Looping and reconfiguration dynamics of a flexible chain with internal friction

Abstract

In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This friction is termed as internal friction in the literature. Using a flexible Gaussian chain with internal friction we analyze the intra- chain reconfiguration and loop formation times for all three topology classes namely end-to- end, end-to-interior and interior-to-interior. In a nutshell, bypassing expensive simulations we show how simple models like that of Rouse and Zimm can support the single molecule experiment and computer simulation results on intra-chain diffusion coefficients, looping time and even can predict the effects of tail length on the looping time.

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Cited by in corpus (7)

• Chain reconfiguration in active noise
• Reconfiguration Dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant
• Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity
• Looping dynamics of flexible chain with internal friction at different degree of compactness
• Rouse model with fluctuating internal friction
• Shear viscosity for finitely extensible chains with fluctuating internal friction and hydrodynamic interactions
• How important are fluctuations in the treatment of internal friction in polymers?