Proteins in a shear flow

TL;DR

This study uses Brownian dynamics simulations to explore how single proteins, ubiquitin and integrin, unfold under shear flow, revealing a sequence of metastable states and the influence of hydrodynamic interactions and anchoring.

Contribution

It provides new insights into protein unfolding mechanisms in shear flow, highlighting the roles of metastable states, hydrodynamic interactions, and anchoring effects.

Findings

Proteins unfold through metastable states at moderate shear rates.

Full unfolding occurs only at very high shear rates.

Hydrodynamic interactions hinder the unfolding process.

Abstract

The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and find that at moderate shear rates they unfold through a sequence of metastable states - a pattern which is distinct from a smooth unraveling found in homopolymers. Full unfolding occurs only at very large shear rates. Furthermore, the hydrodynamic interactions between the amino acids are shown to hinder the shear flow unfolding. The characteristics of the unfolding process depend on whether a protein is anchored or not, and if it is, on the choice of an anchoring point.