Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows.

ABSTRACT: Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence. Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows. Using molecular dynamics simulations, we study folding of another benchmark system-Trp-cage miniprotein, which has different content of secondary structure elements and mechanism of folding. Calculating the probability fluxes of transitions i

SUBMITTER: Andryushchenko VA 

PROVIDER: S-EPMC5716548 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature