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Further study of the zinc coordination in the active site of the human DPP III ­- ONIOM calculations

The first step in understanding the chemical reactions in the DPP III active site is to determine the coordination of the central zinc ion. Discrepancy between the experimental data (PDB ID: 3FVY) and the results of MD simulations [1, 2] indicate that this question is still to be answered. The main issues are: a)does the Glu451 participates in Zn2+ coordination (MD simulations indicate that it does), and b)how many water molecules coordinate the metal ion (one or two, according to the crystal structure or the structures obtained from MD simulations, respectively). To address this problem we performed series of ONIOM (Our own N­-layered Integrated molecular Orbital and molecular Mechanics) QM/MM calculations. The initial structures were either taken from the MD simulations or from the experimental data. For this purpose the protein was divided into two layers which were handled at different levels of theory. The quantum mechanical (QM) layer (consisting of His450, Glu451, His455 and Glu508 side chains, the zinc ion and two water molecules) was treated by the DFT method using B3LYP functional and different basis sets (from 3­21g to 6­311++g(d, p)). The molecular mechanic (MM) part (the rest of the protein) was treated by the AMBER force field (param96). To take into account solvation, additional 50 water molecules, close to the central zinc ion, were considered as a part of the MM layer as well. Some of these water molecules were fixed during the minimization. [1] Tomić A, Abramić M, Špoljarić J, Agić D, Smith MD, Tomić S (2011) Human dipeptidyl peptidase III: insight into ligand binding from a combined experimental and computational approach. J Mol Recogn 24:804­-814. [2] Tomić A, Gonzalez M, Tomić S The large scale conformational change of the human DPP III ­ substrate prefers the "closed" form, J Chem Inf Model 52 (2012)1583-1594

QM/MM ONIOM calculations; human dipeptidyle peptidase

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