Free Energy Landscapes of Iduronic Acid and Related Monosaccharides

Abstract

The pyranose ring of l-iduronic acid (IdoA), a major constituent of the anticoagulant heparin, is an equilibrium of multiple ring puckers that have evaded quantification by experiment or computation. In order to resolve this enigma, we have calculated the free energy landscape of IdoA and two related monosaccharides from extensive microsecond simulations. After establishing that the simulated puckers had reached equilibrium, hypotheses were confirmed that (a) IdoA 1 C 4- and 4 C 1-chair conformations exchange on the microsecond time scale, (b) C5 epimerization leads to a 4 C 1-chair, and (c) IdoA 2-O-sulfation (IdoA2S) stabilizes the 1 C 4 conformer. The IdoA and IdoA2S 1 C 4 conformers were isoenergetic and computed to be 0.9 and 2.6 kcal mol−1 lower in free energy than their respective 4 C 1-chair conformations. The simulations also predicted that the IdoA 2 S O-skew-boat was less populated than previously thought. Novel chemical synthesis and ultra-high-field NMR supported these observations, but slight discrepancies in observed and predicted NMR vicinal couplings implied that the simulation overestimated the population of the IdoA 4 C 1-chair with respect to 1 C 4-chair due to small force field inaccuracies that only manifest in long simulations. These free-energy calculations drive improvements in computational methods and provide a novel route to carbohydrate mimetic biomaterials and pharmaceuticals.

Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers

“…37–39 The IdoA 1 C 4 conformer was previously calculated to be 0.9 kcal mol −1 more stable than the 4 C 1 chair, comparable to the 1.38 kcal mol −1 difference found within this study. 40 Neither guluronic nor alluronic acid had been modeled prior to this work and here the 1 C 4 conformers have been found to be 0.65 kcal mol −1 and 0.04 kcal mol −1 lower in energy than their 4 C 1 conformations, respectively.…”

Computational drill down on FGF1-heparin interactions through methodological evaluation

“…GAGs pyranose rings were harmonically restrained for consistency with the experimental data from the analyzed crystal structures. Moreover, although it is known that the used charges [57] can induce instabilities in the equilibrium of IdoA2S ring conformation [60], the time scales of the MD simulations used for post-processing of the docking poses are for practical reasons significantly shorter than the μs time scales required for the establishment of the equilibrium for the pyranose ring interconversion [18]. For the simulation of HE dp6 and its derivatives, we used IdoA2S with no substitution ( e.g.…”

“…Besides, information about GAG puckering conformations, which is a crucial aspect for their binding specificity [15] and bioactivity [16], and therefore key for modeling GAG-protein interactions [17], is rarely experimentally available a priori . Unfortunately, conventional molecular dynamics (MD) approaches cannot easily deal with this due to the μs time scales needed to be able to observe equilibrium between different ring puckering [18, 19]. By virtue of all these challenges, and opposite to other biomacromolecular systems, standard computational pipelines for treatment of protein-GAG interactions are not yet fully established but rather currently intensively pursued.…”

Synthesis of 3-O-Sulfated Oligosaccharides to Understand the Relationship between Structures and Functions of Heparan Sulfate

“…Moreover, the conformation of the IdoA and IdoA2S residues adopt both chair ( 1 C 4 ) and skew boat ( 2 S O ) conformations 6 . The conformations of GlcA, GlcA2S and GlcN residues exist in the chair ( 4 C 1 ) conformation 7–8 .…”