%0 Journal Article
%T Conformational Search on the Lewis X Structure by Molecular Dynamic: Study of Tri- and Pentasaccharide
%A N. Khebichat
%A K. Nekkaz
%A S. Ghalem
%J International Journal of Carbohydrate Chemistry
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/725271
%X 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 (¦Â-D-Gal-(1,4)-[¦Á-L-Fuc-(1,3)]-¦Â-D-GlcNAc-OMe) and the Lewis X pentasaccharide (¦Â-D-Gal-(1,4)-[¦Á-L-Fuc-(1,3)]-¦Â-D-GlcNAc-(1,3)-¦Â-D-Gal-(1,4)-¦Â-D-Glu-OMe) in explicit water model at 300£¿K for 10£¿ns using the GLYCAM 06 force field. 1. Introduction In nature, carbohydrates form an important family of biomolecules, as simple or complex carbohydrates, either alone or covalently linked to proteins or lipids [1]. They play vital roles in many biological processes, such as recognition, adhesion, and communication between cells. Carbohydrates that are covalently linked to a nonsugar moiety (proteins, peptides, or lipids) are the most prominent cell-surface-exposed structures. The highly diverse structural variability of carbohydrates makes them good candidates for cell receptors and recognition molecules [2]. Determination of the three-dimensional structure of oligosaccharides and understanding the molecular basis of their recognition by receptors represent the main challenges of structural glycobiology. Elucidation of the three-dimensional structures and the dynamical properties of oligosaccharides is a prerequisite for a better understanding of the biochemistry of recognition processes and for the rational design of carbohydrate-derived drugs [1]. The human histo-blood group ABH (O) systems were the first major human alloantigens to be identified. The carbohydrate nature of the A, B, H, and Lewis antigens was established in 1950s [3, 4]. Figure 1 shows a schematic representation of current histo-blood group antigens although additional rare types also exist [5]. The oligosaccharidic epitope of ABH (O) and Lewis histo-blood groups have been the subject of many structural investigations. The energy maps of all of the disaccharides have been established by molecular mechanics methods [6, 7]. Figure 1: Schematic representation of histo-blood group oligosaccharides. The determination of conformational preferences of oligosaccharides is best approached by
%U http://www.hindawi.com/journals/ijcc/2012/725271/