title: Molecular dynamics simulations of asialoglycoprotein receptor ligands.
abstract: Several recent studies have implicated carbohydrates in cell adhesion, inflammation, clearance of glycoproteins from blood circulation, embryonic development, and metastasis among others. Understanding the conformation of these carbohydrate recognition elements and their interaction at the molecular level is essential for the design of oligosaccharide inhibitors/drugs. Given the difficulty in solving carbohydrate structures by X-ray crystallography and since NMR experiments give only time-averaged conformation, molecular dynamics simulations are well suited to determine all the accessible conformations of oligosaccharides. Present communication reports the simulation of some of the oligosaccharide ligands of asialoglycoprotein receptor for 1 ns using Biosym's Insight II molecular modeling package on NCI-FCRDC's Y-MP 8D/8128 supercomputer. Results obtained from these simulations, in addition to explaining the observed differences in the binding affinities of these ligands to the asialoglycoprotein receptor, have led to a modified model for the recognition of the oligosaccharides by the receptor. Accordingly, only the two terminal galactose residues on the 1,3-arm of the triantennary oligosaccharide (GlcNAc2Man3 core of the N-linked oligosaccharides with N-acetyllactosamine in beta 1,2- and beta 1,4-linkages on the 1,3-linked core mannose) are primarily required for recognition, and the terminal galactose on the 1,6-arm (N-acetyllactosamine in beta 1,2-linkage on the 1,6-linked core mannose) provides additional binding energy. It has been shown that the oligosaccharides studied here have significant flexibility and the flexibility is more around the 1,3-linkage than the 1,6-linkage. The need for simulation for longer periods and with multiple initial conformations is also discussed in the present report.
authors.affiliation: Laboratory of Mathematical Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: P V
authors.initials: PV
authors.lastname: Balaji
authors.forename: P K
authors.initials: PK
authors.lastname: Qasba
authors.forename: V S
authors.initials: VS
authors.lastname: Rao
mesh_terms: D037263:Asialoglycoprotein Receptor; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003196:Computer Graphics; D003198:Computer Simulation; D004187:Disaccharides; D005690:Galactose / Q000737:chemistry; D005936:Glucans / Q000737:chemistry; D006027:Glycosides / Q000737:chemistry; D006860:Hydrogen Bonding; D007536:Isomerism; D008024:Ligands; D008358:Mannose / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000737:chemistry* / Q000378:metabolism*; D011956:Receptors, Cell Surface / Q000378:metabolism*; D013997:Time Factors
chemical_list: D037263:Asialoglycoprotein Receptor; D004187:Disaccharides; D005936:Glucans; D006027:Glycosides; D008024:Ligands; D009844:Oligosaccharides; D011956:Receptors, Cell Surface; C032438:chitobiose; D008358:Mannose; D005690:Galactose