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

TL;DR

This study investigates how internal friction affects the reconfiguration and looping dynamics of a single polymer chain under different degrees of compactness, using extended models and experimental comparisons.

Contribution

It introduces the CRIF and CZIF models to analyze polymer dynamics with internal friction under confinement, incorporating denaturant effects and hydrodynamics.

Findings

Results align well with experimental data.

Internal friction significantly influences chain reconfiguration.

Degree of compactness affects looping times.

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.