DSpace
 

DSpace at IIT Bombay >
IITB Publications >
Article >

Please use this identifier to cite or link to this item: http://dspace.library.iitb.ac.in/jspui/handle/10054/9466

Title: Molecular dynamics simulations of alpha 2 -> 8-linked disialoside: Conformational analysis and implications for binding to proteins
Authors: VASUDEVAN, SV
BALAJI, PV
Keywords: t-cell activation
crystal-structure
d-glucose
3-dimensional structures
glycosidic linkage
polysialic acid
tetanus toxin
sialic-acid
oligosaccharides
polysaccharide
Issue Date: 2002
Publisher: JOHN WILEY & SONS INC
Citation: BIOPOLYMERS, 63(3), 168-180
Abstract: Computational methods have played a key, role in elucidating the various three-dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac-alpha2-->8-Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac-alpha2 --> 8-Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth. development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the alpha2-8-linked disialoside has four: C2-O, O-C8', C8'-C7', and C7'-C6'. The present report describes the results from nine 1 ns MD simulations of alpha2-->8-linked disialoside (Neu5Ac-alpha2-->8-Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O-C8' bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast. conformations around the C2-O and C8'-C7' bonds werefound to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7'-C6' bond were found to be in either the - sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7'-C6' bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide's flexibility. (C) 2002 John Wiley Sons, Inc.
URI: http://dx.doi.org/10.1002/bip.10019
http://dspace.library.iitb.ac.in/xmlui/handle/10054/9466
http://hdl.handle.net/10054/9466
ISSN: 0006-3525
Appears in Collections:Article

Files in This Item:

There are no files associated with this item.

View Statistics

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

 

Valid XHTML 1.0! DSpace Software Copyright © 2002-2010  Duraspace - Feedback