Molecular dynamics (MD) simulations will be performed on carbohydrates and related systems. Simulations will address the flexibility and the dynamics between different residues in oligosaccharides and short chain models of polysaccharides. Larger and more complex oligosaccharide structures are to be simulated. These partial structures are constituents of biomembrane glycoconjugates. Subsequent MD simulations on the formation of complexes between carbohydrates as ligands to proteins will be initiated. We will employ both the NAMD and CHARMM programs with improved force fields, of an all-atom CHARMM-type, for simulations in the microsecond time window that now is possible to carry out. Testing of a related novel force field as part of the development is also underway.
We have been running CHARMM version 36 from Harvard University at NSC:s Triolith as an essential part of our approach to investigate carbohydrate dynamics by a combination of molecular simulations and in particular NMR experiments. NAMD is also used in our studies due to its higher speed compared to CHARMM.
We also continuously perform quantum mechanical (QM) calculations using the Gaussian09 program suite for various systems related to carbohydrates.
Some examples include calculating the energy barrier and NMR parameters for the rotation of N-acetyl and N-formyl groups, and building a library of ligands to perform docking simulations with glycosyl transferases.