Studies on the conformational behaviour of GlcNAc-Man3-GlcNAc2 oligosaccharides using molecular dynamics simulations.

Abstract:

:Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-transferase II, GIcNAc-Man3-GlcNAc2, were investigated by molecular modelling methods. Molecular dynamics (MD) and molecular mechanics calculations on two hexasaccharides, namely GlcNAc-Man3-GlcNAc2-Asn and GlcNAc-Man3-GlcNAc2-OMe were performed by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simulation temperatures and for two values of dielectric constant, epsilon=1 and epsilon=4. From each 3 ns trajectory, 3050 structures have been optimized. The local minima obtained have been clustered into families exhibiting similar values of glycosidic torsional angles phi, psi, and omega. The influence of the simulation conditions and force fields used on the conformational behaviour and structure of the title oligosaccharides is discussed.

journal_name

Glycoconj J

journal_title

Glycoconjugate journal

authors

Kozar T,Tvaroska I,Carver JP

doi

10.1023/a:1006976408074

subject

Has Abstract

pub_date

1998-02-01 00:00:00

pages

187-91

issue

2

eissn

0282-0080

issn

1573-4986

journal_volume

15

pub_type

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