Ab Initio QM/MM molecular dynamics simulations of glycosyltransferases
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| Year of publication | 2014 |
| Type | Conference abstract |
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| Description | Force field based molecular dynamics simulations of proteins and their complex with various ligands represent a useful tool in investigation of important biological processes and can complement knowledge gained from experimental studies. However these techniques are not usable, when the process of interest involves changes in the electronic structure, as is the case in enzymatic reactions. In such cases a quantum mechanics methodology, that can describe a chemical reaction, is required. But such methods are computationally very demanding so in order to study large biologically relevant systems we need to combine the two approaches, using highly accurate quantum-mechanics for the chemically relevant region of the enzymatic reaction and highly efficient molecular mechanics for the rest of the protein and solvent. In our work we utilize density functional theory based Car–Parrinello molecular dynamics method in a hybrid QM/MM approach to study enzymatic reaction of polypeptide UDP-GalNAc transferase (ppGalNAcT2), a metal dependent retaining glycosyltransferase of GT-A fold catalyzing the first step in mucin type O-glycosylation, that is the transfer of GalNAc moiety from UDP-GalNAc to the hydroxyl group of either threonine or serine residue on the target protein. |
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