Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by ¹³C NMR Spin Relaxation and Stochastic Modeling

Abstract

Among biomolecules, carbohydrates are unique in that not only can linkages be formed through different positions, but the structures may also be branched. The trisaccharide β-d-Glcp-(1→3)[β-d-Glcp-(1→2)]-α-d-Manp-OMe represents a model of a branched vicinally disubstituted structure. A C site-specific isotopologue, with labeling in each of the two terminal glucosyl residues, enabled the acquisition of high-qualityC NMR relaxation parameters, T and T, and heteronuclear NOE, with standard deviations of ≤0.5%. For interpretation of the experimental NMR data, a diffusive chain model was used, in which the dynamics of the glycosidic linkages is coupled to the global reorientation motion of the trisaccharide. Brownian dynamics simulations relying on the potential of mean force at the glycosidic linkages were employed to evaluate spectral densities of the spin probes. Calculated NMR relaxation parameters showed a very good agreement with experimental data, deviating <3%. The resulting dynamics are described by correlation times of 196 and 174 ps for the β-(1→2)- and β-(1→3)-linked glucosyl residues, respectively, i.e., different and linkage dependent. Notably, the devised computational protocol was performed without any fitting of parameters.

Stochastic Modelling of 13C NMR Spin Relaxation Experiments in Oligosaccharides

“…We tested our method on a collection of oligosaccharides, for which previous analyses based on specific stochastic models were presented. The following systems are considered: -L-Rha p - -(1→2)- -L-Rha p -OMe (two residues, R2R ); experimental data: Reference [ 28 ] -D-Glc p -(1→6)- -D-[6- C]-Man p -OMe (two residues, BGL ); experimental data: Reference [ 29 ] -D-Glc p -(1→3)[ -D-Glc p -(1→2)]- -D-Man p -OMe (three residues, GGM ); experimental data: Reference [ 30 ] -D-Man p -(1→2)- -D-Man p -(1→6)- -D-[6- C]-Man p -OMe (three residues, TRI ); experimental data: Reference [ 31 ] -L-Fuc p -(1→2)- -D-Gal p -(1→3)- -D-Glc p NAc-(1→3)- -D-Gal p -(1→4)-D-Glc p - (five residues, LNF ); experimental data: Reference [ 31 ] …”

“… -D-Glc p -(1→3)[ -D-Glc p -(1→2)]- -D-Man p -OMe (three residues, GGM ); experimental data: Reference [ 30 ]…”

Conformational Studies of Oligosaccharides

“…For example, l ‐rhamnose is absent in most mammals, but widely distributes in lipopolysaccharides (LPS) of Gram‐negative bacteria and in capsular polysaccharides of Gram‐positive bacteria. The conformational preference of rhamnose‐containing glycans was studied with a disaccharide model (α‐ l ‐Rhap‐(1–2)‐α‐ l ‐Rhap‐OMe, Figure , top) . NMR and computational analysis permitted the identification of two preferred conformations in water, existing in a 3:2 ratio.…”

Stochastic modeling of macromolecules in solution. I. Relaxation processes

“…The constant friction approximation is usually acceptable for small molecules and for molecules not showing large amplitude motions. [83][84][85] Examples of trajectories for 2-alanine, 4-alanine, 6-alanine and 10-alanine of diagonal friction matrix elements log |(ω ξ ) ii | in time are shown in Figure 14. Fluctuations are observed which can be significant; however their overall effect is damped if one considers the average eigenvalues of ω ξ and their standard deviation, Figure 15.…”

“…This is, however, not always necessary as the friction tensor calculated in the absolute energy minimum can be sufficient to describe the most important features of the long-time dynamics of the system. 85 Since including the dependence on the configuration requires a larger computational effort, one should decide whether the constant-friction approximation is inappropriate based on the quality of the agreement with experimental data. For the goal of this and of the following paper, 56 which is to show how to build a stochastic model of a system from its all-atom description without resorting to phenomenological parameters, we have purposely chosen the simplest implementation.…”