Molecular Conformations of Di-, Tri-, and Tetra-α-(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations.

Aysegül Turupcu,Markus Blaukopf,Chris Oostenbrink,Paul Kosma

doi:10.3390/ijms21010030

Abstract

By using molecular dynamics simulations with an efficient enhanced sampling technique and in combination with nuclear magnetic resonance (NMR) spectroscopy quantitative structural information on -2,8-linked sialic acids is presented. We used a bottom-up approach to obtain a set of larger ensembles for tetra- and deca-sialic acid from model dimer and trimer systems that are in agreement with the available J-coupling constants and nuclear Overhauser effects. The molecular dynamic (MD) simulations with enhanced sampling are used to validate the force field used in this study for its further use. This empowered us to couple NMR observables in the MD framework via J-coupling and distance restraining simulations to obtain conformations that are supported by experimental data. We used these conformations in thermodynamic integration and one-step perturbation simulations to calculate the free-energy of suggested helical conformations. This study brings most of the available NMR experiments together and supplies information to resolve the conflict on the structures of poly--2,8-linked sialic acid.

Highlights

Neuraminic acids are commonly found in the carbohydrate moiety of glycoproteins and glycolipids, typically at the outermost non-reducing ends
We have studied the conformational freedom of the α-2,8-linkage between two subsequent sialic acid monomers with an enhanced conformational searching and sampling method, local elevation with umbrella sampling (LEUS)
Our simulations showed that the nuclear magnetic resonance (NMR) observations can be satisfied with a set of conformations that are very similar to the ones observed in our LEUS simulations

Summary

Introduction

Neuraminic (sialic) acids are commonly found in the carbohydrate moiety of glycoproteins and glycolipids, typically at the outermost non-reducing ends. Sialic acids can form polymers with degrees of polymerization varying from 8 to 200, called polysialic acids (polySia) [1]. Structural studies on the conformation of oligomers of different degrees of polymerization suggested a flexible helical structure by early NMR [6,7]. One model was built from 3JHH coupling constants by setting the appropriate torsional angles and using the antibody binding site as a target This resulted in a helical model with 6 residues per turn [8], contradicting another helical polymer model, which was built by setting torsional angles satisfying coupling constants and suggests 3–4 residues per turn [9]. Yongye et al [10] suggested another helical type by taking trisialic acid as a model through a combination of NMR and MD studies. The actual conformation(s) are still unclear since there is no consensus on either the type of the helical conformation or on the random coil

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