A mesoscopic model for protein enzymatic dynamics in solution

Abstract

A multi-scale, coarse-grained description of protein conformational dynamics in a solvent is presented. The focus of the paper is on the description of the conformational motions that may accompany enzyme catalysis as the enzyme executes a catalytic cycle, starting with substrate binding and ending with product release and return to the original unbound enzyme. The protein is modeled by a network of beads representing amino acid residues, the solvent is described by multiparticle collision dynamics, and substrate binding and unbinding events are modeled stochastically by conformation-dependent transitions that modify the bonding in the network to correspond to the different binding states of the protein. The solvent dynamics is coupled to that of the protein and hydrodynamic interactions, which are important for the large-scale protein motions, are taken into account. The multi-scale model is used to study the dynamics of the adenylate kinase enzyme in solution. A potential function that describes the different binding and conformational states of the protein and accounts for partial unfolding during the catalytic cycle is constructed as a network built from elastic network and soft potential links. The conformational dynamics of the protein as it undergoes cyclic enzymatic dynamics, as well as its translational diffusion and orientational motion, are investigated using both multiparticle collision dynamics and dynamics that suppresses hydrodynamic coupling. Hydrodynamic interactions are found to have important effects on the large scale conformational motions of the protein and significantly affect the translational diffusion coefficients and orientational correlation times.