Coarse Master Equations for Peptide Folding Dynamics

@article{citeulike:2447536, abstract = {Abstract: We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are validated by comparing their analytical correlation functions with those obtained directly from the molecular dynamics simulations. We find that the master equations properly capture the character and relaxation times of the entire spectrum of conformational relaxation processes. By using the eigenvectors of the transition rate matrix, we are able to systematically coarse-grain the system. We find that a two-state description, with a folded and an unfolded state, roughly captures the slow conformational dynamics. A four-state model, with two folded and two unfolded states, accurately recovers the three slowest relaxation process with time scales between 1.5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition.}, address = {Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520}, author = {Buchete, N. V. and Hummer, G. }, citeulike-article-id = {2447536}, doi = {http://dx.doi.org/10.1021/jp0761665}, journal = {J. Phys. Chem. B}, keywords = {dynamics, equation, folding, master, molecular, protein}, month = {January}, posted-at = {2008-04-17 13:16:30}, priority = {2}, title = {Coarse Master Equations for Peptide Folding Dynamics}, url = {http://dx.doi.org/10.1021/jp0761665}, year = {2008} }

TY - JOUR ID - citeulike:2447536 L3 - citeulike-article-id:2447536 N2 - Abstract: We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are validated by comparing their analytical correlation functions with those obtained directly from the molecular dynamics simulations. We find that the master equations properly capture the character and relaxation times of the entire spectrum of conformational relaxation processes. By using the eigenvectors of the transition rate matrix, we are able to systematically coarse-grain the system. We find that a two-state description, with a folded and an unfolded state, roughly captures the slow conformational dynamics. A four-state model, with two folded and two unfolded states, accurately recovers the three slowest relaxation process with time scales between 1.5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition. JF - J. Phys. Chem. B AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 TI - Coarse Master Equations for Peptide Folding Dynamics KW - dynamics KW - equation KW - folding KW - master KW - molecular KW - protein AU - Buchete, NV AU - Hummer, G PY - 2008/01/31/ UR - http://dx.doi.org/10.1021/jp0761665 ER -