Hydrodynamic Interactions in Protein Folding

TL;DR

This paper investigates how hydrodynamic interactions influence protein folding and dynamics, demonstrating that HI facilitate folding and speed up flap closing in HIV-1 protease, with effects on time correlation functions near the native state.

Contribution

It introduces a coarse-grained model incorporating hydrodynamic interactions using the Rotne-Prager tensor, revealing their role in protein folding and dynamics.

Findings

Hydrodynamic interactions facilitate protein folding.

HI accelerate flap closing in HIV-1 protease.

HI influence time correlation functions near the native state.

Abstract

We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also study HIV-1 protease and show that HI make the flap closing dynamics faster. The HI are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state.