title: A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.
abstract: We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500 Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed.
authors.affiliation: Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia; Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address: damien.hall@anu.edu.au.
authors.forename: Damien
authors.initials: D
authors.lastname: Hall
authors.affiliation: Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Songling
authors.initials: S
authors.lastname: Li
authors.affiliation: Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Yamashita
authors.affiliation: Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Ryuzo
authors.initials: R
authors.lastname: Azuma
authors.affiliation: Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.
authors.forename: John A
authors.initials: JA
authors.lastname: Carver
authors.affiliation: Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address: standley@ifrec.osaka-u.ac.jp.
authors.forename: Daron M
authors.initials: DM
authors.lastname: Standley
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D045304:Cytochromes c / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D000596:Amino Acids; D045304:Cytochromes c
keywords: Algorithm; Distance matrix; Protein–polymer interaction; Surface arc-length