Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session I

6 – POS Board 6 Self-entanglement of Bovine Serum Albumin in Shear Flow Agnieszka Budek 1 , Marek Cieplak 2 , Piotr Szymczak 1 .

1 University of Warsaw, Warszawa, Poland, 2 Polish Academy of Science, Warszawa, Poland. Shear flow is known to speed up the protein aggregation process. This can occur for a variety of reasons, including partial unfolding of the protein structures induced by the flow. However, the experimental evidence regarding the influence of shear flow on the protein tertiary structure is rather contradictory. Some studies indicate unfolding of protein under relatively low shear rates, other do not show any impact on protein structure even after exposure to shear rates which are a few orders of magnitude higher. Also, some experiments indicate that effects of the shear can be a cumulative nature and should be described in terms of the strain history. To investigate this problem we perform Brownian Dynamics simulations of shear-induced unfolding of bovine serum albumin. This protein was reported to unfold at surprisingly low shear rates [1]. Using a coarse-grained model of a protein, we track the conformational changes induced by the flow and observe that after an extended exposure to shear albumin loses its ability to refold even when the flow has been turned off. Instead, it is trapped in a metastable state characterized by a strong self-entanglement which topologically constrains the molecule to fold into the native state. This state becomes more populated with time, which can explain the cumulative effect of the shear observed in the experiments. [1] Soft Matter, Bekard et al., 8, 385-389, 2012

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