BIOPHYSICAL THEORY AND MODELING |
Determination of barrier heights and prefactors from protein folding rate data
Steven Samuel Plotkin 1*
1 University of British Columbia
* To whom correspondence should be addressed. E-mail: steve{at}physics.ubc.ca.
Submitted on September 9, 2004
Revised on January 2, 2005
Accepted on 2 March 2005
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Abstract |
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We determine both barrier heights and prefactors for protein folding by applying constraints determined from experimental rate measurements to a Kramers theory for folding rate. The theoretical values are required to match the experimental values at two conditions of temperature and denaturant that induce the same stability. Several expressions for the prefactor in the Kramers rate equation are examined: a random energy approximation, a correlated energy approximation, and an approximation using a single Arrhenius activation energy. Barriers and prefactors are generally found to be large as a result of implementing this recipe, i.e. the folding landscape is cooperative and smooth. Interestingly, a prefactor with a single Arrhenius activation energy admits no formal solution.
Key Words:
Energy landscape, Kramers rate, Protein folding, folding barrier, folding funnel, kinetics
