Diffusive reaction dynamics on invariant free energy profiles

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 37, 2008, Pages 13841-13846

  Krivov, Sergei V ^a   Karplus, Martin ^a,b  

^a UNIVERSITÉ LOUIS PASTEUR   (France)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Diffusion; One dimensional free energy surfaces; Protein folding; Variable diffusion coefficient

Indexed keywords

ALANINE DERIVATIVE; BETA HAIRPIN MINIPROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; DIFFUSION COEFFICIENT; ENERGY; HISTOGRAM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; SIMULATION;

DIFFUSION; DIPEPTIDES; MODELS, BIOLOGICAL; PROTEIN FOLDING; PROTEINS;

EID: 52949137003     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0800228105     Document Type: Article

References (35)

1. Dobson CM, Sali A, Karplus M (1998) Protein folding: A perspective from theory and experiment. Angew Chem Int Ed 37:868-893.
2. Shea JE, Brooks CL (2001) From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem 52:499-535.
3. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG (1996) Protein folding funnels: The nature of the transition state ensemble. Fold Des 1:441-450.
4. Sabelko J, Ervin J, Gruebele M (1999) Observation of strange kinetics in protein folding. Proc Natl Acad Sci USA 96:6031-6036.
5. Karplus M (2000) Aspects of protein reaction dynamics: Deviations from simple behavior. J Phys Chem B 104:11-27.
6. Kramers HA (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7:284-304.
7. Hagen SJ, Hofrichter J, Szabo A, Eaton WA (1996) Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding. Proc Natl Acad Sci USA 93:11615-11617.
8. Yang WY, Gruebele M (2003) Folding at the speed limit. Nature 423:193-197.
9. Chan HS, Dill KA (1998) Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30:2-33.
10. Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding "speed limit." Curr Opin Struct Biol 14:76-88.
11. Krivov SV, Karplus M (2004) Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci USA 101:14766-14770.
12. Palyanov AY, Krivov SV, Karplus M, Chekmarev SF (2007) A lattice protein with an amyloidogenic latent state: Stability and folding kinetics. J Phys Chem B 111:2675-2687.
13. Socci ND, Onuchic JN, Wolynes PG (1996) Diffusive dynamics of the reaction coordinate for protein folding funnels. J Chem Phys 104:5860-5868.
14. Krivov SV, Karplus M (2006) One-dimensional free-energy profiles of complex systems: Progress variables that preserve the barriers. J Phys Chem B 110:12689-12698.
15. Krivov SV, Karplus M (2002) Free energy disconnectivity graphs: Application to peptide models. J Chem Phys 117:10894-10903.
16. Rhee YM, Pande VS (2005) One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. J Phys Chem B 109:6780-6786.
17. Best RB, Hummer G (2005) Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 102:6732-6737.
18. Ma A, Dinner AR (2005) Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 109:6769-6779.
19. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich ES (1998) On the transition coordinate for protein folding. J Chem Phys 108:334-350.
20. Das P, Moll M, Stamati H, Kavraki LE, Clementi C (2006) Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci USA 103:9885-9890.
21. Mu Y, Nguyen PH, Stock G (2005) Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins 58:45-52.
22. Chandler D (1978) Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J Chem Phys 68:2959-2970.
23. Chandler D (1987) Introduction to Modern Statistical Mechanics (Oxford Univ Press, New York), p 288.
24. EW, Vanden-Eijnden E (2004) Metastability, conformational dynamics, and transition pathways in complex systems. Multiscale Modelling and Simulation, eds Attinger S, Koumoutsakos P (Springer), pp 277-312.
25. Brooks BR, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
26. Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105:1902-1921.
27. Schaefer M, Bartels C, Karplus M (1998) Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model. J Mol Biol 284:835-848.
28. van der Vaart A, Karplus M (2005) Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J Chem Phys 122:114903.
29. Levy RM, Karplus M, McCammon JA (1979) Diffusive Langevin dynamics of model alkanes. Chem Phys Lett 65:4-11.
30. Truhlar D, Garrett B, Klippenstein S (1996) Current status of transition-state theory. J Phys Chem 100:12771-12800.
31. Ferrara P, Caflisch A (2000) Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc Natl Acad Sci USA 97:10780-10785.
32. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342:299-306.
33. Ferrara P, Apostolakis J, Caflisch A (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 46:24-33.
34. Benkovic SJ, Hammes GG, Hammes-Schiffer S (2008) Free-energy landscape of enzyme catalysis. Biochemistry 47:3317-3321.
35. Min W, Xie X, Bagchi B (2008) Two-dimensional reaction free energy surfaces of catalytic reaction: Effects of protein conformational dynamics on enzyme catalysis. J Phys Chem B 112:454-466.