title: Restrained vs free dynamics simulations of oligosaccharides: application to solution dynamics of biantennary and bisected biantennary N-linked glycans.
abstract: We have examined the dynamic behavior in solution of the biantennary glycan GlcNAc beta 1-2Man alpha 1-6(GlcNAc beta 1-2Man alpha 1-3)Man beta 1- 4GlcNAc beta 1-4GlcNAc, and its "bisected" analogue GlcNAc beta 1-2Man alpha 1-6(GlcNAc beta 1-2Man alpha 1-3)(GlcNAc beta 1- 4)Man beta 1-4GlcNAc beta 1-4GlcNAc, by use of both free dynamics simulations and restrained dynamics simulations using distance restraints derived from 1H NMR rotating frame Overhauser effect measurements. Data resulting from each type of simulation are compared with experimental data and are critically evaluated. Both methods suggest that most glycosidic linkages exhibit significant torsional oscillations in solution, and the dynamic behavior of certain linkages, notably Man alpha 1-6Man and Man alpha 1-3Man, were found to be restricted by the presence of the bisecting GlcNAc residue. The average structures so obtained were found to agree closely with those predicted in previous investigations where torsional oscillations about glycosidic linkages were not considered. In particular, the characteristic chemical shift perturbations induced by the bisecting GlcNAc residue could be explained in terms of the dynamic differences between the two glycans.
authors.affiliation: Department of Biochemistry, University of Dundee, U.K.
authors.forename: T J
authors.initials: TJ
authors.lastname: Rutherford
authors.forename: S W
authors.initials: SW
authors.lastname: Homans
mesh_terms: D000117:Acetylglucosamine / Q000737:chemistry*; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry; D006027:Glycosides / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry*; D012996:Solutions
chemical_list: D004187:Disaccharides; D006027:Glycosides; D009844:Oligosaccharides; D011134:Polysaccharides; D012996:Solutions; D000117:Acetylglucosamine