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Updated: Jul 10, 2026

Characterizing Single-Molecule Conformational Changes Under Shear Flow with Fluorescence Microscopy
Published on: January 25, 2020
Proteins in a shear flow
1Institute of Theoretical Physics, Warsaw University, ul. Hoza 69, 00-681 Warsaw, Poland. piotrek@fuw.edu.pl
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.
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