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Abstract: The conformational dynamics of a single protein molecule in a shear flow isinvestigated using Brownian dynamics simulations. A structure-based coarsegrained model of a protein is used. We consider two proteins, ubiquitin andintegrin, and find that at moderate shear rates they unfold through a sequenceof metastable states - a pattern which is distinct from a smooth unravelingfound in homopolymers. Full unfolding occurs only at very large shear rates.Furthermore, the hydrodynamic interactions between the amino acids are shown tohinder the shear flow unfolding. The characteristics of the unfolding processdepend on whether a protein is anchored or not, and if it is, on the choice ofan anchoring point.

Author: P. Szymczak, Marek Cieplak


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