title: Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin.
abstract: A topological list, consisting of segments of regular secondary structures and a list of buried and solvent accessible residues, is automatically predicted from multiple aligned sequences in a protein family. This topological list is translated into geometric constraints for distance geometry calculation in torsion angle space. A new self-correcting distance geometry method detects and eliminates false distance constraints. In an application to the four-helix bundle protein, myohem-erythrin, the right-handed global fold was correctly reproduced with a root-mean-square deviation of 2.6 A, when the topological list was derived from the X-ray structure. A predicted topological list, coupled with constraints from the residues in the active site of myohemerythrin, predicted the correct fold with a root-mean-square deviation of 4 A for backbone atoms.
authors.affiliation: Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
authors.forename: G
authors.initials: G
authors.lastname: Hänggi
authors.forename: W
authors.initials: W
authors.lastname: Braun
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006422:Hemerythrin / Q000031:analogs & derivatives* / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009348:Nematoda / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012984:Software
chemical_list: D006422:Hemerythrin; C008571:myohemerythrin