A minimum-reaction-flux solution to master-equation models of protein folding

Master equations are widely used for modeling protein folding. Here an approximate solution to such master equations is presented. The approach used may be viewed as a discrete variational transition-state theory. The folding rate constant k(f) is approximated by the outgoing reaction flux J, when the unfolded set of macrostates assumes an equilibrium distribution. Correspondingly the unfolding rate constant k(u) is calculated as Jp(u)/(1-p(u)), where p(u) is the equilibrium fraction of the unfolded state. The dividing surface between the unfolded and folded states is chosen to minimize the reaction flux J. This minimum-reaction-flux surface plays the role of the transition-state ensemble and identifies rate-limiting steps. Test against exact results of master-equation models of Zwanzig [Proc. Natl. Acad. Sci. USA 92, 9801 (1995)] and Munoz [Proc. Natl. Acad. Sci. USA 95, 5872 (1998)] shows that the minimum-reaction-flux solution works well. Macrostates separated by the minimum-reaction-flux surface show a gap in p(fold) values. The approach presented here significantly simplifies the solution of master-equation models and, at the same time, directly yields insight into folding mechanisms. (c) 2008 American Institute of Physics.