Chain reconfiguration in active noise

In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time of the position correlation between two residues of the protein. In this paper we theoretically calculate the reconfiguration time for a single flexible polymer in presence of active noise. The study suggests that though the MSD grows faster, the chain reconfiguration is always slower in presence of long-lived active noise with exponential temporal correlation. Similar behavior is observed for a worm like semi-flexible chain and a Zimm chain. However it is primarily the characteristic correlation time of the active noise and not the strength that controls the increase in the reconfiguration time. In a nutshell, such active noise makes the polymer to move faster but the correlation loss between the monomers becomes slower.Comment: 18 pages, 8 figure

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

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

Looping and reconfiguration dynamics of a flexible chain with internal friction

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