Global optimisation by replica exchange with scaled hybrid Hamiltonians

Molecular Simulation

Volumn 34, Issue 6, 2008, Pages 575-590

  Xu, Weixin ^a   Yang, Ye ^a   Mu, Yuguang ^a   Nordenskiöld, Lars ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

All atom simulation; Global optimisation; Replica exchange with scaled hybrid Hamiltonian; Trpzip2 hairpin

Indexed keywords

AMINES; AMINO ACIDS; BINDING SITES; DYNAMICS; HAMILTONIANS; HYDROGEN; HYDROGEN BONDS; MODEL STRUCTURES; MOLECULAR DYNAMICS; NONMETALS; NUCLEAR MAGNETIC RESONANCE; QUANTUM CHEMISTRY; SHAPE OPTIMIZATION; STRUCTURAL OPTIMIZATION;

ALL-ATOM SIMULATION; COMPACT PACKING; EXPLICIT WATER; EXTENDED STRUCTURES; FOLDING MECHANISMS; FOLDING PROCESSES; GLOBAL OPTIMISATION; HEAVY ATOMS; LATE STAGE; MOLECULAR DYNAMICS SIMULATION; NMR MODELS; OPTIMISATION; REPLICA EXCHANGE; REPLICA-EXCHANGE WITH SCALED HYBRID HAMILTONIAN; ROOT MEAN SQUARED; STRUCTURAL DATA; STRUCTURE PREDICTION; TRANSITION STATE ENSEMBLE;

GLOBAL OPTIMIZATION;

EID: 49549116236     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020801947020     Document Type: Article

References (81)

1. S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi, Optimization by simulated annealing, Science 220 (1983), pp. 671-679.
2. D.J. Wales and H.A. Scheraga, Global optimization of clusters, crystals, and biomolecules, Science 285 (1999), pp. 1368-1372.
3. U.H. E. Hansmann and Y. Okamoto, New Monte Carlo algorithms for protein folding, Curr. Opin. Struct. Biol. 9 (1999), pp. 177-183.
4. A. Mitsutake, Y. Sugita, and Y. Okamoto, Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 60 (2001), pp. 96-123.
5. B.A. Berg and T. Neuhaus, Multicanonical ensemble: A new approach to simulate first-order phase transitions, Phys. Rev. Lett. 68(1992), pp. 9-12.
6. E. Marinari and G. Parisi, Simulated tempering: A new Monte Carlo scheme, Europhys. Lett. 19 (1992), pp. 451-458.
7. A.P. Lyubartsev, A.A. Martsinovski, S.V. Shevkunov, and P.N. Verentsov-Velayaminov, New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles, J. Chem. Phys. 96 (1992), pp. 1776-1783.
8. U.H.E. Hansmann, Parallel tempering algorithm, for conformational studies of biological molecules, Chem. Phys. Lett. 281 (1997), pp. 140-150.
9. Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 314 (1999), pp. 141-151.
10. R. Zhou, B.J. Berne, and R. Germain, The free energy landscape for beta hairpin folding in explicit water, Proc. Natl. Acad. Sci. USA 98 (2001), pp. 14931-14936.
11. A.E. Garcia and J.N. Onuchic, Folding aprotein in a computer: An atomic description of the folding/unfolding of protein A, Proc. Natl. Acad. Sci. USA 100 (2003), pp. 13898-13903.
12. H. Fukunishi, O. Watanabe, and S. Takada, On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction, J. Chem. Phys. 116 (2002), pp. 9058-9067.
13. M.M. Seibert, A. Partriksson, B. Hess, and D. van der Spoel, Reproducible polypeptide folding and structure prediction using molecular dynamics simulations, J. MoI. Biol. 354 (2005), pp. 173-183.
14. D.M.. Zucherman and E. Lyman, A second look at canonical smapling of biomolecules using replica exchange simulation, J. Chem. Theory. Comput. 2 (2006), pp. 1200-1202.
15. X. Per.io.le and A.E. Mark, Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit water, J. Chem. Phys. 126 (2007), pp. 014903-014911.
16. P. Liu, B. Kim, R.A. Friesner, and B.J. Berne, Replica exchange with solute tempering: A method for sampling biological systems in explicit water, Proc. Natl. Acad. Sci. USA 102 (2005), pp. 13749-13754.
17. T.Z. Lwin and R. Luo, Overcoming entropic barrier with coupled sampling at dual resolutions, J. Chem. Phys. 123 (2005), pp. 1949041-19490410.
18. X. Cheng, G. Cui, V. Hornak, and C. Simmerling, Modified replica exchange simulation methods for local structure refinement, J. Phys. Chem. B 109 (2005), pp. 8220-8230.
19. E. Lyman, F.M. Ytreberg, and D.M. Zuckerman, Resolution exchange simulation, Phys. Rev. Lett. 96 (2006), pp. 028104-028105.
20. A. Okur, L. Wickstrom, M. Layten, R. Geney, K. Song, V. Hornak, and C. Simmerling, Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model, J. Chem. Theory. Comput. 2 (2006), pp. 420-433.
21. Y. Mu and Y. Yang, Modeling of water explicitly In the replica-exchange simulation method for protein folding, NIC Series:http://www.fz-juelich.de/nic-series/volume34/mu.pdf. 34 (2006), pp. 119-224.
22. D. Qiu, P.S. Shenkin, F.P. Hollinger, and W.C. Still, The GB/SA continuum model for solvation: A fast analytical method for the calculation of approximate Bom radii, J. Phys. Chem. A 101 (1997), pp. 3005-3014.
23. R.M. Hughes and M.L. Waters, Model systems for β-hairpins and β-sheets, Curr. Opin. Struct. Biol. 16 (2006), pp. 514-524.
24. A.G. Cochran, N.J. Skelton, and M.A. Starovasnik, Tryptophan zippers: Stable, monomeric β-hairpins, Proc. Natl. Acad. Sci. USA 98 (2001), pp. 5578-5583.
25. S. Gianni, N.R. Guydosh, F. Khan, T.D. Caldas, U. Mayor, G.W. White, M.L. DeMarco, V. Daggett, and A.R. Fersht, Unifying features in protein-folding mechanisms, Proc. Natl. Acad. Sci. USA 100 (2003), pp. 13286-13291.
26. M. Petrovich, A.L. Jonsson, N. Ferguson, V. Daggett, and A.R. Fersht, phi-Analysis at the experimental limits: Mechanism of beta-hairpin formation, J. Mol. Biol. 360 (2006), pp. 865-881.
27. V. Munoz, E.R. Henry, J. Hofrichter, and W.A. Eaton, A statistical model for β-hairpin kinetics, Proc. Natl. Acad. Sci. USA 95 (1998), pp. 5872-5879.
28. A. Kolinski, B. Ilkowski, and J. Skolnick, Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques, Biophys. J. 77 (1999), pp. 2942-2952.
29. V.S. Pande and D.S. Rokhsar, Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G, Proc. Natl. Acad. Sci. USA 96 (1999), pp. 9062-9067.
30. A.R. Dinner, T. Lazaridis, and M. Karplus, Understanding β-hairpin formation, Proc. Natl. Acad. Sci. USA 96 (1999), pp. 9037-9068.
31. V. Munoz, P.A. Thompson, J. Hofrichter, and W.A. Eaton, Folding dynamics and mechanism of β-hairpin formation, Nature 390 (2003), pp. 196-199.
32. K. Klimov and D. Thirumalai, Mechanisms and kinetics of β-hairpin formation, Proc. Natl. Acad. Sci. USA 97 (2000), pp. 2544-2549.
33. B. Zagrovic, E.J. Sorin, and V.S. Pande, β-hairpin folding simulations in atomistic detail using an implicit solvent model, J. Mol. Biol. 313 (2001), pp. 151-169.
34. A.E. Garcia and K.Y. Sanbonmatsu, Exploring the energy landscape of a β-hairpin in explicit solvent, Proteins 42 (2001), pp. 345-354.
35. P.G. Bolhuis, Transition-path sampling of β-hairpin folding, Proc. Natl. Acad. Sci. USA 100 (2003), pp. 12129-12134.
36. N. Kobayashi, S. Honda, H. Yoshii, and E. Munekata, Role of side chains in the cooperative β-hairpin folding of the short C-terminal fragment derived from streptococcal protein G, Biochemistry 39 '(2000), pp. 6564-6571.
37. R.H. Zhou, B.J. Berne, and R. Germain, The free energy landscape for βhairpin folding in explicit water, Proc. Natl. Acad. Sci. USA 98 (2001), pp. 14931-14936.
38. J. Tsai and M. Levitt, Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G, Biophys. Chem. 101 (2002), pp. 187-201.
39. Y.Q. Zhou and A. Linhananta, Role of hydrophilic and hydrophobic contacts infolding of the second β-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model, Proteins 47 (2002), pp. 154-162.
40. Xu. Wu, S. Wang, and B.R. Brooks, Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation, J. Am. Chem. Soc. 124 (2002), pp. 5282-5283.
41. G.H. Wei, N. Mousseau, and P. Derreumaux, Complex folding pathways in a simple β-hairpin, Proteins 56 (2004), pp. 464-474.
42. K.A. Olsen, R.M. Fesinmeyer, J.M. Stewart, and N.H. Andersen, Hairpin folding rates reflect mutations within and remote from the turn region, Proc. Natl. Acad. Sci. USA 102 (2005), pp. 15483-15487.
43. P.H. Nguyen, Y.G. Mu, and G. Stock, Structure and energy landscape of a photoswithchable peptide: A replica exchange molecular dynamics study, Proteins 60 (2005), pp. 485-494.
44. G. Bussi, F.L. Gervasio, A. Laio, and M. Parrinello, Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics, J. Am. Chem., Soc. 128 (2006), pp. 13435-13441.
45. S. Patel, P. Sista, P.V. Balaji, and Y.U. Sasidhar, β-hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease, J. MoI. Graph. Model 25 (2006), pp. 103-115.
46. D.G. Du, M. Tucker, and F. Gai, Understanding the mechanism of beta-hairpin folding via phi-value analysis, Biochemistry 45 (2006), pp. 2668-2678.
47. J. Zhang, M. Qin, and W. Wang, Folding mechanism of β-hairpins studied by replica exchange molecular simulations, Proteins 62 (2006), pp. 672-685.
48. A.M. J. J. Bonvin and W.F. van. Gunsteren, β-hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat, J. Mol. Biol. 296 (2000), pp. 255-268.
49. D.G. Du, Y.J. Zhu, C.Y. Huang, and F. Gai, Understanding the key factors that control the rate of β-hairpin folding, Proc. Natl. Acad. Sci. USA 101 (2004), pp. 15915-15920.
50. H.J.C. Berendsen, D. van der Spoel, and R. van Drunen, A message-passing parallel molecular dynamics implementation, Comp. Phys. Comm. 91 (1995), pp. 43-56.
51. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118(1996), pp. 11225-11236.
52. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije, LINCS: A linear constraint solver for molecular simulations, J. Comp. Chem, 18 (1997), pp. 1463-1472.
53. R. V. Pappu, R.K. Hart, and J. W. Ponder, Analysis and application of potential energy smoothing and search methods for global optimization, J. Phys. Chem. B 102 (1998), pp. 9725-9742.
54. W.X. Xu, J. Wang, and W. Wang, Folding behavior of chaperonin-mediated substrate protein. Proteins 61 (2005), pp. 777-794.
55. E. Gallicchio, M. Andrec, A.K. Felts, and R.M. Levy, Temperature weighted histogram analysis method, replica exchange, and transition paths, J. Phys. Chem. B 109 (2005), pp. 6722-6731.
56. G. Zuo, J. Wang, and W. Wang, Folding with downhill behavior and low cooperativity of proteins, Proteins 63 (2006), pp. 165-173.
57. J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, and K.A. Dill, Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations, J. Chem, Theory. Comput. 3 (2007), pp. 26-41.
58. A.M. Ferrenberg and R.H. Swendsen, Optimized Monte Carlo data analysis, Phys. Rev. Lett. 63 (1989), pp. 1195-1198.
59. Y.G. Mu, L. Nordenskiold, and J.P. Tam, Folding, misfolding, and amyloid protofibril formation of WW domain FBP28, Biophys. J. 90 (2006), pp. 3983-3992.
60. Y.G. Mu, P.H. Nguyen, and G. Stock, Energy landscape of a small peptide revealed by dihedral angle principal component analysis, roteins 58 (2005), pp. 45-52.
61. C.D. Snow, L. Qiu, D. Du, F. Gai, S.J. Hagen, and V.S. Pande, Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy, Proc. Natl. Acad. Sci. USA 101 (2004), pp. 4077-4082.
62. A. Baumketner and J.E. Shea, The thermodynamics of folding of a β- hairpin peptide probed through replica exchange molecular dynamics simulations, Theor. Chem. Acc. 116 (2006), pp. 262-273.
63. K.Y. Sanbonmatsu and A.E. Garcia, Structure of Met-Enkephalin in explicit aqueous solution using replica exchange molecular dynamics, Proteins 46 (2002), pp. 225-234.
64. R. Koradi, M. Billeter, and K. Wüthrich, MOLMOL: A program for display and analysis of macromolecular structures, J. Mol. Graph. 14 (1996), pp. 51-55.
65. N.H. Andersen, K.A. Olsen, R.M. Fesinmeyer, X. Tan, F.M. Hudson, L.A. Eidenschink, and S.R. Farazi, Minimization and optimization of designed β-hairpin folds, ββmultiple turns in , proteins, J. Am. Chem, Soc. 128 (2006), pp. 6101-6110.
66. S. Kumar and R. Nussinov, Salt bridge stability in monomeric proteins, J. Mol., Biol, 293 (1999), pp. 1241-1255.
67. A.S. Thomas and A.H. Elcock, Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures, J. Am. Chem. Soc. 126 (2004), pp. 2208-2214.
68. W.Y. Yang, J.W. Pitera, W.C. Swope, and M. Gruebele, Heterogeneous folding of the trpzip hairpin; Full atom simulation and experiment, J. Mol. Biol. 336 (2004), pp. 241-251.
69. S. Deechongkit, H. Nguyen, E.T. Powers, P.E. Dawson, M. Gruebele, and J.W. Kelly, Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics, Nature 430 (2004), pp. 101-105.
70. E.G. Huntchinson and J.M. Thornton, A revised set of potentials for β-turn formation in proteins, Protein Sci. 3 (1994), pp. 2207-2216.
71. K. Guruprasad, M.S. Prasad, and G.R. Kumar, Analysis of γβ, βy, γγ, ββ multiple turns in proteins, J. Pept. Res. 56 (2000), pp. 250-263.
72. A.K. Felts, E. Gallicchio, A. Wallqvist, and R.M. Levy, Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Born solvent model, Proteins 48 (2002), pp. 404-422.
73. J.P. Ulmschneider and W.L., Jorgensen, Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation, J. Am. Chem. Soc. 126 (2004), pp. 1849-1857.
74. R. Zhou and B.J. Berne, Can a continuum solvation model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl. Acad. Sci, USA 99 (2002), pp. 12777-12782.
75. H. Y. Liu and X. Zou, Electrostatics ofligand binding: Parametrization of the generalized Born model and comparison with the PoissonBoltzmann approach, J. Phys. Chem. B 110 (2006), pp. 9304-9313.
76. J. Chen, W. Im, and C.L. Brooks, Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field, J. Am. Chem. Soc. 128 (2006), pp. 3728-3736.
77. S.H. Lin, P.K. Maiti, and W.A. Goddart, III, Dynamics and thermodynamics of water in PAMAM dendrimers at subnanosecond time scales, J. Phys. Chem. B 109 (2005), pp. 8663-8672.
78. S. Woutersen, Y.G. Mu, G. Stock, and P. Hamm, Subpicosecond conformational dynamics of small peptides probed by two-dimensional vibrational spectroscopy, Proc. Natl. Acad. Sci. USA. 98 (2001), pp. 11254-11258.
79. D. Roe, A. Okur, L. Wickstrom, V. Hornak, and C. Simmerling, Secondary structure bias in generalized Born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation, J. Phys. Chem. B. 111 (2007), pp. 1846-1857.
80. A. Onufriev, D. Bashford, and D.A. Case, Exploring protein native states and large-scale conformational changes with a modified generalized Born model, Proteins 55, pp. 383-394.
81. M. Stork and P. Tavan, Electrostatics of proteins in dielectric solvent continua, I. Newton's third law marries qE forces, J. Chem. Phys. 126 (2007), pp. 165105-165115.