Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins

Physical Chemistry Chemical Physics : PCCP
Xiakun Chu, Jin Wang

Abstract

Successful extensions of protein-folding energy landscape theory to intrinsically disordered proteins' (IDPs') binding-coupled-folding transition can enormously simplify this biomolecular process into diffusion along a limited number of reaction coordinates, and the dynamics subsequently is described by Kramers' rate theory. As the critical pre-factor, the diffusion coefficient D has direct implications on the binding kinetics. Here, we employ a structure-based model (SBM) to calculate D in the binding-folding of an IDP prototype. We identify a strong position-dependent D during binding by applying a reaction coordinate that directly measures the fluctuations in a Cartesian configuration space. Using the malleability of the SBM, we modulate the degree of conformational disorder in an isolated IDP and determine complex effects of intrinsic disorder on D varying for different binding stages. Here, D tends to increase with disorder during initial binding but shows a non-monotonic relationship with disorder in terms of a decrease-followed-by-increase in D during the late binding stage. The salt concentration, which correlates with electrostatic interactions via Debye-Hückel theory in our SBM, also modulates D in a stepwise way. The...Continue Reading

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Citations

Nov 12, 2019·Journal of Biomolecular Structure & Dynamics·Jing YangYongqi Huang
Sep 5, 2020·Applied Physics Reviews·Xiakun Chu, Jin Wang
Jun 3, 2021·International Journal of Molecular Sciences·Bin Sun, Peter M Kekenes-Huskey
Jan 24, 2020·Journal of Chemical Theory and Computation·Xiakun ChuJin Wang
Nov 10, 2021·Reports on Progress in Physics·Wen-Ting ChuJin Wang

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Methods Mentioned

BETA
protein folding
differential scanning calorimetry
protein-folding

Software Mentioned

Contacts of Structural Units ( CSU )
Gromacs
SMOG
PLUMED

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