Cooperative denaturation kinetics of homogeneous polymers

Abstract

The kinetics of denaturation of a homogeneous, helical biopolymer with nearest neighbor interactions are described, using a kinetic Ising model in which the configuration of its neighbors dictates the transition probability for a single residue in the chain. The actual kinetics that are simulated using Monte Carlo techniques are compared with the results of analytical kinetic equations for the fraction of helix, (s), generated using the mean-field approximation. This mean-field rate equation is expanded as a hierarchy of terms that characterize the nature of rate constants for interacting systems. The first term in the expansion is first order in (s) and varies linearly with the interaction energy. Subsequent rate terms involve higher powers of (s) and demonstrate the need for nonlinear equations in systems with larger interaction energies. Both the simulations and the mean-field approximation show an intrinsic induction period for the single-step kinetic process. They also yield an apparent first-order rate constant that changes as the reaction proceeds. However, only the simulated kinetics yield ordered regions of chain and a nonzero, nearest-neighbor correlation function.