Conformations of the iduronate ring in short heparin fragments described by time-averaged distance restrained molecular dynamics

Abstract

The polyconformational behavior of L-iduronic acid (L-IdoA2S) in heparin derivatives has been previously analyzed in terms of intra-ring proton-proton vicinal coupling constants ((3)JHH) through mathematical fit of experimental and theoretical values (Ferro DR, Provasoli A, Ragazzi M, Casu B, Torri G, Bossennec V, Perly B, Sinay P, Petitou M, Choay J. 1990. Conformer Populations of L-Iduronic Acid Residues in Glycosaminoglycan Sequences. Carbohydr Res. 195:157-167; Muñoz-García JC, López-Prados J, Angulo J, Díaz-Contreras I, Reichardt N, de Paz JL, Martín-Lomas M, Nieto PM. 2012. Effect of the substituents of the neighboring ring in the conformational equilibrium of iduronate in heparin-like trisaccharides. Chemistry. 18:16319-16331.). However, this methodology is subjected to the experimental uncertainties of the J-coupling measurements, the force field deviations and the goodness of the least-squares fit. In the present work, we have used time-averaged distance restrained molecular dynamics (tar-MD) to largely reduce these errors, which enables accurate quantification of the population of conformers, or puckers, of the L-IdoA2S residue, in a set of eight heparin-like trisaccharides following the general sequence d-glucosamine (GlcN)-IdoA-GlcN, directly from the time evolution of the puckering coordinates θ and . Thus, by carrying out tar-MD simulations in explicit water, with the exclusive nuclear overhauser enhancement (NOE)-derived distance H2-H5 of the L-IdoA2S (2)SO conformer as the unique imposed constraint, we have been able to accurately and easily determine the different extents to which the iduronate ring populates the polar ((1)C4 chair) and equatorial ((2)SO skew-boat) areas of the puckering sphere depending on the sulfation pattern of the flanking GlcN residues, under low temperature conditions (278 K). The results indicate that 6-O-sulfation at the reducing-end GlcN residue facilitates the (1)C4 to (2)SO transitions of the iduronate ring by augmenting the flexibility of the C2-C3 torsion, driving the conformational equilibrium toward a majority of equatorial conformers.

Chondroitin Sulfate Tetrasaccharides: Synthesis, Three‐Dimensional Structure and Interaction with Midkine

“…We processed the structures to extract geometrical values for comparison with experimental data from NMR spectroscopy results and we found that they agreed consistently. The coupling constants were calculated as the weighted average over the length of the whole simulation for each frame, by considering the modified Altona equation for the calculated instant values . Only residue D, and to a lesser extent B, presented some conformational flexibility that was reflected in the calculated coupling constant values, which deviated from those obtained experimentally (see Table S2 in the Supporting Information).…”

“…Interprotonic inter‐residue distances, however, were consistent with the NOE‐based experimentally obtained results (Table ). We then decided to use time‐averaged distance‐restrained MD (tar‐MD) with the distances between the protons H1 to H3 and H1 to H5 of the rings B and D as experimental restraints . In this case, we obtained monoconformational behaviour for all rings, including D (Figures and ).…”

“…Analysis of the tar‐MD trajectories was carried out with the ptraj module of Amber 11 . This protocol was previously discussed in detail by us …”

Perspective on computational simulations of glycosaminoglycans

“…Representation of glycosidic torsion angles Φ,Ψ. (a) and (b) Glycosidic torsional angle Φ, Ψ distribution with respect to GlcN‐IdoA2S and Ido2A‐GlcN linkages for a library of eight sequences . (c) Schematic structure of GAG disaccharide with Δ‐uronic acid and GlcNAc with varying sulfation of total three sequences (1: ΔUA2S‐GlcNAc6S, 2: ΔUA2S‐GlcNS, 3: ΔUA2S‐GlcNS6S).…”

“…The topology and coordinates files were built with LEaP module of AMBER11, while GLYCAM_06h parameters were used to model the heparin molecule including O ‐sulfonate and N ‐sulfamate groups. Here, the partial charge remodification of O ‐ and N ‐atoms bound to the SO 3 − group was performed using the GLYCAM procedure so as to ensure an appropriate integral charge for the oligosaccharide, while parameters for TIP3P water and counter ions were used from AMBERff 12SB parameters …”