A docking model for convulxin and convulxin-like proteins with human glycoprotein VI

COMP 201

Yufeng J. Tseng, yjtseng@csie.ntu.edu.tw and Cheng-chieh Tsai, mustkevin@gmail.com. Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Computer Science and Information Science, National Taiwan University, Rm 529, No. 1 Roosevelt Rd. Sec. 4, Taipei, 106, Taiwan
Convulxin, one of C-type lectin-like proteins, was extracted from the South American rattlesnake and has been use as platelet agonist. However, the fragments of convulxin displayed antagonist properties. There is no developed binding model to explore the mechanism of convulxin. Herein, we used the human glycoprotein VI receptor and convulxin structures from PDB (2GI7, 1UMR) to predict the binding model with Genetic Algorithm which build in the AUTODOCK. We also present a new type of C-type lectin-like protein with homology modeling structure that can be used to predict and explain the previous experimental binding activities. Convulxin and this new convulxin like protein share similar binding site and activity pattern but different from the collagen binding site at glycoprotein VI which proposed in the previous literature. Our model suggest that these two protein shares similar binding model and both protein fragment have the potential as potent platelet antagonist.

Poster Session
6:00 PM-8:00 PM, Tuesday, August 18, 2009 Walter E. Washington Convention Center -- Ballroom A, Poster

Division of Computers in Chemistry

The 238th ACS National Meeting, Washington, DC, August 16-20, 2009