Proteins in a shear flow

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.

to be published in J. Chem. Phys

References in corpus (6)

• Universality classes in folding times of proteins
• Molecular dynamics of folding of secondary structures in Go-type models of proteins
• Sequencing of folding events in Go-like proteins
• Stretching of proteins in a uniform flow
• Chirality and Protein Folding
• Influence of Hydrodynamic Interactions on Mechanical Unfolding of Proteins

Cited by in corpus (4)

• An O(N^2) Approximation for Hydrodynamic Interactions in Brownian Dynamics Simulations
• Hydrodynamic Interactions in Protein Folding
• Tumbling motion of a single chain in shear flow: a crossover from Brownian to non-Brownian behavior
• Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions