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Rapid Generation of a Representative Ensemble of N-Glycan Conformations
Glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces where their oligosaccharide moieties are implicated in a wide range of cellcell and cellmatrix recognition events. Glycans constitute highly flexible molecules. Only a small number of glycan X-ray structu...
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Published in: | In silico biology 2002, Vol.2 (3), p.427-439 |
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Main Authors: | , , , |
Format: | Article |
Language: | English |
Subjects: | |
Online Access: | Get full text |
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Summary: | Glycosylated proteins are ubiquitous components of extracellular
matrices and cellular surfaces where their oligosaccharide moieties are
implicated in a wide range of cellcell and cellmatrix
recognition events. Glycans constitute highly flexible molecules. Only a small
number of glycan X-ray structures is available for which sufficient electron
density for an entire oligosaccharide chain has been observed. An unambiguous
structure deter-mination based on NMR-derived geometric constraints alone is
often not possible. Time consuming computational approaches such as Monte Carlo
calculations and molecular dynamics simulations have been widely used to
explore the conformational space accessible to complex carbohydrates. The
generation of a comprehensive data base for N-glycan fragments based on long
time molecular dynamics simulations is presented. The fragments are chosen in
such a way that the effects of branched N-glycan structures are taken into
account. The prediction database consti-tutes the basis of a procedure to
generate a complete set of all possible conformations for a given N-glycan. The
constructed conformations are ranked according to their energy content. The
resulting conformations are in reason-able agreement with experimental data. A
web interface has been established (http://www.dkfz.de/spec/glydict/), which
enables to input any N-glycan of interest and to receive an ensemble of
generated conformations within a few minutes. |
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ISSN: | 1386-6338 1434-3207 |
DOI: | 10.3233/ISB-00061 |