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Biophys. J. BioFAST: First Published June 9, 2006. doi:10.1529/biophysj.106.086264
© 2006 by the Biophysical Society.

A more recent version of this article appeared on September 1, 2006.
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PROTEINS

TOWARD AN ACCURATE THEORETICAL FRAMEWORK FOR DESCRIBING ENSEMBLES FOR PROTEINS UNDER STRONGLY DENATURING CONDITIONS

Hoang T Tran 1 and Rohit V Pappu 2*

1 Washington University in St.Louis
2 Washington University

* To whom correspondence should be addressed. E-mail: pappu{at}biomed.wustl.edu.

Submitted on March 31, 2006
Revised on May 12, 2006
Accepted on 31 May 2006


  Abstract
Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows: Average shapes are consistent with prolate ellipsoids; Ensembles are characterized by large correlated fluctuations; Sequence-specific conformational preferences are restricted to local length scales that span 5-9 residues; Beyond local length scales, chain properties follow well-defined power laws that are expected for generic polymers in the EV limit; The average available volume is filled inefficiently and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.

Key Words: Correlated Fluctuations, Denatured States, Excluded Volume, Solvent Quality




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Copyright © 2006 by the Biophysical Society.