A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein

Damien Hall; Songling Li; Kazuo Yamashita; Ryuzo Azuma; John A Carver; Daron M Standley

doi:10.1016/j.bpc.2014.01.005

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein

Biophys Chem. 2014 Jun:190-191:50-5. doi: 10.1016/j.bpc.2014.01.005. Epub 2014 Feb 13.

Authors

Damien Hall¹, Songling Li², Kazuo Yamashita², Ryuzo Azuma², John A Carver³, Daron M Standley⁴

Affiliations

¹ 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: [email protected].
² Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
³ Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.
⁴ Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address: [email protected].

PMID: 24589301
DOI: 10.1016/j.bpc.2014.01.005

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.

Keywords: Algorithm; Distance matrix; Protein–polymer interaction; Surface arc-length.

Publication types

Letter

MeSH terms

Algorithms*
Amino Acids / chemistry*
Cytochromes c / chemistry*
Surface Properties

Substances

Amino Acids
Cytochromes c