Direct determination of reaction paths and stationary points on potential of mean force surfaces

Journal of Molecular Graphics and Modelling

Volumn 24, Issue 2, 2005, Pages 82-93

  Li, Guohui ^a   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Minimum energy path; Nudged elastic band; Potential of mean force; Simulation

Indexed keywords

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); MOLECULAR DYNAMICS; REACTION KINETICS;

CANONICAL DISTRIBUTION; ENERGY FUNCTIONS; POTENTIAL OF MEAN FORCE (PMF);

THERMODYNAMICS;

ALANINE DERIVATIVE; DIPEPTIDE; PROTON;

ACCURACY; ALGORITHM; CALCULATION; CHEMICAL REACTION; CONFERENCE PAPER; CONFORMATION; ENERGY; ENTROPY; FORCE; ISOMERIZATION; KINETICS; MOLECULAR DYNAMICS; MOLECULE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REACTION ANALYSIS; SAMPLING; SOLVATION; STATISTICS; SURFACE PROPERTY; TEMPERATURE; THERMODYNAMICS; VACUUM;

ALANINE; COMPUTER SIMULATION; DIPEPTIDES; KINETICS; MODELS, CHEMICAL; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTONS; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 25444532015     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.06.001     Document Type: Conference Paper

References (84)

1. A. Rahman MD simulation of LJ liquid Phys. Rev. 136A 1964 405
2. B.J. Berne, J. Jortner, and R. Gordon Vibrational relaxation of diatomic molecules in gas and liquids J. Chem. Phys. 47 1967 1600
3. P.J. Rossky, and M. Karplus Solvation. A molecular dynamics study of a dipeptide in water J. Am. Chem. Soc. 101 1979 1913 1937
4. J.A. McCammon, B.R. Gelin, and M. Karplus Dynamics of folded proteins Nature 267 1977 585 590
5. J. Berne, G. Ciccotti, and D.F. Coker Classical and Quantum Dynamics in Condensed Phase Simulations 1998 World Scientific Singapore
6. S.D. Schwartz Progress on Theoretical Chemistry and Physics 2000 Kluwer Academic Dordrecht
7. M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652
8. D. Heidrich The Reaction Path in Chemistry: Current Approaches and Perspectives 1995 Kluwer Dordrecht
9. R. Elber Reaction path studies of biological molecules R. Elber Recent Developments in Theoretical Studies of Proteins 1996 World Scientific New York
10. K. Fukui The path of chemical reactions - the IRC approach Acc. Chem. Res. 14 1981 363 368
11. R.A. Marcus Analytical mechanics of chemical reactions, III. Natural collision coordinates J. Chem. Phys. 49 1968 2610 2616
12. D.G. Truhlar Potential Energy Surfaces and Dynamics Calculations 1981 Plenum Press New York
13. H.B. Schlegel Optimization of equilibrium geometries and transition structures Adv. Chem. Phys. 67 1987 249
14. P. Hanggi, P. Talkner, and M. Borkovec Reaction-rate theory: fifty years after Kramers Rev. Mod. Phys. 62 1990 251 341
15. M. Karplus Aspects of protein reaction dynamics: deviation from simple behavior J. Phys. Chem. 104 2000 11 27
16. M. Berkowitz J. Chem. Phys. 79 1983 5563
17. R. Elber, and D. Shalloway Temperature dependent reaction coordinates J. Chem. Phys. 112 2000 5539 5545
18. S. Huo, and J.E. Straub MaxFlux J. Chem. Phys. 107 1997 5000
19. R. Crehuet, and M.J. Field A temperature-dependent nudged-elastic-band algorithm J. Chem. Phys. 118 2003 9563 9571
20. H. Frauenfelder, S.G. Sligar, and P.G. Wolynes The energy landscape and motions of proteins Science 254 1991 1598 1603
21. S. Fischer, and M. Karplus Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition state in systems with many degrees of freedom Chem. Phys. Lett. 194 1992 252 261
22. R. Elber, and M. Karplus A method for determining reaction paths in large molecule: application to myoglobin Chem. Phys. Lett. 139 1987 375 380
23. G. Henkelman, B.P. Uberuaga, and H. Jonsson A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 113 2000 9901 9904
24. R. Olender, and R. Elber Calculation of classical trajectories with a very large time step: formalism and numerical examples J. Chem. Phys. 105 1996 9299 9315
25. A. Ghosh, R. Elber, and H. Scherage An atomically detailed study of the folding pathways of protein A with the stochastic difference equation Proc. Natl. Acad. Sci. U.S.A. 99 2002 10394 10398
26. S. Huo, and J.E. Straub Proteins: structure, function and genetics Proteins 36 1999 249s
27. Q. Cui, and M. Karplus Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton transfer rate constants J. Am. Chem. Soc. 124 2002 3093 3124
28. P.G. Bolhuis Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu. Rev. Phys. Chem. 53 2002 291 318
29. D. Parsserone, M. Ceccarelli, and M. Parrinello A concerted variational strategy for investigating rare events J. Chem. Phys. 118 2003 2025 2032
30. P.G. Bolhuis, C. Dellago, and D. Chandler Reaction coordinates of biomolecular isomerization Proc. Natl. Acad. Sci. U.S.A. 97 2000 5877 5882
31. R. Elber Bridging the gas between long time trajectories and reaction pathways Adv. Chem. Phys. 126 2003 93
32. R. Zwanzig Nonequilibrium Statistical Mechanics 2001 Oxford University Press Oxford
33. A. Laio, and M. Parrinello Escaping free energy minima Proc. Natl. Acad. Sci. U.S.A. 99 2002 12562 12566
34. G. Hummer, and I.G. Kevrekidis Coarse molecular dynamics of a peptide fragment: free energies, kinetics, and long-time dynamics computations J. Chem. Phys. 118 2003 10762 10773
35. M. Iannuzzi, A. Laio, and M. Parrinello Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics Phys. Rev. Lett. 90 2003 238302
36. J. Apostolakis, P. Ferrara, and A. Caflisch Calculation of conformational transitions and barriers in solvated systems: application to the alanine dipeptide in water J. Chem. Phys. 110 1999 2099 2108
37. J. Mahadevan, K.-H. Lee, and K. Kuczera Conformational free energy surfaces of Ala10 and Aib10 peptide helices in solution J. Phys. Chem. B 105 2001 1863 1876
38. P.L. Geissler, C. Dellago, and D. Chandler Kinetic pathway of ion pair dissociation in water J. Phys. Chem. B 103 1999 3706 3710
39. D.G. Truhlar, and B.C. Garrett Multidimensional transition state theory and the validity of Grote-Hynes theory J. Phys. Chem. B 104 2000 1069 1072
40. K.C. Holmes, and M.A. Geeves Structural mechanism of muscle contraction Annu. Rev. Biochem. 68 1999 687 728
41. F. Julicher, A. Ajdari, and J. Prost Modeling molecular motors Rev. Mod. Phys. 69 1997 1269 1281
42. A.R. Dinner Understanding protein folding via free-energy surfaces from theory and experiment TiBS 25 2000 331 339
43. E.M. Boczko, and C.L. Brooks III First-principles calculation of the folding free energy of a 3-helix bundle protein Science 269 1995 393 396
44. J.E. Shea, and C.L. Brooks III From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding Annu. Rev. Phys. Chem. 52 2001 499 535
45. 2+-ATPase Biophys. J. 86 2004 743 763
46. Y.A. Berlin Conformationally gated rate processes in biological macromolecules J. Phys. Chem. A 105 2001 5666 5678
47. G. Basu A collective motion description of the 3-10/alpha-helix transition - implications for a natural reaction coordinate J. Am. Chem. Soc. 116 1994 6307 6315
48. J.E. Shea, J.N. Onuchic, and C.L. Brooks III Probing the folding free energy landscape of the src-SH3 protein domain Proc. Natl. Acad. Sci. U.S.A. 99 2002 16064 16068
49. P. Roche Molecular dynamics of the FixJ receiver domain: movement of the beta 4-alpha 4 loop correlates with the in and out flip of Phe101 Protein Sci. 11 2002 2622 2630
50. A.M. Berezhkovskii Reaction dynamics on a thermally fluctuating potential J. Chem. Phys. 111 1999 9952 9957
51. J.N. Onuchic, and P.G. Wolynes Energy landscapes, glass transitions, and chemical-reaction dynamics in biomolecular or solvent environment J. Chem. Phys. 98 1993 2218 2224
52. R. Olender, and R. Elber J. Mol. Struct. Theochem. 398-399 1997 63 72
53. T. Lazaridis Reaction paths and free energy profile for conformational transitions: AN internal coordinate approach J. Chem. Phys. 95 1991 7612 7625
54. J.J. Portman, S. Takada, and P.G. Wolynes Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach J. Chem. Phys. 114 2001 5069 5081
55. J.J. Portman, S. Takada, and P.G. Wolynes Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics J. Chem. Phys. 114 2001 5082 5096
56. N.D. Socci, J.N. Onuchic, and P.G. Wolynes Diffusive dynamics of the reaction coordinate for protein folding funnels J. Chem. Phys. 104 1996 5860 5868
57. G.M. Torrie, and J.P. Valleau Non-physical sampling distributions in Monte Carlo free energy estimation: umbrella sampling J. Comp. Phys. 23 1977 187 199
58. C. Bartels, and M. Karplus Probability distributions for complex systems: adaptive umbrella sampling of the potential energy J. Phys. Chem. B 102 1998 865 880
59. S. Kumar The weighted histogram analysis method for free energy calculations on biomolecules. 1. The method J. Comput. Chem. 13 1992 1011 1021
60. E. Neria, S. Fischer, and M. Karplus Simulation of activation free energies in molecular systems J. Chem. Phys. 105 1996 1902 1921
61. R. Elber Calculation of the potential of mean force using molecular dynamics with linear constraints: an application to a conformational transition in a solvated dipeptide J. Chem. Phys. 93 1990 4312 4321
62. E.W.W. Ren, and E. Vanden-Eijnden Phys. Rev. B 66 2002 052301
63. Y. Brumer Calculating approximate quantum mechanical rates without an a priori reaction coordinate J. Chem. Phys. 116 2002 8376 8383
64. H. Jonsson Theoretical studies of atomic-scale processes relevant to crystal growth Annu. Rev. Phys. Chem. 51 2000 623 653
65. G. Henkelman, and H. Jonsson Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 113 2000 9978 9985
66. E.A. Carter, G. Ciccotti, and J.T. Hynes Constrained reaction coordinate dynamics for the simulation of rare events Chem. Phys. Lett. 156 1989 472 477
67. M. Sprik, and G. Ciccotti Free energy from constrained molecular dynamics J. Chem. Phys. 109 1998 7737 7744
68. T. Mulders Free energy as the potential of mean constraint force J. Chem. Phys. 104 1996 4869 4870
69. J. Schlitter, and M. Klahn A new concise expression for the free energy of a reaction coordinate J. Chem. Phys. 118 2003 2057 2060
70. W.K. den Otter, and W.J. Briels The calculation of free-energy differences by constrained molecular dynamics simulations J. Chem. Phys. 109 1998 4139 4146
71. E. Darve, and A. Pohorille Calculating free energies using average force J. Chem. Phys. 115 2001 9169 9183
72. M. Fixman Classical statistical mechanics of constraints: A theorem and application to polymers Proc. Natl. Acad. Sci. U.S.A. 71 1974 3050 3053
73. H. Decornez, K. Drukker, and S. Hammes-Schiffer Solvation and hydrogen-bonding effects on proton wires J. Phys. Chem. 103 1999 2891 2898
74. M. Elstner Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties Phys. Rev. B58 1998 7260 7268
75. Y. Wang, and K. Kuczera Exploration of conformational free energy surfaces of helical Ala and Aib peptides J. Phys. Chem. B 101 1997 5205 5213
76. W. Press Numerical Recipes in Fortran 77 second ed. 1996 Cambridge University Press Cambridge
77. J.P. Ryckaert, G. Ciccotti, and H.J. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
78. R.A. Copeland, and S.I. Chan Proton translocation in proteins Annu. Rev. Phys. Chem. 40 1989 671 698
79. M. Wikstrom Proton translocation by bacteriorhodopsin and heme-copper oxidases Curr. Opin. Struct. Biol. 8 1998 480 488
80. G.A. Voth Path-integral centroid methods in quantum statistical mechanics and dynamics Adv. Chem. Phys. XCIII 1996 135 218
81. S.R. Billeter Hydride transfer in liver Alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion J. Am. Chem. Soc. 123 2001 11262 11272
82. J. Gao, and D.G. Truhlar Quantum mechanical methods for enzyme kinetics Annu. Rev. Phys. Chem. 53 2002 467 505
83. R. Pomes, and B. Roux Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules Biophys. J. 75 1998 33 40
84. T. Kruger, M. Elstner, P. Schiffels, and T. Frauenheim Validation of the density function based tight-binding approximation method for the calculation of reaction energies and other data J. Chem. Phys. 122 2005 Art. 114110