Conformational Dynamics of a Central Trisaccharide Fragment of the Le^aLe^x Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations

Abstract

Certain carbohydrate structures are recognized as cancer antigens, and identification of these and relevant epitopes are essential in fighting the disease. The trisaccharide β‐D‐GlcpNAc‐(1→3)‐β‐D‐Galp‐(1→4)‐β‐D‐GlcpNAc‐OMe represents a model for the central region of the LeaLex hexasaccharide and it has herein been investigated by 1D 1H,1H‐NOESY experiments to obtain effective interresidue proton–proton distances as well as by 2D J‐HMBC experiments to determine transglycosidic 3JCH coupling constants. Molecular dynamics (MD) simulations using explicit water as solvent and three different carbohydrate force fields, namely, GLYCAM06, PARM22/SU01, and CHARMM2011, were employed for the interpretation of experimental data. Overall, the force field based MD simulations are able to reproduce the experimental data and the ψ torsion angle at the β‐(1→3)‐linkage is concluded to be flexible. In addition, different minor states were present for the three force fields with either anti‐ψ or non‐exo‐anomeric conformations. Transitions between the exo‐anomeric and the non‐exo‐anomeric conformations for the φ torsion angle at the β‐(1→4)‐linkage in one of the MD simulations were analyzed in detail. It was found that hydrogen‐bonding water molecules, interresidue hydrogen bonds and the transitions between antiperiplanar and synperiplanar conformations for the τH torsion angle of an N‐acetyl group were all essential in the description of the glycosidic transition process. In particular, the transition of τH may be a general way of regulating other transitions into less populated but biologically important conformational regions.

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility

“…Molecular dynamics (MD) simulations have been used previously to study conformational properties of glycosidic linkages in oligosaccharides (Campen et al, 2007;Peric-Hassler et al, 2010;Zaccheus et al, 2012;Wang et al, 2013), although hemicelluloses were not specifically targeted. Here, we use MD to study different disaccharides and tetrasaccharides mimicking the possible sugar combinations from the backbone of glucomannan, xylan and xyloglucan.…”

Recognition of Dimeric Lewis X by Anti-Dimeric Lex Antibody SH2

“…Extended epitope presentation from the non-reducing end Le x trisaccharide in DimLe x to the mAb SH2 binding site should also be considered in the context of the β- d -Glc N Ac-(1→3)- d -Gal glycosidic bond conformation. Indeed, this glycosidic bond, that links the non-reducing end Le x trisaccharide to the reducing end Le x moiety in DimLe x ( 6 ) or to galactose in Lex[1,3]Gal (9), has been shown to be highly flexible in various oligosaccharides [ 60 , 61 , 62 , 63 , 64 , 65 , 66 ]. Conformations around glycosidic bonds are defined by two dihedral angles: Φ (O5-C1-O1-Cx) and Ψ (C1-O1-Cx + 1).…”

Glycan synthesis, structure, and dynamics: A selection

“…In the trisaccharide β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-β-D-GlcpNAcOMe (Fig. 4), a model for the central region of the Le a Le x hexasaccharide, we observed a minor conformation appearing to be more easily accessible when the nearby N-acetyl group was in a conformation having τ ≈ 165º [24]. Upon closer investigation, a plausible causal relationship was found involving R. PENDRILL et al…”

“…This chain of events was initiated by the disruption of the interresidue O5'ؒؒؒHO3 hydrogen bond and the simultaneous formation of a hydrogen bond with the same donor atom but involving the N-acetyl carbonyl oxygen instead. Since the latter hydrogen bond is only accessible in a small region of the conformational space for the N-acetyl group, it appears that this functional group effectively regulates the conformation at other flexible sites in the molecule [24].…”