Protein Folding Dynamics in the Space of Experimentally Measured Variables: Turbulence Phenomena

Abstract

The process of folding of villin subdomain HP-35 has been studied using the method of molecular dynamics. To characterize protein conformations, two variables are introduced that correspond to the distances between fluorophores in experiments on protein folding with the Förster resonance energy. The simulation results show that the field of probability flows of transitions between protein states is filled with eddies. It has been found that, in contrast to the previously studied cases of hydrodynamic turbulence and turbulence in protein folding in three-dimensional conformational space, the structure functions of the flows of various orders depend linearly on the increment in the conformational space. An explanation of this linear dependence based on the β-model is proposed. It is shown that this dependence is not due to the choice of variables to describe the folding process.