CARB 46 |
| Glycosaminoglycans (GAGs) are sulfated, carbohydrate polymers in which a uronic acid-glucosamine disaccharide unit repeats. To date, 23 different repeat units have been identified in GAGs with several intra-residue conformational states. These structural features introduce phenomenal structural diversity in GAG sequences. Despite the involvement of GAGs in several biological processes, little is known about specific recognition sequences. The prediction of specific protein-binding GAG sequences using in silico screening would be a rapid approach to understand GAG structure-activity relationships. We have designed a molecular docking approach based on a dual filtering protocol – GOLD score and sequential reproducibility – to derive structural and conformational information on GAG sequence(s) that recognize proteins. This protocol accurately identifies the high-affinity pentasaccharide sequence of heparin from nearly 7,000 possible sequences as the most optimal GAG sequence. Additionally, the binding geometry and mode of the pentasaccharide-sequence matches to within 2.5 Å RMSD when compared to the X-ray crystal structure. |
|
General Posters
6:00 PM-8:00 PM, Tuesday, 28 March 2006 Georgia World Congress Center -- Ex. Hall B4, Poster
Division of Carbohydrate Chemistry |