Docking simulation on the inhibitor of exo-polygalacturonase

COMP 232

Yong-Jae Lee, yjl@pusan.ac.kr1, Eun-Hee Kim2, and Sungu Hwang, sungu@pusan.ac.kr2. (1) Department of Horticultural Bioscience, Pusan National University, 50 Cheonghak-ri, Samnangjin-eup, Miryang, 627-706, South Korea, (2) Department of Nanomedical Engineering, Pusan National University, 50 Cheonghak-ri, Samnangjin-eup, Miryang, 627-706, South Korea
Docking simulation on the inhibitor of a protein called polygalacturonase (PG), which is relevant to control cell walls, was performed to slow down the ripening of fruit. The simulation was conducted by using a docking program, Glide by applying the various structure of inhibitors to Exo-PG of Yersinia enterocolitica, YeGH28. In order to find proper inhibitors that have more affinity and are structurally similar to natural inhibitor of Exo-PG found in X-ray structural data, a trial set is prepared by changing positions of ľOH attached carbon atoms. In addition, substitution was made in the linkage of the natural inhibitor to research the effect of different binding. Result showed that the ligand whose ľOH is positioned alternately had the strongest affinity to the protein. Redocking was conducted to find whether there is any synergestic effect between the positional effect and substitution.
 

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