Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the ϕ, ψ-conformational space of the α-(1→2)-linked mannose disaccharide present in N- and O-linked glycoproteins

Abstract

The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.

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

“…Scalar coupling constants were calculated using the pertinent Karplus equations for 3 J H5g,H6gR/S , 2 J H6gR,H6gS , and 3 J C4g,H6gR/S published by Thibaudeau et al 55 and for 3 J C1f,H6gR/S and 3 J C6g,H1f published by Säwén et al 56 Effective distances were calculated from the MD simulation using . In order to include in equation 10 areas of the conformational space not sampled by the MD simulation, r -6 was determined from a potential-energy relaxed threedimensional map calculated at 10° intervals with a dielectric constant of 3 and subsequently interpolated to a resolution of 5°.…”

Structure assignment and H/D-exchange behavior of several glycosylated polyphenols

“…In those cases, Karplus-relations for the two different diastereotopic protons H6 pro-R and H6 pro-S and their coupling to C4 and H5 have been developed. [25][26][27][28][29][30] However, to the best of our knowledge, there do not seem to be any publications that propose a quantitative description of dihedral angles  and  (i.e. ') for 6-O-substituted sugars based on a Karplus-relation for coupling of H6-C4.…”

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

“…[35] Recently, Serianni and co-workers proposed a 2 J C2,H1 relation for the φ torsion angle. [36] Since the trisaccharide was 13 C-labeled at C2 and C2 the magnitude of the heteronuclear two-bond coupling constants to the anomeric protons could be determined from the J-HMBC experiments with high precision, i.e.…”

“…In the present study, eight conformationally dependent coupling constants were determined for the trisaccharide; these coupling constants may be used together with previously determined trans-glycosidic 3 J C,H , and seven interresidue 1 H, 1 H-T-ROEs, one of which was directly determined herein confirming the previously estimated one, in further conformational analysis of the trisaccharide. In particular, it is anticipated that the utilization of the recently developed Karplus-type relationships [35] for 3 J C,H and 3 J C,C together with new force field parameterizations [42] for MD simulations and their validation [43] will facilitate a detailed description of the conformational dynamics of the trisaccharide. This study highlights that different approaches are available in order to obtain in particular 3 J C,H coupling constants and that the choice of magnetic field strength is an additional variable parameter available to resolve spectral overlap (Fig.…”