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J Comput Biol. 2007 Jun;14(5):578-93.

Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values.

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1
School of Computing, National University of Singapore, Singapore.

Abstract

This paper presents a new method for studying protein folding kinetics. It uses the recently introduced Stochastic Roadmap Simulation (SRS) method to estimate the transition state ensemble (TSE) and predict the rates and the Phi-values for protein folding. The new method was tested on 16 proteins, whose rates and Phi-values have been determined experimentally. Comparison with experimental data shows that our method estimates the TSE much more accurately than an existing method based on dynamic programming. This improvement leads to better folding-rate predictions. We also compute the mean first passage time of the unfolded states and show that the computed values correlate with experimentally determined folding rates. The results on Phi-value predictions are mixed, possibly due to the simple energy model used in the tests. This is the first time that results obtained from SRS have been compared against a substantial amount of experimental data. The results further validate the SRS method and indicate its potential as a general tool for studying protein folding kinetics.

PMID:
17683262
DOI:
10.1089/cmb.2007.R004
[Indexed for MEDLINE]

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