Computational prediction of glycosamineglycanes binding to GAPDH and its implication in neurodegenerative disease

TORRES BUGEAU, CLARISA; AVILA, CÉSAR; CHEHÍN ROSANA

Florianópolis

Congreso; X-Meeting; 2011

Sociedad Brasilera de Bioinformática y Biología Computacional

Neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) have common cellular and molecular mechanisms including protein aggregation. The aggregates usually consist of fibers containing misfolded proteins termed amyloid. These aggregates are composed mainly by Abeta peptide and alpha-synuclein in AD and PD respectively. However, glycosaminoglycans (GAGs) along with other proteins like ubiquitin, tau and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are routinely found associated with these amyloid deposits. GAPDH is a well-studied protein as a glycolytic enzyme. Nevertheless, current evidence reveals that this protein can form fibrillar aggregates which were found in the post mortem brains of patients with PD and AD. In our lab, the ability of heparin and heparan sulfate to trigger the amyloid aggregation of GAPDH at physiological conditions of pH and temperature has been demonstrated through the use of various biophysical techniques. We also demonstrated that chondroitin sulphates A, B and C together with dextran sulphate had negligible effect in GAPDH aggregation. In order to explain the different effect of GAGs, a global search for heparin binding sites on GAPDH was conducted using the program AutoDock (version 4.2). Due to the high charge density and the weak surface complementarily of the sulphated sugar chain, prediction of heparin binding sites on protein presents a challenging task for computational docking. The structures of several protein-heparin complex, such as thrombin light chain and acidic and basic fibroblast growth factor, obtained from the PDB were used to evaluate the prediction capability of the docking protocol developed by us. In order to predict the heparin binding site on GAPDH this procedure was used. The docking results suggest that the position of the sulphate groups on the polymeric sugar chain seems to be more important than their density since only heparin and HS contain N-sulphation and 3-free hydroxyl in the glucosamine unit and 2-O-sulphation in the uronic unit readily available to interact with Lys104, Lys183 and Lys191 on GAPDH. Given the importance of protein-glycosaminoglycan interactions, the identification of protein sequences that interact specifically with heparin could shed light on the mechanism of protein aggregation. Considering the ability of heparin-induced GAPDH oligomers promoting the AS fibrilation and thus reducing the AS cytotoxicity, the results presented herein could have impact in drug design.