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© Oxford University Press

Connection topology of proteins

A. Aszói and W.R. Taylor

Laboratory of Mathematical Biology, National Institute for Medical Research The Ridgeway, Mill Hill, London NW7 1AA, UK

One-dimensional amino acid sequences and three-dimensional folded polypeptide chains were modelled as non-directed graphs in which nodes corresponded to amino acids and arcs repre sented connections between them. In the case of folded chains, non-backbone connections were assigned to amino acid pairs if their distance was lower than a threshold. Two topological indices, the connectedness number and the effective chain length were devised to compare folding topologies. Loops created by non-backbone connections in the structure graphs were studied by simple graphical representations, revealing the hierarchy in native protein structures.

Received on November 1, 1992; accepted on March 15, 1993

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