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Predicting protein folding rates from geometric contact and amino acid sequence
Author(s) -
Ouyang Zheng,
Liang Jie
Publication year - 2008
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.034660.108
Subject(s) - folding (dsp implementation) , protein folding , contact order , topology (electrical circuits) , voronoi diagram , amino acid , native state , physics , crystallography , biological system , chemistry , mathematics , combinatorics , biology , geometry , biochemistry , engineering , electrical engineering
Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the native protein. That and subsequent studies showed, if the native structure of a protein is known, its 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 α , 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 α is a consistently excellent predictor of folding speeds of both two‐state fast folders and more complex multistate 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.