Reaction coordinates and rates from transition paths.

@article{citeulike:507286, abstract = {The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.}, address = {Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 132, Bethesda, MD 20892-0520, USA.}, author = {Best, R. B. and Hummer, G. }, citeulike-article-id = {507286}, doi = {10.1073/pnas.0408098102}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {folding}, month = {May}, number = {19}, pages = {6732--6737}, posted-at = {2006-05-02 08:27:39}, priority = {2}, title = {Reaction coordinates and rates from transition paths.}, url = {http://dx.doi.org/10.1073/pnas.0408098102}, volume = {102}, year = {2005} }

TY - JOUR ID - citeulike:507286 L3 - citeulike-article-id:507286 TI - Reaction coordinates and rates from transition paths. JF - Proc Natl Acad Sci U S A VL - 102 IS - 19 SP - 6732 EP - 6737 AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 132, Bethesda, MD 20892-0520, USA. SN - 0027-8424 N2 - The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding. KW - folding AU - Best, RB AU - Hummer, G PY - 2005/05/10/ UR - http://dx.doi.org/10.1073/pnas.0408098102 ER -