R.C. Melo^1,2, C. Ribeiro^1,2, C.S. Murray², C.J.M. Veloso^1,2, C.H. da Silveira^1,2, G. Neshich³, W. Meira Jr.², R.L. Carceroni² and M.M. Santoro^1
1Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
²Departamento de Ciência da Computação, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
³Embrapa Informação Tecnólogica, Campinas, SP, Brasil
Corresponding author: R.C. Melo
E-mail: [email protected]/[email protected]

Genet. Mol. Res. 6 (4): 946-963 (2007)
Received August 03, 2007
Accepted September 25, 2007
Published October 05, 2007

ABSTRACT. We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature.

Key words: BPTI, Protein-protein interactions, Contact maps, Serine proteases