Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology

PLoS Computational Biology

Volumn 6, Issue 6, 2010, Pages 1-12

  Lezon, Timothy R ^a   Bahar, Ivet ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; ENTROPY; STRUCTURAL DYNAMICS; TOPOLOGY;

COLLECTIVE MODES; CROSS-CORRELATIONS; ELASTIC NETWORK MODELS; ENTROPY MAXIMIZATION; GLOBAL DYNAMICS; INTER-RESIDUE CONTACT; MEAN SQUARE FLUCTUATION; MODEL PREDICTION; NATIVE CONTACTS; SOFT MODES;

PROTEINS;

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; ENTROPY; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN SECONDARY STRUCTURE; ALGORITHM; BIOLOGY; CHEMISTRY; HYDROGEN BOND; METABOLISM; METHODOLOGY; NORMAL DISTRIBUTION; PROTEIN CONFORMATION; PROTEIN DATABASE;

PROTEIN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENTROPY; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; NORMAL DISTRIBUTION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 77955496805     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000816     Document Type: Article

References (64)

1. Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 17: 633-640.
2. Tobi D, Bahar I (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A 102: 18908-18913.
3. Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5: 789-796.
4. Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438: 117-121.
5. Jimenez A, Clapes P, Crehuet R (2008) A dynamic view of enzyme catalysis. J Mol Model 14: 735-746.
6. Zheng W (2009) Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase. Proteins 76: 747-762.
7. Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol Biosyst 4: 287-292.
8. Ming D, Wall ME (2005) Allostery in a coarse-grained model of protein dynamics. Physical Review Letters 95.
9. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2: 173-181.
10. Tirion MM (1996) Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Phys Rev Lett 77: 1905-1908.
11. Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alphaamylase inhibitor. Proteins 40: 512-524.
12. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505-515.
13. Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14: 1-6.
14. Hinsen K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33: 417-429.
15. Hinsen K, Thomas A, Field MJ (1999) Analysis of domain motions in large proteins. Proteins 34: 369-382.
16. Hinsen K, Petrescu A-J, Dellerue S (2000) Harmonicity in slow protein dynamics. Chem Phys 261: 25-37.
17. Yang L, Song G, Jernigan RL (2009) Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A 106: 12347-12352.
18. Kondrashov DA, Cui Q, Phillips GN, Jr. (2006) Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J 91: 2760-2767.
19. Kundu S, Melton JS, Sorensen DC, Phillips GN, Jr. (2002) Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 83: 723-732.
20. Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL (2006) The Extent of Cooperativity of ProteinMotions Observed with Elastic NetworkModels Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput 2: 696-704.
21. Petrone P, Pande VS (2006) Can conformational change be described by only a few normal modes? Biophys J 90: 1583-1593.
22. Jaynes E (1957) Information Theory and Statistical Mechanics. Phys Rev 106: 620-630.
23. Jaynes E (1957) Information Theory and Statistical Mechanics II. Phys Rev 108: 171-190.
24. Schneidman E, Berry MJ, Segev R, Bialek W (2006) Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 440: 1007-1012.
25. Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV (2006) Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci U S A 103: 19033-19038.
26. Hoang TX, Seno F, Trovato A, Banavar JR, Maritan A (2008) Inference of the solvation energy parameters of amino acids using maximum entropy approach. Journal of Chemical Physics 129.
27. Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980.
28. Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J 94: 3424-3435.
29. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
30. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1988) Numerical Recipes in C. Cambridge: Cambridge University Press.
31. Moritsugu K, Smith JC (2007) Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J 93: 3460-3469.
32. Lyman E, Pfaendtner J, Voth GA (2008) Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys J 95: 4183-4192.
33. Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 106: 14349-14354.
34. Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5: e1000393.
35. Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320: 1471-1475.
36. Liu L, Koharudin LM, Gronenborn AM, Bahar I (2009) A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. Proteins 77: 927-939.
37. Mittermaier AK, Kay LE (2009) Observing biological dynamics at atomic resolution using NMR. Trends in Biochemical Sciences 34: 601-611.
38. Kruschel D, Zagrovic B (2009) Conformational averaging in structural biology: issues, challenges and computational solutions. Molecular Biosystems 5: 1606-1616.
39. Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, et al. (2003) The precision of NMR structure ensembles revisited. J Biomol NMR 25: 225-234.
40. Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433: 128-132.
41. Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M (2007) The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. Journal of Biomolecular Nmr 37: 117-135.
42. Rieping W, Habeck M, Nilges M (2005) Inferential structure determination. Science 309: 303-306.
43. Laughton CA, Orozco M, Vranken W (2009) COCO: a simple tool to enrich the representation of conformational variability in NMR structures. Proteins 75: 206-216.
44. Abseher R, Horstink L, Hilbers CW, Nilges M (1998) Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins 31: 370-382.
45. Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, et al. (2007) Insights into equilibrium dynamics of proteins from comparison of NMR and Xray data with computational predictions. Structure 15: 741-749.
46. Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics 25: 606-614.
47. Jernigan RL, Bahar I (1996) Structure-derived potentials and protein simulations. Curr Opin Struct Biol 6: 195-209.
48. Miyazawa S, Jernigan RL (1985) Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
49. Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
50. Rojnuckarin A, Subramaniam S (1999) Knowledge-based interaction potentials for proteins. Proteins 36: 54-67.
51. Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213: 859-883.
52. Hao MH, Scheraga HA (1996) How optimization of potential functions affects protein folding. Proc Natl Acad Sci U S A 93: 4984-4989.
53. Kolinski A, Godzik A, Skolnick J (1993) A General-Method for the Prediction of the 3-Dimensional Structure and Folding Pathway of Globular-Proteins - Application to Designed Helical Proteins. Journal of Chemical Physics 98: 7420-7433.
54. Yang LW, Rader AJ, Liu X, Jursa CJ, Chen SC, et al. (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res 34: W24-W31.
55. Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A 84: 7524-7528.
56. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21: 167-195.
57. Goldstein RA, Luthey-Schulten ZA, Wolynes PG (1992) Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc Natl Acad Sci U S A 89: 9029-9033.
58. Wolynes PG, Onuchic JN, Thirumalai D (1995) Navigating the folding routes. Science 267: 1619-1620.
59. Lezon TR, Banavar JR, Maritan A (2006) The origami of life. Journal of Physics-Condensed Matter 18: 847-888.
60. Bahar I, Atilgan AR, Demirel MC, Erman B (1998) Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 80: 2733-2736.
61. Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I (1998) Identification of kinetically hot residues in proteins. Protein Sci 7: 2522-2532.
62. Haliloglu T, Keskin O, Ma B, Nussinov R (2005) How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J 88: 1552-1559.
63. Ortiz AR, Skolnick J (2000) Sequence evolution and the mechanism of protein folding. Biophys J 79: 1787-1799.
64. Yang Z, Majek P, Bahar I (2009) Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol 5: e1000360.