Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions

Details Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions

2005-02-15

arxiv.org/abs/q-bio/0502016v1

Biology

Quantitative Biology

Biomolecules

24 pages, 3 figures, 2 tables; to appear in "Proteins: Structure, Function, and Bioinformatics"

Scientific paper

In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes from native structures by minimizing the entropic loop-closure cost during folding. The model predicts characteristic folding sequences of structural elements such as helices and beta-strand pairings. Based on few simple rules, the kinetic impact of these structural elements is estimated from the routes and compared to average experimental Phi-values for the helices and strands of 15 small, well-characterized proteins. The comparison leads on average to a correlation coefficient of 0.62 for all proteins with polarized Phi-value distributions, and 0.74 if distributions with negative average Phi-values are excluded. The diffuse Phi-value distributions of the remaining proteins are reproduced correctly. The model shows that Phi-value distributions, averaged over secondary structural elements, can often be traced back to entropic loop-closure events, but also indicates energetic preferences in the case of a few proteins governed by parallel folding processes.

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