Looping dynamics of flexible chain with internal friction at different degree of compactness

Abstract

Recently single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has strong dependence on denaturant concentration. Recent simulations also support such propositions by pointing out weak interactions to be the origin of internal friction in proteins. Here we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential which accounts for the presence of the denaturant, by using recently proposed Compacted Rouse with internal friction (CRIF). We also incorporated the effect of hydrodynamics by extending this further to Compacted Zimm with internal friction (CZIF). All the calculations are carried out within the Wilemski Fixmann (WF) framework. By changing the strength of the confinement we mimicked chains with different degrees of compactness at different denaturant concentrations. While compared with experiments our results are found to be in good agreement.

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Cited by in corpus (4)

• Chain reconfiguration in active noise
• Reconfiguration, swelling and tagged monomer dynamics of a single polymer chain in Gaussian and non-Gaussian active baths
• 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