On the Use of PDB X-Ray Crystal Structures as Force Field Target and Validation Data for Pyranose Ring Puckering

Abstract

The carbon and oxygen atoms of tetrahydropyran form the common substructure of pyranose monosaccharides in vertebrate glycans. This substructure can assume various ring puckering chair and skew-boat conformations, and can thereby impact glycan conformations relevant for biomolecular structure and signaling. The Protein Data Bank (PDB) provides a wealth of experimental glycan structural biology data that can be useful in the development and validation of molecular mechanics force fields for these molecules. However, these experimental data are typically from solvent-depleted crystalline environments at very low temperatures, in contrast to biological conditions that are aqueous and near ambient temperature, which is the regime targeted by biomolecular force fields. To determine if these PDB X-ray crystal data can be of utility as references for carbohydrate force fields, we compared ring puckering conformations from these experimental data to both vacuum and explicit aqueous solvent puckering free energy data from extended-system adaptive biasing force (eABF) molecular dynamics simulations using the previously validated CHARMM36 force field. We found that, for monosaccharides that are not charged (glucose, N-acetylglucosamine, galactose, N-acetylgalactosamine, mannose, xylose, and fucose), both the vacuum and aqueous simulation puckering preferences strongly correlate with PDB data, and therefore with each other. In contrast, all charged monosaccharides that were considered (the conjugate bases of N-acetylneuraminic acid, glucuronic acid, and iduronic acid) had puckering preferences correlating with PDB data only in aqueous simulations and not in vacuum simulations. These results suggest that comparing puckering preferences from aqueous simulations to PDB X-ray crystal puckering conformation data can be a valid and useful component of carbohydrate force field development and validation.