Proteins in a shear flow

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 seq...

Full description

Saved in:
Bibliographic Details
Published in:The Journal of chemical physics 2007-10, Vol.127 (15), p.155106-155106-7
Main Authors: Szymczak, P., Cieplak, Marek
Format: Article
Language:English
Subjects:
Biophysics - methods
Computer Simulation
Diffusion
Models, Chemical
Models, Statistical
Models, Theoretical
Molecular Conformation
Protein Binding
Protein Conformation
Protein Denaturation
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins - chemistry
Stress, Mechanical
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.2795725