Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields

Abstract

D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via...

Chitosan Polysaccharides from a Polarizable Multiscale Approach

“…Recently the F (Θ, Ψ) maps of mannopyrannose disaccharides in aqueous phase computed from both a standard pairwise force field and a polarizable Drude oscillator-based approach have been reported . As for our polarizable force field, the map portions at the vicinity of the F (Θ, Ψ) global minima from the Drude approach are also flatter than from the pairwise force field approach.…”

“…Polarization is modeled in our all atom force field and solvent coarse-grained model from the induced dipole moment approach. Alternative theoretical approaches to handle polarization microscopic effects have been proposed, see in particular the recent all atom polarizable force field based on Drude oscillators to model the behavior of mannopyrannose disaccharides in aqueous phase …”

“…Alternative theoretical approaches to handle polarization microscopic effects have been proposed, see in particular the recent all atom polarizable force field based on Drude oscillators to model the behavior of mannopyrannose disaccharides in aqueous phase. 40 Our multiscale approach may be used to perform in depth analyses of the microscopic factors modulating the interactions among chitosan chains and between chitosan chains and their chemical partners (like the solvent, acids and counterions). However, it may also be used to provide reference data from which to assess and/or calibrate full coarse-grained approaches to efficiently model large chitosan assemblies according to bottom-up schemes.…”

Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

“…However, sampling conformational space and investigation of ring puckering for d -hexopyranoses show that the CARMM36 additive force field tends to overstabilize the 4 C 1 conformation, whereas the Drude polarizable carbohydrate force field results in flexible ring systems, more readily accessible skew and boat conformations, lower free energy barriers, and oversampling of the 1 C 4 conformation for some of the monosaccharides . The inverted 1 C 4 conformation for α- d -mannopyranose was in these MD simulations present to an extent of ∼80%, whereas in a study of α-linked d -mannopyranose disaccharides using the Drude polarizable force field a wider conformational sampling at glycosidic linkages was evident, without any oversampling of inverted chairs . Even though sampling of conformational space by MD simulations using the Drude model is ∼4-fold slower than the additive CHARMM force field, and ∼8-fold slower than using a hydrogen mass repartitioning (HMR) approach by increasing the mass of hydrogen by distributing a heavy atom mass to hydrogen atom(s) attached to the heavy atom, the modeling is performed in a more realistic way, for glycans per se but in particular for understanding and unveiling the structural basis of ligand recognition and specificity in carbohydrate–protein interactions, which calls for further developments of the Drude polarizable force fields.…”

Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

“…These investigations of sugars having the pyranoid ring form have included, inter alia, a series of α-linked mannobioses substituted at position 2-, 3-, 4-, or 6. [15] Furthermore, studies of a 2-linked sugar residue [16,17] where the substitution takes place at a secondary alcohol and those of 6linked sugar residues [18,19] where the substitution takes place at a primary alcohol have also been performed. To complete the investigations of substitutions at different positions we herein focus on 3-as well as 4-linked residues where the substitution takes place at a secondary alcohol.…”