Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

Abstract

The conformational flexibility and dynamics of two (1-->6)-linked disaccharides that are related to the action of the glycosyl transferase GnT-V have been investigated. NMR NOE and T-ROE spectroscopy experiments, conformation-dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as alpha-d-[6-(13)C]-Manp-OMe derivatives, which reduced the (1)H NMR spectral overlap and facilitated the determination of two- and three-bond (1)H,(1)H, (1)H,(13)C and (13)C,(13)C-coupling constants. The population distribution for the glycosidic omega torsion angle in alpha-d-Manp-(1-->6)-alpha-d-Manp-OMe for gt/gg/tg was equal to 45:50:5, whereas in alpha-d-Manp-OMe it was determined to be 56:36:8. The dynamic model that was generated for beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe by MD simulations employing the PARM22/SU01 CHARMM-based force field was in very good agreement with experimental observations. beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe is described by an equilibrium of populated states in which the phi torsion angle has the exo-anomeric conformation, the psi torsion angle an extended antiperiplanar conformation and the omega torsion angle a distribution of populations predominantly between the gauche-trans and the gauche-gauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site-specific (13)C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.

Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-l-Fucp-(1→6)-α-d-Glcp-OMe in Water Solution

“…Effective correlation times were also determined from the ratio between the cross-relaxation rates from NOESY and T-ROESY experiments 17 which are in very good agreement with that calculated from translational diffusion (Table 3). To further investigate the dynamics 13 C T 1 relaxation rates were measured (Figure 11a, Table 4).…”

“…[13][14][15][16][17][18] The conformational and dynamical properties of other (1→6)-linked disaccharides 17,[19][20][21] and larger oligosaccharides having this linkage 15,22 have been investigated.…”

NMR analysis of conformationally dependent nJC, H and nJC, C in the trisaccharide α‐L‐Rhap‐(1 → 2)[α‐L‐Rhap‐(1 → 3)]‐α‐L‐Rhap‐OMe and a site‐specifically labeled isotopologue thereof

“…It is furthermore possible to obtain also n J C,H coupling constants when site-specifically 13 C-labeled compounds are available. [41] The spin-simulation software was also used for 1-c 2 where, in conjunction with a 1 H, 13 C-coupled 13 C NMR spectrum (Fig. 9), a 1 H NMR spectrum was predicted in excellent agreement with experimental spectrum at 500 MHz (Fig.…”

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with13C CPMAS NMR as a Verification Method

“…Spin coupling constants ( 3 JC,H) along the glycosidic linkage were calculated and used to validate the obtained structures. [35] Solid-state 13 C NMR spectroscopy could be employed to derive structural information. The studies of oligosaccharides and polysaccharides yielded 13 C chemical shifts of the glycosidic carbons, which were used to construct chemical shift surfaces (CSSs).…”