title: Assessment of homology with the helical mimicry algorithm.
abstract: Homologies based on structural motifs characterize conserved structures and mechanisms of maintaining function. An algorithm was developed to quantitate homology among segments of two proteins based upon structural characteristics of an amphipathic alpha-helix. This helical mimicry algorithm scored homology among sequences of two proteins in terms of: (i) presence of Leu, Ile, Val, Phe, or Met in a longitudinal, hydrophobic strip-of-helix at positions n, n + 4, n + 7, n + 11, etc. in the primary sequence, (ii) identity or chemical similarity of amino acids at intervening positions and (iii) exchanges of amino acids from positions n 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 the surfaces of homologous helices may conserve function, they did not maintain specific interactions of those residues with apposing groups.
authors.affiliation: Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655.
authors.forename: C M
authors.initials: CM
authors.lastname: Bositis
authors.forename: N
authors.initials: N
authors.lastname: Craft
authors.forename: R A
authors.initials: RA
authors.lastname: Lew
authors.forename: E J
authors.initials: EJ
authors.lastname: Fowlie
authors.forename: J
authors.initials: J
authors.lastname: Queenan
authors.forename: R E
authors.initials: RE
authors.lastname: Humphreys
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002645:Chickens; D006801:Humans; D008969:Molecular Sequence Data; D009113:Muramidase / Q000235:genetics*; D009154:Mutation; D017386:Sequence Homology, Amino Acid
chemical_list: D009113:Muramidase