Conformationally Gated Rate Processes in Biological Macromolecules

Abstract

The concept of gating has been applied to the theoretical description of rate processes coupled to conformational rearrangements of biological macromolecules both out of equilibrium and near equilibrium. The out-of-equilibrium rearrangements are discussed in terms of requirements imposed by the complexity of biomolecules. These include (i) a variety of relaxation time scales for different degrees of freedom, (ii) constraints arising from their interactions, and (iii) the hierarchy of conformational substates. The simplest possible model that satisfies the requirements i−iii is developed. The model suggests that the motion along the reaction coordinate is gated by slower degrees of freedom. We show that under this assumption dynamics of the reaction coordinate resembles anomalous (non-Gaussian) diffusion. Expressions for observables derived within our model predict (i) a suppression of reaction coordinate dynamics in biomolecules imbedded in rigid matrixes, (ii) a transition from the familiar Debye exponen...