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Predicting protein folding rates from geometric contact and amino acid sequence

¹ University of Illinois at Chicago;
² University of Illinois at chicago

(RECEIVED January 22, 2008; ACCEPTED April 7, 2008)

Protein folding speeds are known to vary over more than 8 orders of magnitude. Plaxco, Simons, and Baker first showed a correlation of folding speed with the topology of the native protein. That and subsequent studies showed that if the native structure of a protein is known, it's folding speed can be predicted reasonably well through a correlation with the "localness" of the contacts in the protein. In the present work, we develop a related measure, the geometric contact number, n, which is the number of nonlocal contacts that are well-packed, by a Voronoi criterion. We find, first, that in 80 proteins, the largest such database of proteins yet studied, n is a consistently excellent predictor of folding speeds of both two-state fast-folders and more complex multi-state folders. Second, we show that folding rates can also be predicted from amino acid sequences directly, without the need to know the native topology or other structural properties.

Keywords: Protein Structure/Folding; Computational Analysis of Protein Structure; folding rate; geometric contact number; zippers model

³ E-mail: jliang{at}uic.edu

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