期刊
PROTEIN SCIENCE
卷 17, 期 7, 页码 1256-1263出版社
WILEY
DOI: 10.1110/ps.034660.108
关键词
protein folding; geometric contact number; zippers model; folding rate
资金
- NIGMS NIH HHS [R01 GM068958, R01 GM079804, GM081682, GM079804-01A1, GM68958] Funding Source: Medline
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 alpha, 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 alpha 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.
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