GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins.
In previous work [Pol-Fachin, L.; Fernandes, C. L.; Verli, H.; Carbohydr. Res.2009, 344, 491-500], we had demonstrated that GROMOS96 43a1 force field and Löwdin HF/6-31G * *-derived atomic charges, adequately represent a glycoprotein's conformational ensemble in aqueous solutions, taking as the starting geometries NMR-determined structures. Based on such data, the present work intends to evaluate the use of the main solution conformations of isolated disaccharides, to build the carbohydrate moiety of glycoproteins, for which no previous experimental information is available. The observed results suggested that the entire glycoprotein scaffold appears unable to promote major modifications in the conformational behavior of glycosidic linkages. Additionally, when compared to energy contour plots, the results support the use of solution ensembles, to refine vacuum conformations of carbohydrate databases in the assembling of glycoproteins 3D structures. Finally, such approach is applied to build a full glycosylated model for COX-1 and COX-2 enzymes.
Fernandes
C L
CL
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil.
Sachett
L G
LG
Pol-Fachin
L
L
Verli
H
H
D000818:Animals; D018801:CD2 Antigens / Q000737:chemistry*; D018957:CD59 Antigens / Q000737:chemistry*; D002240:Carbohydrate Sequence; D006063:Chorionic Gonadotropin / Q000737:chemistry*; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry*; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D051379:Mice; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry; D011451:Prostaglandin-Endoperoxide Synthases / Q000737:chemistry; D013816:Thermodynamics
D018801:CD2 Antigens; D018957:CD59 Antigens; D006063:Chorionic Gonadotropin; D004187:Disaccharides; D006023:Glycoproteins; D009844:Oligosaccharides; D011134:Polysaccharides; C051590:CD59 protein, human; D011451:Prostaglandin-Endoperoxide Synthases