title: Molecular modeling of sialyloligosaccharide fragments into the active site of influenza virus N9 neuraminidase.
abstract: Molecular modeling studies have been carried out to investigate the interactions between substrate sialyloligosaccharide (SOS) fragments bearing different glycosidic linkages and influenza virus N9 neuraminidase, a surface glycoprotein of influenza virus subtype N9. The studies revealed that the allowed orientation for sialic acid (SA) is less than 1% in the Eulerian space at the active site. The active site of this enzyme has enough space to accommodate various SOS fragments, NeuNAcalpha(2-3)Gal, NeuNAcalpha(2-6)Gal, NeuNAcalpha(2-8)NeuNAc and NeuNAcalpha(2-9)NeuNAc, but on specific conformations. In the bound conformation, among these substrates there exists a conformational similarity leading to a structural similarity, which may be an essential requirement for the cleavage activity of the neuraminidases irrespective of the type of glycosidic linkage.
authors.affiliation: Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India. bio@md3.vsnl.net.in
authors.forename: K
authors.initials: K
authors.lastname: Veluraja
authors.forename: M X
authors.initials: MX
authors.lastname: Suresh
authors.forename: T H
authors.initials: TH
authors.lastname: Christlet
authors.forename: Z A
authors.initials: ZA
authors.lastname: Rafi
mesh_terms: D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D020134:Catalytic Domain; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000737:chemistry* / Q000378:metabolism*; D009844:Oligosaccharides / Q000737:chemistry* / Q000378:metabolism*; D009975:Orthomyxoviridae / Q000201:enzymology*; D011487:Protein Conformation; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D009844:Oligosaccharides; C016735:sialooligosaccharides; D009439:Neuraminidase