  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.
