Ganesh Kamath1, Olgun Guvench1, Shannon Greene1, and Alexander D. MacKerell2. (1) Pharmaceutical Sciences, University of Maryland, University of Maryland at Baltimore, 20 Penn Street, Baltimore, MD 21201, (2) University of Maryland, Department of Pharmaceutical Sciences, 20 Penn Street, Baltimore, MD 21201
Carbohydrates play a central role in molecular biology where they serve as a storehouse for energy, as structural elements, and as components of molecular-recognition networks. Molecular mechanics simulations provide a means to investigate the biological functions of carbohydrates at an atomic level of detail. Toward this end, the present work details recent efforts at developing an all-atom additive CHARMM molecular mechanics carbohydrate force field. The results include parametrization via the reproduction of conformational, spectroscopic, and thermodynamic aspects of small-molecule compounds that correspond to fragments of pyranose monosaccharides. Additionally, over 1600 pyranose monosaccharide conformational energies at the quantum mechanical MP2/cc-pVTZ//MP2/6-31G(d) level are used as target data for the parametrization of intramolecular conformational energetics. The resultant parameters are tested in crystalline and solvated monosaccharide condensed phase simulations. The force field is also extended to enable modeling of di- and polysaccharides. The nonbonded parameters of the glycosidic oxygen are empirically fitted to reproduce water dimer interactions of polysaccharides with varying conformers and glycosidic linkages. Dihedral parameters are fitted to reproduce MP2/cc-pVTZ//MP2/6-31g(d) adiabatic potential phi/psi energy scans for different glycosidic linkages, and the resultant force field parameters are applied to investigate the condensed phase properties of polysaccharides. The parametrization protocol is consistent with that employed for the existing CHARMM protein, nucleic acid, and lipid force fields. Thus, the present force field can be applied to investigate not only carbohydrates alone but also in interaction with these other important biomolecules.