|InterJournal Polymers and Complex Fluids, 560
|Manuscript Number: |
Submission Date: 20531
|Fluctuation analysis in the Transition State ensemble of the SH3 domain|
Subject(s): PX.11, PX.01, CX.30, CX.26
We perform a detailed analysis of the folding kinetics of the SH3 domain fold family of proteins with discrete molecular dynamics. We propose a protein model that reproduces the general experimentally observed thermodynamic and folding kinetic properties of globular proteins. We use our model to study the rare thermal fluctuations that beginning in the folded or unfolded state, reach the transition state ensemble--- a set of unstable conformations that fold to the protein native state with probability 1/2. With the analysis of the rare fluctuations we predict that a set of amino acid contacts are the critical folding nucleus of the SH3 fold and propose a hypothesis that explains this result.
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