title: Reaction coordinates and rates from transition paths.
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.
authors.affiliation: 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.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
authors.forename: Gerhard
authors.initials: G
authors.lastname: Hummer
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D000465:Algorithms; D001499:Bayes Theorem; D001703:Biophysics / Q000379:methods*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015233:Models, Statistical; D036103:Nanotechnology / Q000379:methods; D037742:Nanotubes, Carbon / Q000737:chemistry; D044367:Phase Transition; D011336:Probability; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012984:Software; D014867:Water / Q000737:chemistry
chemical_list: D037742:Nanotubes, Carbon; D014867:Water; D000255:Adenosine Triphosphate