Structural similarity between two-layer alpha/beta and beta-proteins.

This paper demonstrates that overall folds of two-layer alpha/beta-proteins and beta-proteins with aligned beta-sheet packings have a number of common features. First of all, there are similar recurrent folding units, the so-called abcd-units, in proteins of both the classes. There are also some larger commonly occurring structures in many representatives of these classes. The fact that these proteins belong to different structural classes and have different functions supports the idea that some physical principles governing the polypeptide chain folding rather than the evolutionary divergence or functional convergence of proteins are the basis of such similarities. The analysis reported here shows that practically all the known protein structures of these classes can be obtained by stepwise addition of secondary structure element to the abcd-units taking into account three simple rules: (1) crossing of connection regions is prohibited; (2) alpha-helices should be packed into the alpha-layer and beta-strands in to the beta-layer of the growing structure; (3) beta alpha beta-units should be folded into right-handed superhelices; three consecutive beta-strands can be folded into the similar right-handed beta beta beta-superhelix if there is at least one additional beta-strand in the layer between the first and third ones. A possible selection of a conformation of a polypeptide chain segment by its protein environment is also discussed.