ASSESSMENT OF HOMOLOGY WITH THE HELICAL MIMICRY ALGORITHM

Homologies based on structural motifs characterize conserved structure s and mechanisms of maintaining function. An algorithm was developed t o quantitate homology among segments of two proteins based upon struct ural characteristics of an amphipathic alpha-helix. This helical mimic ry algorithm scored homology among sequences of two proteins in terms of: (i) presence of Leu, lie, Val, Phe, or Met in a longitudinal, hydr ophobic strip-of-helix at positions n, n + 4, n + 7, n + 11, etc. in t he primary sequence, (ii) identity or chemical similarity of amino aci ds at intervening positions and (iii) exchanges of amino acids from po sitionsn to n - 1, n + 3, n + 4, n + 1, n - 3, n - 4 around n (on the surface of a putative helix). While such exchanges of amino acids on t he surfaces of homologous helices may conserve function, they did not maintain specific interactions of those residues with apposing groups.