Jan 12, 2016

Analysis of Two-State Folding Using Parabolic Approximation I: Hypothesis

BioRxiv : the Preprint Server for Biology
Robert S Sade

Abstract

A model which treats the denatured and native conformers of spontaneously-folding fixed two-state systems as being confined to harmonic Gibbs energy-wells has been developed. Within the assumptions of this model the Gibbs energy functions of the denatured (DSE) and the native state (NSE) ensembles are described by parabolas, with the mean length of the reaction coordinate (RC) being given by the temperature-invariant denaturant m value. Consequently, the ensemble-averaged position of the transition state ensemble (TSE) along the RC, and the ensemble-averaged Gibbs energy of the TSE are determined by the intersection of the DSE and the NSE-parabolas. The equations derived enable equilibrium stability and the rate constants to be rationalized in terms of the mean and the variance of the Gaussian distribution of the solvent accessible surface area of the conformers in the DSE and the NSE. The implications of this model for protein folding are discussed.

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Mentioned in this Paper

Receptors, Antigen
Gamma-Enolase
Transition protein 2
Coordination and Collaboration
alpha-tocopheryloxybutyric acid
Replication Compartment
Solvents
Reaction Center
Analysis
Surface

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