Hypothesis about the mechanism of protein folding.

A three-step mechanism of protein folding, proposed in our previous paper, is applied here to postulate the nature of the intermediates in the folding of rubredoxin, ferricytochrome c, and lysozyme. Contact maps are calculated for these three proteins, and it is shown that they contain much information (such as the polarity of residues in contact regions) about the structure of the native protein. Elementary processes are described for the formation of contact regions. Based on these concepts, details of the pathways of folding these three proteins from the unfolded to the native structure are postulated, focusing on the formation of ordered backbone structures (such as alpha-helical, extended, and chain-reversal conformations) in step A of the three-step mechanism and on the formation of contact regions in response to medium-and long-range interactions in steps B and C. It was found that chain reversals can often play an important role in forming contact regions in step A (short-range interactions) and in step B (medium-range interactions) but not in step C.