title: Computing the transition state populations in simple protein models.
abstract: We describe the master equation method for computing the kinetics of protein folding. We illustrate the method using a simple Go model. Presently most models of two-state fast-folding protein folding kinetics invoke the classical idea of a transition state to explain why there is a single exponential decay in time. However, if proteins fold via funnel-shaped energy landscapes, as predicted by many theoretical studies, then it raises the question of what is the transition state. Is it a specific structure, or a small ensemble of structures, as is expected from classical transition state theory? Or is it more like the denatured states of proteins, a very broad ensemble? The answer that is usually obtained depends on the assumptions made about the transition state. The present method is a rigorous way to find transition states, without assumptions or approximations, even for very nonclassical shapes of energy landscapes. We illustrate the method here, showing how the transition states in two-state protein folding can be very broad ensembles.
authors.affiliation: Center for Computational Biology, Department of Molecular Genetics, School of Medicine, University of Pittsburgh, PA 15213, USA.
authors.forename: S Banu
authors.initials: SB
authors.lastname: Ozkan
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
mesh_terms: D007700:Kinetics; D008432:Mathematical Computing; D008956:Models, Chemical; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins