Can current force fields reproduce ring puckering in 2-O-sulfo-alpha-L-iduronic acid? A molecular dynamics simulation study.
The monosaccharide 2-O-sulfo-alpha-L-iduronic acid (IdoA2S) is one of the major components of glycosaminoglycans. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium is important for the successful prediction of the free energies of interaction of these carbohydrates with proteins. Here we report unconstrained molecular dynamics simulations of IdoA2S monosaccharide that were carried out to investigate the ability of commonly used force fields to reproduce its ring conformational flexibility in aqueous solution. In particular, the distribution of ring conformer populations of IdoA2S was determined. The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. On the other hand, the GLYCAM06 force field with the TIP3P water potential sampled transitional conformations between the boat and chair forms. Simulations using the GROMOS96 force field showed no pseudorotational equilibrium fluctuations and hence no inter-conversion between the boat and twist boat ring conformers. Calculations of theoretical proton NMR coupling constants showed that the GROMOS96 force field can predict the skew-boat to chair conformational ratio in good agreement with the experiment, whereas GLYCAM06 shows worse agreement. The omega rotamer distribution about the C5-C6 bond was predicted by both force fields to have torsions around 10 degrees , 190 degrees , and 360 degrees .
Gandhi
Neha S
NS
Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845, Australia.
Mancera
Ricardo L
RL
D004574:Electromagnetic Fields; D007067:Iduronic Acid / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
D007067:Iduronic Acid