Protein evolution and protein folding: non-functional conserved residues and their probable role

It is shown that there are two types of conserved residues in evolutionary and functionally related proteins whose sequences have been well diverged in evolution. The first group consists of residues forming the active center, while the second (first established in this work) has nothing to do with function and therefore should be related to protein structure and/or protein folding. The lattter group consists of 4 residues in c-type cytochromes and 6 residues in globins. All these residues belong to alpha-helices and occupy positions (i, i + 4) or (i, i + 3), stabilizing one helical turn in some helices. These residues form an interface between the N- and C-terminal helices in c-type cytochromes and helices A, G, H in globins. These helical complexes form early in protein folding and are relatively stable in both equilibrium and kinetic folding intermediates. The attractive hypothesis is that these helices form folding nuclei in protein in the frame of the nucleation-growth mechanism of protein folding.