Folding Time Predictions from All-atom Replica Exchange Simulations

Journal of Molecular Biology

Volumn 372, Issue 3, 2007, Pages 756-763

  Yang, Sichun ^a,b   Onuchic, José N ^b   García, Angel E ^c   Levine, Herbert ^b  

^a Gordon Center for Integrative Science   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

diffusive model; folding kinetics; hairpin; replica exchange simulation

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN;

ARTICLE; BETA CHAIN; DIFFUSION COEFFICIENT; ENTROPY; HYDROGEN BOND; KINETICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; STOCHASTIC MODEL;

EID: 34548273698     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.010     Document Type: Article

References (52)

1. Onuchic J.N., and Wolynes P.G. Theory of protein folding. Curr. Opin. Struct. Biol. 14 (2004) 70-75
2. Bryngelson J.D., and Wolynes P.G. Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA 84 (1987) 7524-7528
3. Leopold P.E., Montal M., and Onuchic J.N. Protein folding funnels: kinetic pathways through compact conformational space. Proc. Natl Acad. Sci. USA 89 (1992) 8721-8725
4. Duan Y., and Kollman P. Pathways to a protein-folding intermediate observed in a 1-microsecond simulation in aqueous-solution. Science 282 (1998) 740-744
5. Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
6. Sanbonmatsu K., and García A.E. Structure of met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins: Struct. Funct. Genet. 46 (2002) 225-234
7. Zhou R., Berne B.J., and Germain R. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl Acad. Sci. USA 98 (2001) 14931-14936
8. Garcia A.E., and Onuchic J.N. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl Acad. Sci. USA 100 (2003) 13898-13903
9. Yang S., Cho S.S., Levy Y., Cheung M.S., Levine H., Wolynes P.G., and Onuchic J.N. Domain swapping is a consequence of minimal frustration. Proc. Natl Acad. Sci. USA 101 (2004) 13786-13791
10. Chen J., Im W., and Brooks C. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J. Am. Chem. Soc. 126 (2004) 16038-16047
11. Andrec M., Felts A.K., Gallicchio E., and Levy R.M. Protein folding pathways from replica exchange simulations and a kinetic network model. Proc. Natl Acad. Sci. USA 102 (2005) 6801-6806
12. Yang S., Levine H., and Onuchic J.N. Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. J. Mol. Biol. 352 (2005) 202-211
13. Best R.B., and Hummer G. Diffusive model of protein folding dynamics with Kramers turnover in rate. Phys. Rev. Lett. 96 (2006) 228104 (4 pp.)
14. Yang S., Onuchic J.N., and Levine H. Effective stochastic dynamics on a protein folding energy landscape. J. Chem. Phys. 125 (2006) 054910
15. Socci N.D., Onuchic J.N., and Wolynes P.G. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104 (1996) 5860-5868
16. Klimov D.K., and Thirumalai D. Viscosity dependence of the folding rates of proteins. Phys. Rev. Lett. 79 (1997) 317-320
17. Plotkin S.S., and Wolynes P.G. Non-Markovian configurational diffusion and reaction coordinates in protein folding. Phys. Rev. Lett. 80 (1998) 5015-5018
18. Munoz V., and Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA 96 (1999) 11311-11316
19. Schumaker M., Pomes R., and Roux B. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophys. J. 79 (2000) 2840-2857
20. Hummer G., and Kevrekidis I.G. Coarse molecular dynamics of a peptide fragment: free energy, kinetics, and long-time dynamics computations. J. Chem. Phys. 118 (2003) 10762-10773
21. Berezhkovskii A., and Szabo A. One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. J. Chem. Phys. 122 (2005) 014503
22. Wang J., Zhang K., Lu H., and Wang E. Quantifying kinetic paths of protein folding. Biophys. J. 89 (2005) 1612-1620
23. Wang J., Zhang K., Lu H., and Wang E. Dominant kinetic paths on biomolecular binding-folding energy landscape. Phys. Rev. Lett. 96 (2006) 168101 (4 pp.)
24. Kopelevich D.I., Panagiotopoulos A.Z., and Kevrekidis I.G. Coarse-grained kinetic computations for rare events: application to micelle formation. J. Chem. Phys. 122 (2005) 044908
25. Hummer G. Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J. Phys. 7 (2005) 34
26. Leite V.B.P., and Onuchic J.N. Structure and dynamics of solvent landscape in charge transfer reactions. J. Phys. Chem. 100 (1996) 7680-7690
27. Blanco F., Rivas G., and Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous-solution. Nat. Struct. Biol. 1 (1994) 584-590
28. Munoz V., Thompson P.A., Hofrichter J., and Eaton W.A. Folding dynamics and mechanism of beta-hairpin formation. Nature 390 (1997) 196-199
29. Dinner A.R., Lazaridis T., and Karplus M. Understanding beta-hairpin formation. Proc. Natl Acad. Sci. USA 96 (1999) 9068-9073
30. Pande V.S., and Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl Acad. Sci. USA 96 (1999) 9062-9067
31. Klimov D.K., and Thirumalai D. Mechanisms and kinetics of beta-hairpin formation. Proc. Natl Acad. Sci. USA 97 (2000) 2544-2549
32. Ma B., and Nussinov R. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. J. Mol. Biol. 296 (2000) 1091-1104
33. Guo C., Levine H., and Kessler D.A. How does a beta-hairpin fold/unfold? Competition between topology and heterogeneity in a solvable model. Proc. Natl Acad. Sci. USA 97 (2000) 10775-10779
34. García A.E., and Sanbonmatsu K.Y. Exploring the energy landscape of a β-hairpin in explicit solvent. Proteins: Struct. Funct. Genet. 42 (2001) 345-354
35. Zagrovic B., Sorin E.J., and Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313 (2001) 151-169
36. Tsai J., and Levitt M. Evidence of turn and salt bridge contributions to beta-hairpin stability: simulations of-terminal fragment from the B1 domain of protein. Biophys. Chem. 101-102 (2002) 187-201
37. Swope W., Pitera J., Suits F., Pitman M., Eleftheriou M., Fitch B., et al. Describing protein folding kinetics by molecular dynamics simulations: 2. Example applications to alanine dipeptide and a beta-hairpin peptide. J. Phys. Chem., B 108 (2004) 6582-6594
38. Bolhuis P.G. Kinetic pathways of beta-hairpin (un)folding in explicit solvent. Biophys. J. 88 (2005) 50-61
39. Baumketner A., and Shea J.-E. The thermodynamics of folding of a beta-hairpin peptide probed through replica exchange molecular dynamics simulations. Theor. Chem. Acc. (2006) 1-12
40. Munoz V., Ghirlando R., Blanco F., Jas G., Hofrichter J., and Eaton W. Folding and aggregation kinetics of a beta-hairpin. Biochemistry 45 (2006) 7023-7035
41. Bolhuis P.G. Transition-path sampling of beta-hairpin folding. Proc. Natl Acad. Sci. USA 100 (2003) 12129-12134
42. Singhal N., Snow C.D., and Pande V.S. Using path sampling to build better markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J. Chem. Phys. 121 (2004) 415-425
43. Elmer S.P., Park S., and Pande V.S. Foldamer dynamics expressed via Markov state models: I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. J. Chem. Phys. 123 (2005) 114902
44. Park S., and Pande V.S. Validation of Markov state models using Shannon's entropy. J. Chem. Phys. 124 (2006) 054118
45. Chodera J.D., Swope W.C., Pitera J.W., and Dill K.A. Obtaining long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Model. Simul. 5 (2006) 1214-1226
46. Jayachandran G., Vishal V., Garcia A.E., and Pande V.S. Local structure formation in simulations of two small proteins. J. Struct. Biol. 157 (2007) 491-499
47. Voter A.F. Parallel replica method for dynamics of infrequent events. Phys. Rev., B Condens Matter 57 (1998) R13985-R13988
48. Spoel D.V.D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J.C. Gromacs: fast, flexible, and free. J. Comput. Chem. 26 (2005) 1701-1718
49. Kaminski G., Friesner R., Tirado-Rives J., and Jorgensen W. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem., B 105 (2001) 6474-6487
50. van Kampen N.G. Stochastic Processes in Physics and Chemistry (2004), North-Holland, Amsterdam
51. Gardiner C.W. Handbook of Stochastic Methods. 3rd edit. (2004), Springer Verlag, New York
52. Taylor J.R. An Introduction to Error Analysis. 2nd edit (1997), University Science Books, Sausalito, CA