Proteins in a shear flow

Details Proteins in a shear flow Proteins in a shear flow

2007-10-11

arxiv.org/abs/0710.2235v1

Biology

Quantitative Biology

Biomolecules

to be published in J. Chem. Phys

Scientific paper

10.1063/1.2795725

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.

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