Unified regression model of binding equilibria in crowded environments.

Scientific Reports
Byoungkoo LeeRussell Schwartz

Abstract

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment.

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Citations

Sep 17, 2013·Journal of Molecular Graphics & Modelling·Michael Feig, Yuji Sugita
Feb 6, 2013·Nature Structural & Molecular Biology·Vladimir Svetlov, Evgeny Nudler
Feb 12, 2014·The Journal of Chemical Physics·Zhong-Ru XieYinghao Wu

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Methods Mentioned

BETA
protein folding

Software Mentioned

Moonshine
SPT
Matlab
Linux Fedora
2DSOLM
Linux Beowulf
SOLM
GNU
2DSPT
URM

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