Conformational Analysis of a High‐Mannose‐Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR‐Validated Molecular Dynamics Simulation

Abstract

Exploration of the conformational spaces of flexible oligosaccharides is essential to gain deeper insights into their functional mechanisms. Here we characterised dynamic conformation of a high-mannose-type dodecasaccharide with a terminal glucose residue, a critical determinant recognised by molecular chaperones. The dodecasaccharide was prepared by our developed chemoenzymatic technique, which uses C labelling and lanthanide tagging to detect conformation-dependent paramagnetic effects by NMR spectroscopy. The NMR-validated molecular dynamics simulation produced the dynamic conformational ensemble of the dodecasaccharide. This determined its spatial distribution as well as the glycosidic linkage conformation of the terminal glucose determinant. Moreover, comparison of our results with previously reported crystallographic data indicates that the chaperone binding to its target oligosaccharides involves an induced-fit mechanism.

Novel NMR Avenues to Explore the Conformation and Interactions of Glycans

“…Using this methodology, insights into the conformational details of simple oligosaccharides 46 and, in particular, bi-antennary 47 and tetra-antennary complex type 48 and high mannose N-glycans have been deduced. 49 The different NMR-active nuclei in these molecules show isochronous chemical shifts for the units located at the end of the arms, and therefore, their complete NMR analysis is highly difficult or almost impossible. 50 Nevertheless, the initial employment of this approach has also allowed the direct evaluation of the interaction of saccharides (lactose-type), decorated with the lanthanide-binding tag, with a lectin (human galectin-3).…”

The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis

“…NMR has been extensively employed to assess the conformational, dynamic and recognition features of these flexible molecules. Recent developments using paramagnetic NMR approaches ( Suzuki et al, 2017 ; Fernández de Toro et al, 2018 ) or NMR-active nuclei ( 13 C, 19 F) as labels permitted to circumvent the tremendous overlapping problem inherent to glycans ( Fittolani et al, 2021 ; Moure et al, 2021 ), especially in the case of homo-oligosaccharides.…”

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…Density maps or energy maps built for a set of the glycosidic torsion angles (φ, ψ, ω) are a typical way to report conformational preferences of a glycan provided by population analysis of its MD trajectory. As a representative example, conformational characteristics of highly flexible branched oligosaccharide Glc 1 Man 9 GlcNAc 2 (GM9) were investigated by explicit-water REMD study and validated using paramagnetism-assisted NMR spectroscopy [ 149 ] ( Figure 3 a,b). Due to the structural complexity of GM9, adequate exploration of conformational space requires long-timescale simulations.…”

“…Red dots locate glycosidic torsion angles derived from crystallographic data of Glc 1 Man 3 tetrasaccharide ligand complexed with the lectin domain of calreticulin (PDB ID: 3O0W). Panels ( a ) and ( c ) were reproduced with permission from [ 149 ], © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.…”