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The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and showed to be robust enough to enable reliable modeling not only human DPP III and its orthologues but also of the other zinc dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i. e peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising eight different peptidases, five DPP III orthologues, thermolysin, neprilysin and aminopeptidase N, and the results are summarized in the second part of the publication.

Reliable representation of the systems with transition metals is still a weak point of the force field based molecular modeling methods. We tested different strategies for modeling the zinc ion in classical molecular dynamics simulations based on nonpolarizable (nonbonded, hybrid bonded/nonbonded and cationic dummy atom models) as well as on polarizable (Drude-2013) potentials using human dipeptidyl peptidase III (DPP III) as a template. In the experimentally determined human DPP III structure the zinc ion is mostly tetrahedrally coordinated by two histidines, glutamate and one water or the substrate/inhibitor molecule. The quantum mechanics - molecular mechanics (QMMM) calculations showed an exchange of the four- and five-coordinated zinc ion during the reaction. Since neither of the strategies based on the nonpolarizable potential showed good agreement with experimental findings and the results of QMMM calculations, and the simulations utilizing the polarizable potential turned out to be extremely expensive, we modified the approach of Yang et al. [1] by extending the region used in quantum mechanical (QM) calculations based parametrization procedure. Namely, the zinc coordinated water molecule and the residues constituting the second metal ion coordination sphere were included in QM calculations resulting with a new set of the zinc ion parameters, so called 4-ligand-extended parameters, to be used within the AMBER force fields ff12SB and ff14SB. These parameters enabled realistic modeling of the active site configuration in different DPP III orthologues as well as in distant peptidases like thermolysin, neprilysin and aminopeptidase N.