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.
Subject(s)
Neuraminidase/chemistry , Neuraminidase/metabolism , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Orthomyxoviridae/enzymology , Carbohydrate Conformation , Carbohydrate Sequence , Catalytic Domain , Computer Simulation , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Protein Conformation , Substrate Specificity , ThermodynamicsABSTRACT
Conventional space filling molecular modeling in computers, using the scan method, takes considerable computer time and effort. In depicting the CPK-image on a computer screen, the hidden-point removal is the main task and on such an image, the front-line atoms hide the back-benchers and their whereabouts become completely unknown, in a given view of the picture. While in search of a simple and faster algorithm for producing surface graphics of molecules, we have developed a novel method, which is considerably faster than the conventional one and it has an interesting transparency-effect which would be useful in the various fields of molecular designs.
