Reconfiguration dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant

  title={Reconfiguration dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant},
  author={Nairhita Samanta and Rajarshi Chakrabarti},
  journal={Physica A-statistical Mechanics and Its Applications},

Dispersion Forces and the Molecular Origin of Internal Friction in Protein.

It is concluded that cohesive forces among nonbonded atoms are major contributors to the molecular origin of internal friction.

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?

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

Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions

The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time.

How important are fluctuations in the treatment of internal friction in polymers?

The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an

Chain reconfiguration in active noise

In a typical single molecule experiment, the dynamics of an unfolded protein is studied by determining the reconfiguration time using long-range Förster resonance energy transfer, where the

Effect of internal friction on the coil-stretch transition in turbulent flows.

It is shown that although internal friction does not modify the critical Weissenberg number for the coil-stretch transition, it makes the slope of the probability distribution of the extension steeper, thus rendering the transition sharper.

Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity.

The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for

Low-frequency internal friction behaviour of Zr55Al10Ni5Cu30 metallic glass with different quenching temperatures

The correlation between the internal friction behaviour of Zr55Al10Ni5Cu30 BMG samples and their quenching temperatures was investigated. It was found that, below the glass transition temperature,

Wet and dry internal friction can be measured with the Jarzynski equality

In this work an experimental protocol, based in optical tweezers, is used to measure the internal friction caused by internal interactions in polymers

Internal friction can be measured with the Jarzynski equality

A simple protocol for the extraction of the internal friction coefficient of polymers is presented. The proposed scheme necessitates repeatedly stretching the polymer molecule, and measuring the



Peptide chain dynamics in light and heavy water: zooming in on internal friction.

Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggests that solvent and internal friction effects are intrinsically entangled, and suggests a connection between friction and the formation of hydrogen bonds upon folding.

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

The combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing is used to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics.

Concerted dihedral rotations give rise to internal friction in unfolded proteins.

Analysis of the reconfiguration dynamics of the unfolded cold-shock protein revealed that hops in the dihedral space provide the dominant mechanism of internal friction, and the increased number of concerted dihedral moves at physiological conditions suggest that, in such conditions, the concerted motions result in higher frictional forces.

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models.

The Rouse model with internal friction (RIF), and its non-free draining analog, Zimm model withinternal friction, are used to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain.

Molecular Origins of Internal Friction Effects on Protein Folding Rates

All-atom simulations of peptide and protein folding in explicit solvent find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction.

Rouse Model with Internal Friction: A Coarse Grained Framework for Single Biopolymer Dynamics

Recent work has highlighted an intimate link between the internal friction of single biopolymers and dynamics on an underlying energy landscape of conformational change. Here, we examine the

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

The motions involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, finding that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosities because of internal friction.

Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy

It is found that the internal friction affecting the folding rates of spectrin domains is highly localized to the early transition state, suggesting an important role of rather specific interactions in the rate-limiting conformational changes.

Dependence of Internal Friction on Folding Mechanism

It is shown that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier, suggesting an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.