Protein flexibility from discreate molecular dynamic simulation using quasi - Physical potentials

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 1, 2010, Pages 83-94

  Emperador, Agustí ^a,b   Meyer, Tim ^a,b   Orozco, Modesto ^a,b,c  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b BARCELONA SUPERCOMPUTING CENTER   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Coarse grained protein models; Discrete molecular dynamics; Principal component analysis; Protein flexibility

Indexed keywords

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN DATABASE;

PROTEIN;

COMPUTER SIMULATION; DATABASES, PROTEIN; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEINS;

EID: 77949346997     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22563     Document Type: Article

References (81)

1. Ma J, Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sei USA 1998; 95: 8502-8507. (Pubitemid 28350517)
2. Daniel RM, Dumm RV, Finney JL, Smith CJ. The role of dynamics in enzyme activity. Annu Rev Biophys Biomol Struct 2003; 32: 69-92.
3. Eisenmesser EZ, Bosco DA, Akke MD, Kern D. Enzyme dynamics during catalysis. Science 2002; 295: 1520-1523.
4. Luo J, Bruice TC. Anticorrelated motions as a driving force in enzyme catalysis: the dehydrogenase reaction. Proc Natl Acad Sci USA 2004; 101: 13152-13156. (Pubitemid 39209634)
5. Hinsen K, Thomas A, Field MJ. Analysis of domain motions in large proteins. Proteins 1999; 34: 369-382. (Pubitemid 29071678)
6. Waldron TT, Murphy KP. Stabilization, of proteins by Iigand binding: application to drug screening and determination of unfolding energetics. Biochemistry 2003; 42: 5058-5064.
7. Yang L-W, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005; 13: 893-904. (Pubitemid 40804392)
8. Sacquin-Mora S, Lavery R. Investigating the local flexibility of functional residues in hemoproteins. Biophys J 2006; 90: 2706-2717.
9. Remy I, Wilson IA, Michnick SW. Erythropoietin receptor activation by a ligand-induced conformation, change. Science 1999; 283: 990-993. (Pubitemid 129505219)
10. Henzler-Wildman KA, Ming L, Vu T, Kerns SJ, Karplus M, Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007; 450: 913-916. (Pubitemid 350231333)
11. league SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2008; 2: 527-541.
12. Marvin JS, Hellinga HW. Manipulation of Iigand binding affinity by exploitation of conformational coupling. Nature Struct Biol 2001; 8: 795-798.
13. Falke JJ. A moving story. Science 2002; 295: 1480-1481.
14. Kenakin T. Agonist receptor efficacy 1: mechanisms of efficacy and receptor promiscuity. Trends Pharmacol. Sci 1995; 16: 188-192.
15. Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at single protein site: a matter of pre-existing populations. Protein Sci 2002;11: 184-197. (Pubitemid 34075781)
16. Shoichet BK, Baase WA, Kuroki R, Matthews B. A. relationship between protein stability and protein function. Proc Natl Acad Sci USA 1995; 92: 452-456.
17. Karplus M., McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002; 9: 646-652.
18. Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005; 102: 6679-6685.
19. Karplus M, McCammon JA. The dynamics of proteins. Sci Am 1986; 254: 42-51.
20. McCammon JA, Gelin BR, Karplus M.. Dynamics of folded proteins. Nature 1977; 267: 585-590.
21. Allen MP, Tildesley DJ. Computer simulation, of liquids. Oxford: Clarendon Press; 1989.
22. Brooks CL, III, Karplus M, Petti BM. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. Cambridge: Cambridge University Press, 1987.
23. Warshel A. Bicycle-pedal, model for the first step in the vision, process. Nature 1976; 260: 679-683.
24. Van Gunsteren WF, Karplus M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry 1982; 21: 2259-2274.
25. Berendsen. HJC, Postma JPM., Van Gunsteren. WF, DiNoIa A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684-3690.
26. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005; 15: 586-592. (Pubitemid 41393491)
27. Rueda M, Chacon P, Orozco M. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure 2007; 15: 565-575. (Pubitemid 46722600)
28. McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids. Cambridge: Cambridge University Press, 1987.
29. Karanicolas J, Brooks CL. The origins of asymmetry in. the folding transition states of protein L and protein G. Protein Sci 2002; 11: 2351-2361.
30. Paci E, Vendruscolo M, Marplus M. Native and non-native interactions along protein folding and unfolding pathways. Proteins: Struct Funct Genet 2002; 47: 379-392. (Pubitemid 34438687)
31. Zarrine-Afsar A, Waliin S, Necuiai AM, Neudekker P, Howell PL, Davidson. AR, Cahn HS. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Proc Natl Acad Sci USA 2008; 105: 9999-10004.
32. Alder BJ, Wainwright TE. Studies in molecular dynamics. I. General method. J Chem. Phys 1959; 31: 459-1166
33. Smith WS, Hall. CK, Freeman BD. Molecular dynamics for polymeric fluids using discontinuous potentials. J Comput Phys 1997; 134: 16-30.
34. Emperador A, Carrillo O, Rueda M, Orozco M. Exploring the suitability of coarse-grained techniques for the representation of protein, dynamics. Biophys J 2008; 95: 2127-2138.
35. Emperador A, Meyer T, Orozco M. United-atom, discrete molecular dynamics of proteins using physics-based potentials. J Chem Theory Comput 2008; 4: 2001-2010.
36. Taketomi H, Ueda Y, Go N. Studies of protein folding, unfolding and fluctuations by computer simulations. Int J Pept Protein Res 1975; 7: 445-459.
37. Ding F, Tsao D, Nie H, Dokholyan NV. Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure 2008; 16: 1010-1018. (Pubitemid 351899281)
38. Ding F, Buldyrev SV, Dokholyan NV. Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J 2005; 88: 147-155. (Pubitemid 40070665)
39. Zhou YQ, Karplus M. Interpreting the folding kinetics of helical proteins. Nature 1999; 401: 400-403. (Pubitemid 29454967)
40. Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich. EI. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 1998; 3: 577-587. (Pubitemid 29023621)
41. Linhananta A, Zhou Y. The role of side chain packing and native contact interactions in folding: discontinuous molecular dynamics folding simulations of an all-atom. Go model of fragment B of Staphylococcal protein A. J Chem Phys 2002; 117: 8983-8995. (Pubitemid 35457605)
42. Luo Z, Ding J, Zhou Y. Temperature-dependent folding pathways of pinl WW domain; an all-atom molecular dynamics simulation of a Go model. Biophys J 2007; 93: 2152-2161. (Pubitemid 47437598)
43. Zhou Y, Linhananta A. Role of hydrophilic and hydrophobic contacts in folding of the second b-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model. Proteins: Struct Fund Genet 2002; 47: 154-162. (Pubitemid 34263329)
44. Ding F, Sharma S, Chalasani P, Demidov W, Broude NE, Dokholyan NV. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 2008; 14: 1164-1173. (Pubitemid 351717496)
45. Sharma S, Ding F, Dokholyan NV. Multiscale modeling of nucleosome dynamics. Biophys J 2007; 92: 1457-1470.
46. Ding F, Dokholyan NV, Buldyrev SV, Stanley EH, Shakhnovich EI. Molecular dynamic simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism.. J Mol Biol 2002; 324: 851-857. (Pubitemid 36044117)
47. Chen Y, Dokholyan NV. A single disulfide bond differentiates aggregation pathways of ß2-microglobulm. J Mol. Biol 2005; 354: 473-482. (Pubitemid 41579859)
48. Ding F, LaRocque JJ, Dokholyan NV. Direct observation of protein folding, aggregation, and a prion-like conformational conversion. J Biol Chem 2005; 280: 40235-40240. (Pubitemid 41779161)
49. Khare SD, Ding F, Gwanmesia KM, Dokholyan NV. Molecular origin of polyglutamine-mediated protein, aggregation in neurodegenerative diseases. PLoS Comput Biol 2005; 1: 230-235.
50. Marchut AJ, Hall CK. Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations. Biophys J 2006; 90: 4574-4584. (Pubitemid 43830901)
51. Nguyen HD, Hall CK. Molecular dynamics simulations of spontaneous fibril, formation by random-coil peptides. Proc Nad Acad Sei USA 2004; 101: 16180-16185. (Pubitemid 39552819)
52. Peng S, Ding F, Urbane B, Buldyrev SV, Cruz L, Stanley HE, Dokholyan NV. Discrete molecular dynamics simulations of peptide aggregation. Phys Rev E 2004; 69: 041908.
53. Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV. Mechanism for the alpha-helix to beta-hairpin transition. Proteins: Struct Funct Genet 2003; 53: 220-228.
54. Urbane B, Cruz L, Buldyrev SV, Bitan G, Teplow DB, Stanley HE. In silico study of amyloid beta protein folding and oligomerization. Proc Natl Acad Sei USA 2004; 101: 17345-17350.
55. Yun S, Urbane B, Cruz L, Bitan G, Teplow DB, Stanley HE. Role of electrostatic interactions in amyloid beta-protein (ABeta) oligomer formation: a discrete molecular dynamics study. Biophys J 2007; 92: 4064-4077. (Pubitemid 46910591)
56. Borreguero JM, Urbane B, Lazo ND, Buldyrev SV, Teplow DB, Stanley HE. Folding events in the 21-30 region of amyloid beta-protein (ABeta) studied in silico. Proc Natl Acad Sci USA 2005; 102: 6015-6020.
57. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins: Struct Funct Genet 1999; 35: 133-152. (Pubitemid 29165128)
58. Rueda M, Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi JL, Orozco M. A consensus view of protein dynamics. Proc Natl Acad Sei USA 2007; 104: 796-801.
59. Cornell. WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman P. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995; 117: 51795197.
60. MacKerell AD, Bashford D, Beilott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen. DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102: 3586-3616. (Pubitemid 128576688)
61. MacKerell AD, Wiorkiewicz-Kuczera J, Jr, Karplus M. An all-atom empirical energy function for the simulation of nucleic acids. J Am Chem Soc 1995;117: 11946-11975. (Pubitemid 126634921)
62. Damm W, Frontera A, Tirado-Rives J, Jorgensen WL. OPLS allatom force field for carbohydrates. J Comput Chem 1997; 18: 1955-1970. (Pubitemid 127598549)
63. Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225-11236. (Pubitemid 26399746)
64. Kaminski G, Duffy EM, Matsui T, Jorgensen WL. Free energies of hydration and pure liquid properties of hydrocarbons from, the OPLS all-atom model. J Phys Chem 1994; 98: 13077-13082.
65. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum, chemical calculations on peptides. J Phys Chem B 2001; 105: 6474-6487. (Pubitemid 35339015)
66. Darden TL, York D, Pedersen L. Particle Mesh Ewald: AN N-log(N) method for Ewald sums in large systems. J Chem. Phys 1993; 98: 10089-10092.
67. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian, equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1997; 23: 327-341.
68. Andersen HC. Rattle: a velocity version of the SHAKE algorithm for molecular dynamics calculations. J Comput Phys 1983; 52: 24-34.
69. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926-935.
70. Mahoney MW, Jorgensen WL. A. five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 2000; 112: 8910-8922.
71. Case DA, Pearlman DA, Caldwell JW, Cheatham TE, Ross WS, Simmerling CL, Darden TL, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER8. San Francisco: University of California, 2004.
72. Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 1999; 151: 283-312.
73. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot. C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26: 1781-1802.
74. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005; 33: 2302-2309.
75. Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins .1993; 17: 412-425.
76. Hess B. Similarities between principal components of protein dynamics and random diffusion. Phys Rev E 2000; 62: 8438-8448. (Pubitemid 32087906)
77. Noy A, Meyer T, Rueda M., Ferrer C, Valencia A, Perez A, Orozco M, de la Cruz X, Luque FJ. Data mining of molecular dynamics trajectories of nucleic acids. J Biomol Struct Dyn 2006; 23: 357-484. (Pubitemid 43099656)
78. Orozco M, Perez A, Noy A, Luque FJ. Theoretical methods for the simulation of nucleic acids. Chem Soc Rev 2003; 32: 350-364. (Pubitemid 38353226)
79. Brlischweiler R. Collective protein dynamics and nuclear spin, relaxation. J Chem Phys 1995; 102: 3396-3403.
80. Zhou Y, Vitkup D, Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J MoI Biol 1999; 285: 1371-1375, (Pubitemid 29060440)
81. Zhou Y, Karplus M. Folding thermodynamics of a model threehelix bundle protein. Proc Natl Acad Sei USA 1997; 94: 14429-14432. (Pubitemid 28041390)