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Biophys J, October 2000, p. 1787-1799, Vol. 79, No. 4

Sequence Evolution and the Mechanism of Protein Folding

Angel R. Ortiz and Jeffrey Skolnick

Department of Molecular Biology, TPC-5, The Scripps Research Institute, La Jolla, California 92037 USA

The impact on protein evolution of the physical laws that govern folding remains obscure. Here, by analyzing in silico-evolved sequences subjected to evolutionary pressure for fast folding, it is shown that: First, a subset of residues in the thermodynamic folding nucleus is mainly responsible for modulating the protein folding rate. Second and most important, the protein topology itself is of paramount importance in determining the location of these residues in the structure. Further stabilization of the interactions in this nucleus leads to fast folding sequences. Third, these nucleation points restrict the sequence space available to the protein during evolution. Correlated mutations between positions around these hot spots arise in a statistically significant manner, and most involve contacting residues. When a similar analysis is carried out on real proteins, qualitatively similar results are obtained.

Biophys J, October 2000, p. 1787-1799, Vol. 79, No. 4
© 2000 by the Biophysical Society   0006-3495/00/10/1787/13  $2.00


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