Molecular dynamic studies of heparin binding to glyceraldehyde-3-phosphate dehydrogenase

AVILA CL,; CHEHÍN RN

Rosario

Congreso; IV Congreso Argentino de Bioinformática & IV Conferencia de SOIBIO; 2013

Sociedad Iberoamericana de bioinformática

Background Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme from the glycolytic pathway, which has been suggested to be involved in Parkinson´s disease. Although it was found associated to alfa-synuclein (AS) and glycosaminoglycans (GAG) in Lewy bodies (LB) isolated from biopsies of patients with PD [1,2], its role in the pathogenesis of the disease remains unclear. We demonstrated that upon binding, heparin as well as other highly sulfated GAGs are able to trigger GAPDH amyloid aggregation [3]. We also showed that some of the prefibrillar intermediates present in the early stages of GAPDH aggregation are able to interact with toxic species of AS, preventing in vitro some of the AS deleterious effects. In this way, the study of the GAPDH fibrillation pathway induced by heparin acquires relevance as it might be used in the treatment of PD. Results In this work, we use molecular dynamics simulations to model the early events in GAPDH aggregation, i.e. heparin binding to protein. We performed 20 free binding simulations of four heparin tetrasaccharides to protein, 100 ns each, using the CHARMm forcefield. Cluster analysis of the trajectories allowed us to get a glimpse on the most common binding modes. The putative binding pose, as obtained from one of the largest clusters, shows the sulfate groups from the 2-deoxy-2-sulfamido-alfa-D-glucopyranosyl-6-O-sulfate (GlcNS(6S)) ring positioned at phosphate binding pockets in GAPDH. It should be noted that in the crystallographic structure of the holo GAPDH from Bacillus stearothermophilus (PDB ID: 1GD1) this pockets are occupied by sulfate ions [4]. Conclusion The interactions described herein might explain the ability of heparin to trigger GAPDH fibrillation as only heparin and heparan sulfate contain N-sulfated residues in the glucosamine unit as opposed to other GAGs such as chondroitin sulfates which are unable to induce aggregation of GAPDH. References 1. Tsuchiya K, Tajima H, Kuwae T, Takeshima T, Nakano T, Tanaka M, Sunaga K, Fukuhara Y, Nakashima K, Ohama E, Mochizuki H, Mizuno Y, Katsube N, Ishitani R: Proapoptotic protein glyceraldehyde-3-phosphate dehydrogenase promotes the formation of Lewy body-like inclusions. Eur J Neurosci 2005, 21:317-326 2. Leverenz JB, Umar I, Wang Q, Montine TJ, McMillan PJ, Tsuang DW, Jin J, Pan C, Shin J, Zhu D, Zhang J: Proteomic identification of novel proteins in cortical lewy bodies, Brain Pathol 2007, 17:139-145. 3. Torres-Bugeau CM, Avila CL, Raisman-Vozari R, Papy-Garcia D, Itri R, Barbosa LR, Cortez LM, Sim VL, Chehin RN: Characterization of Heparin-induced Glyceraldehyde-3-phosphate Dehydrogenase Early Amyloid-like Oligomers and Their Implication in alpha-Synuclein Aggregation. J Biol Chem 2012, 287:2398-2409. 4. Skarzynski T, Moody PC, Wonacott AJ: Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution. J Mol Biol 1987, 193:171-87.