14. Chou YT, Swain JF, Gierasch LM (2002) Functionally significant mobile regions of Escherichia coli SecA ATPase identified by NMR. J Biol Chem 277:50985-50990
15. Clore GM, Szabo A, Bax A et al (1990) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112:4989-4991
16. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302
17. Dalgarno DC, Levine BA, Williams RJ (1983) Structural information from NMR secondary chemical shifts of peptide alpha C-H protons in proteins. Biosci Rep 3:443-452
18. Damberg P, Jarvet J, Graslund A (2005) Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation. J Am Chem Soc 127:1995-2005
19. Dedios AC, Oldfield E (1994) Chemical-shifts of carbonyl carbons in peptides and proteins. J Am Chem Soc 116:11485-11488
20. Dyson HJ, Wright PE (1998) Equilibrium NMR studies of unfolded and partially folded proteins. Nat Struct Biol 5(Suppl):499-503
21. Eghbalnia HR, Wang L, Bahrami A et al (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 32:71-81
22. Elofsson A, Nilsson L (1993) How consistent are molecular-dynamics simulations - comparing structure and dynamics in reduced and oxidized Escherichia-Coli thioredoxin. J Mol Biol 233:766-780
23. Farrow NA, Zhang O, Forman-Kay JD et al (1997) Characterization of the backbone dynamics of folded and denatured states of an SH3 domain. Biochemistry 36:2390-2402
24. Fiaux J, Bertelsen EB, Horwich AL et al (2002) NMR analysis of a 900K GroEL GroES complex. Nature 418:207-211
25. Fushman D, Cahill S, Cowburn D (1997) The main-chain dynamics of the dynamin pleckstrin homology (Ph) domain in solution - analysis of N-15 relaxation with monomer/dimer equilibration. J Mol Biol 266:173-194
26. Glushka J, Lee M, Coffin S et al (1989) N-15 chemical-shifts of backbone amides in bovine pancreatic trypsin-Inhibitor and apamin. J Am Chem Soc 111:7716-7722
27. Grathwoh C, Wuthrich K (1974) C-13 NMR of protected tetrapeptides TFA-GLY-GLY-L-X-L-ALA-OCH3, where X stands for 20 common amino-acids. J Magn Reson 13:217-225
28. Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274-1279
29. Horita DA, Zhang W, Smithgall TE et al (2000) Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations. Protein Sci 9:95-103
30. Huang X, Peng JW, Speck NA et al (1999) Solution structure of core binding factor beta and map of the CBF alpha binding site. Nat Struct Biol 6:624-627
31. Ishima R, Torchia DA (2000) Protein dynamics from NMR. Nat Struct Biol 7:740-743
32. Jin DQ, Andrec M, Montelione GT et al (1998) Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. J Biomol NMR 12:471-492
33. Kay LE (1998) Protein dynamics from NMR. Nat Struct Biol 5(Suppl):513-517
34. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: A program for display and analysis of macromolecular structures. J Mol Graphics 14:51-55
35. Korzhnev DM, Orekhov VY, Arseniev AS (1997) Model-free approach beyond the borders of its applicability. J Magn Reson 127:184-191
36. Lacroix E, Bruix M, Lopez-Hernandez E et al (1997) Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli. J Mol Biol 271:472-487
37. Le HB, Oldfield E (1996) Ab initio studies of amide-N-15 chemical shifts in dipeptides: Applications to protein NMR spectroscopy. J Phys Chem 100:16423-16428
38. Lecroisey A, Martineau P, Hofnung M et al (1997) NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. J Biol Chem 272:362-368
39. Levitt MH (2001) Spin dynamics: Basics of nuclear magnetic resonance. Wiley, Chichester
40. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Model 7:306-317
41. Lindorff-Larsen K, Best RB, Depristo MA et al (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128-132
42. Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546-4559
43. Lukin JA, Gove AP, Talukdar SN et al (1997) Automated probabilistic method for assigning backbone resonances of (C-13,N-15)-labeled proteins. J Biomol NMR 9:151-166
44. McConnell HM (1958) Reaction Rates by Nuclear Magnetic Resonance. J Chem Phys 28:430-431
45. Merutka G, Dyson HJ, Wright PE (1995) Random Coil H-1 Chemical-Shifts Obtained as a Function of Temperature and Trifluoroethanol Concentration for the Peptide Series Ggxgg. J Biomol NMR 5:14-24
46. Mielke SP, Krishnan VV (2004) An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts. J Biomol NMR 30:143-153
47. Neal S, Nip AM, Zhang H et al (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 26:215-240
48. Oldfield E (1995) Chemical shifts and three-dimensional protein structures. J Biomol NMR 5:217-225
49. Osapay K, Case DA (1994) Analysis of proton chemical shifts in regular secondary structure of proteins. J Biomol NMR 4:215-230
50. Palmer AG 3rd (2001) NMR probes of molecular dynamics: Overview and comparison with other techniques. Annu Rev Biophys Biomol Struct 30:129-155
51. Palmer AG 3rd, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 339:204-238
52. Pang Y, Buck M, Zuiderweg ER (2002) Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics. Biochemistry 41:2655-2666
53. Pardi A, Wagner G, Wuthrich K (1983) Protein conformation and proton nuclear-magnetic-resonance chemical shifts. Eur J Biochem 137:445-454
54. Penkett CJ, Redfield C, Jones JA et al (1998) Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus. Biochemistry 37:17054-17067
55. Petsko GA, Ringe D (1984) Fluctuations in protein structure from X-ray diffraction. Annu Rev Biophys Bioeng 13:331-371
56. Richarz R, Wuthrich K (1978) C-13 Nmr Chemical-Shifts of Common Amino-Acid Residues Measured in Aqueous-Solutions of Linear Tetrapeptides H-Gly-Gly-X-L-Ala-Oh. Biopolymers 17:2133-2141
57. Sahu SC, Bhuyan AK, Udgaonkar JB et al (2000) Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study. J Biomol NMR 18:107-118
58. Sanders CR, Landis GC (1994) Facile acquisition and assignment of oriented sample NMR-spectra for bilayer surface-associated proteins. J Am Chem Soc 116:6470-6471
59. Schwarzinger S, Kroon GJ, Foss TR et al (2001) Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 123:2970-2978
60. Schwarzinger S, Kroon GJ, Foss TR et al (2000) Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView. J Biomol NMR 18:43-48
61. Scott WRP, Hunenberger PH, Tironi IG et al (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596-3607
62. Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and C-alpha and C-beta C-13 nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492
63. Sun HH, Sanders LK, Oldfield E (2002) Carbon-13 NMR shielding in the twenty common amino acids: Comparisons with experimental results in proteins. J Am Chem Soc 124:5486-5495
64. Szilagyi L (1995) Chemical-shifts in proteins come of age. Prog Nucl Magn Reson Spectrosc 27:325-443
65. Thanabal V, Omecinsky DO, Reily MD et al (1994) The 13C chemical shifts of amino acids in aqueous solution containing organic solvents: application to the secondary structure characterization of peptides in aqueous trifluoroethanol solution. J Biomol NMR 4:47-59
66. van Gunsteren WF, Mark AE (1998) Validation of molecular dynamics simulation. J Chem Phys 108:6109-6116
67. Vila JA, Ripoll DR, Baldoni HA et al (2002) Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: A theoretical study. J Biomol NMR 24:245-262
68. Wand AJ (2001) Dynamic activation of protein function: A view emerging from NMR spectroscopy. Nat Struct Biol 8:926-931
69. Wang Y, Jardetzky O (2002a) Investigation of the neighboring residue effects on protein chemical shifts. J Am Chem Soc 124:14075-14084
70. Wang Y, Jardetzky O (2002b) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861
71. Wang Y, Jardetzky O (2004) Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from PHI, PSI i-1, and CHI-1 torsion angles. J Biomol NMR 28:327-340
72. Wang Y, Wishart DS (2005) A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins. J Biomol NMR 31:143-148
73. Wang T, Cai S, Zuiderweg ER (2003) Temperature dependence of anisotropic protein backbone dynamics. J Am Chem Soc 125:8639-8643
74. Wishart DS, Nip AM (1998) Protein chemical shift analysis: A practical guide. Biochem Cell Biol 76:153-163
75. Wishart DS, Sykes BD (1994) The 13C chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171-180
76. Wishart DS, Sykes BD (1994) Chemical shifts as a tool for structure determination. Methods Enzymol 239:363-392
77. Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311-333
78. Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647-1651
79. Wishart DS, Bigam CG, Holm A et al (1995) 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 5:67-81
80. Wolf-Watz M, Grundstrom T, Hard T (2001) Structure and backbone dynamics of Apo-CBFbeta in solution. Biochemistry 40:11423-11432
81. Xu XP, Case DA (2002) Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408-423
82. Zhang F, Bruschweiler R (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc 124:12654-12655
83. Zhang H, Neal S, Wishart DS (2003) RefDB: A database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173-195