Influence of the Hydrodynamic Interaction on Kinetics and Thermodynamics of Minimal Protein Models

Abstract

In this paper we study the influence of the hydrodynamic interaction on the folding process in minimal protein models. In minimal models entire protein residues (or groups of residues) are represented at a simplified level by interacting beads. In a viscous medium such as water the beads are subject to the hydrodynamic interaction: when one of the beads is set in motion incited thereby velocity field exert force on all the remaining beads. This effective interaction is accounted for in our simulations through the Rotne–Prager mobility tensor. We considered two types of chain molecules, a β hairpin and an α helix, designed to represent the proteins' most common secondary structure elements. Both thermodynamical and dynamical properties of the examined models were studied by using Brownian dynamics simulations. It was found that the effect of the hydrodynamic interaction on the folding process of a protein depends on the geometry of its native state. In the case of the β protein the hydrodynamic interaction lowers the temperature of collapse and folding transitions. Kinetically, the position at which the temperature dependence of the folding time has a minimum is shifted significantly towards lower temperatures and the minimal folding time itself grows by a factor of 2. As to the α helix, the hydrodynamic interaction affects neither its thermodynamics nor kinetics. We speculate that the observed difference in the behaviour of β and α proteins is connected with the differing mechanisms by which these proteins fold.