title: Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: insights from an analytically solvable model.
abstract: Conformational rearrangements in biomolecules (such as protein folding or enzyme-ligand binding) are often interpreted in terms of low-dimensional models of barrier crossing such as Kramers' theory. Dimensionality reduction, however, entails memory effects; as a result, the effective frictional drag force along the reaction coordinate nontrivially depends on the time scale of the transition. Moreover, when both solvent and "internal" friction effects are important, their interplay results in a highly nonlinear dependence of the effective friction on solvent viscosity that is not captured by common phenomenological models of barrier crossing. Here, these effects are illustrated using an analytically solvable toy model of an unstructured polymer chain involved in an inter- or intramolecular transition. The transition rate is calculated using the Grote-Hynes and Langer theories, which--unlike Kramers' theory--account for memory. The resulting effective frictional force exerted by the polymer along the reaction coordinate can be rationalized in terms of the effective number of monomers engaged in the transition. Faster transitions (relative to the polymer reconfiguration time scale) involve fewer monomers and, correspondingly, lower friction forces, because the polymer chain does not have enough time to reconfigure in response to the transition.
authors.affiliation: Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA. makarov@cm.utexas.edu
authors.forename: Dmitrii E
authors.initials: DE
authors.lastname: Makarov
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D007700:Kinetics; D008390:Markov Chains; D008962:Models, Theoretical
chemical_list: D001704:Biopolymers