Sequence evolution and the mechanism of protein folding

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