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How does the tail length and the separation between the tagged monomers influence the reconfiguration of a chain with internal friction for different solvent-quality?

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Published under licence by IOP Publishing Ltd
, , Citation Nairhita Samanta and Rajarshi Chakrabarti 2016 J. Phys.: Conf. Ser. 759 012014 DOI 10.1088/1742-6596/759/1/012014

1742-6596/759/1/012014

Abstract

Recent experiments involving single proteins have shown the importance of internal friction in protein dynamics. In addition to internal friction, solvent-quality also plays an important role in elucidating the structure and dynamics of proteins. Using a single chain based model where internal friction is introduced via dashpots between the neighbouring monomers and the solvent- quality is taken care of by introducing a mean field Flory type parameter, we monitor the effect of separation of two tagged monomers along the chain and the tail length on the reconfiguration time. We show that irrespective of the degree of compactness, the reconfiguration time remains unchanged beyond a tail length. Our calculations can also reproduce different trends observed in experiments.

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10.1088/1742-6596/759/1/012014