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

2019

Preprint

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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 average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the hypothetical limit of zero solvent viscosity. The validity of the protocol is established through Brownian dynamics simulations of a single-mode spring-dashpot model for a polymer. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Internal friction can be measured with the Jarzynski equality

2019

Preprint

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“…66) and as an analytical expression for asymptotic values of the ratio at high shear rates (see Eq. (17) in Ref. 66).…”

Section: Comparison Of a Model With Large IV Parameter With A Rigimentioning

confidence: 94%

“…[1][2][3][4] The inclusion of a resistive force proportional to the rate of change of the connector vector between beads in addition to the spring force has been shown to lead to a finite limiting value for the infinite frequency limit of the dynamic viscosity, 3 instantaneous stress jumps at the inception of steady shear flow, 5 and to a shear-rate dependent viscosity. 6,7 More recently, several experimental, [8][9][10][11][12] theoretical [13][14][15][16][17][18][19] and simulation studies [20][21][22][23] have shown that the presence of internal friction modulates conformational changes in a number of different biological contexts. This includes slowing down the process of protein folding, 8 affecting the dynamics of intermolecular interactions in intrinsically disordered proteins, 10,11 and influencing stretching transitions in single biomolecule force spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

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

The Journal of Chemical Physics

2018

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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 a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on the magnitude of the stress jump at the inception of shear flow, and on the transient viscometric functions, but a negligible effect on the steady state viscometric functions at high shear rates. Zero-shear rate viscometric functions of free-draining dumbbells remain essentially independent of the internal viscosity parameter, as predicted by the Gaussian approximation, but the inclusion of hydrodynamic interactions induces a dependence on both the hydrodynamic interaction and the internal viscosity parameter. Large values of the internal viscosity parameter lead to linear viscoelastic predictions that mimic the behavior of rigid dumbbell solutions. On the other hand, steady-shear viscometric functions at high shear rates differ in general from those for rigid dumbbells, depending crucially on the finite extensibility of the dumbbell spring.

“…For dry internal friction, a spring-dashpot model [1,3,44,45] is considered where the molecule is represented as massless beads connected by a spring and dashpot in parallel with each other. The spring accounts for entropic elasticity, while dissipative effects due to internal friction are captured by the dashpot [46].…”

Section: Introductionmentioning

confidence: 99%

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

2020

Phys. Rev. Research

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The existence of two types of internal friction-wet and dry-is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule, and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of: (a) a single-mode nonlinear spring-dashpot model for a polymer, and (b) a finitely extensible bead-spring chain with cohesive intra-chain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally. arXiv:1904.07473v2 [cond-mat.soft]