Conformational search on the Lewis X structure by molecular dynamic: study of tri- and penta-saccharide

Abstract

Carbohydrates play vital roles in many biological processes, such as recognition, adhesion and signalling between cells. The Lewis X determinant is a trisaccharide fragment implicated as a specific differentiation antigen, tumor antigen and key component of the ligand for the endothelial leukocyte adhesion molecule, so it is necessary or essential to determine and to know their conformational and structural properties. In this work, conformational analysis was performed using molecular dynamics (MD) simulation with the AMBER10 program package in order to study the dynamic behavior of of the Lewis X trisaccharide (D-Gal-(1,4)-[ -L-Fuc-(1,3)]-D-GlcNAc-OMe), and Lewis X pentasaccharide (-D-Gal-(1,4)-[ -LFuc-(1,3)]-D-GlcNAc-(1,3)-D-Gal-(1,4)-D-Glu-OMe) in explicit water model at 300 K for 10 ns using the GLYCAM 06 force field.