Reliable protein folding on non-funneled energy landscapes: the free energy reaction path

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory bas...

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Bibliographic Details
Published in:arXiv.org 2008-02
Main Authors: Gregg, Lois, Blawzdziewicz, Jerzy, O'Hern, Corey S
Format: Article
Language:English
Subjects:
Computer simulation
Folding
Free energy
Mathematical models
Organic chemistry
Protein folding
Proteins
Online Access:Get full text
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Summary:A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory based on this insight predicts that (1) proteins with non-funneled energy landscapes can fold reliably to their native state, (2) reliable folding can occur as an equilibrium or out-of-equilibrium process, and (3) reliable folding only occurs when the rate r is below a limiting value, which can be calculated from measurements of the free energy. We test these predictions against numerical simulations of model proteins with a single energy scale.
ISSN:2331-8422
DOI:10.48550/arxiv.0802.0209