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Characterization of the interaction between cahapsin B and glicosaminoglicans using computational mehtods

Abstract

The goal of the project is the molecular characterization the interaction between cystein-proteases and glicosaminoglicans through computational simulation. The main focus is cathepsin B, a thiol proteases that is implicated in various physio-pathologies, such as invasion and tumoral metastasis, muscular dystrophy and arthritis, where it is related to the degradation of extracellular matrix components, rich in glycosaminoglycans. Almeida e col. (J. Biol. Chem. 276, 944-951, 2001) have shown that the interaction between cathepsin B and others cystein-proteases with glycosaminoglycans, heparan sulfate and heparin, in particular, modulates its activity and increase structural stability against alcaline denaturation, effect accompanied by changing in its alpha-helical content, suggesting a mechanism that may explain why this protease can keep active, at physiological pH, at extracellular matrix of tumoral cells. A large number of protein that interact with glycosaminoglycan has been observed experimentally, but less than a dozen complexes has been determined with atomic resolution by X-ray crystallography. So far, none cystein-protease/glycosaminoglycan complex has been resolved with atomic resolution, showing that the complex crystallization is a experimental challenge. Among the few proteins complexed with heparin, resolved with atomic resolution, one can cite antithronbim III and fibroblast growth factors. The study of the interaction will start from the heparin disaccharide topology, based on the GROMOS96 force field, whose charge distribution was determined by quantum calculation. The cathepsin B molecular dynamics will be done in different temperatures and conditions in order to obtain the relaxed structure for docking. The complex cathepsin B-heparin will be build by molecular docking using the Generalized Simulated Annealing (GSA) algorithm, followed by molecular dynamics to check the complex stability and structural changes on the protein... (AU)

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