New zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases

Tomić, Antonija; Horvat, Gordan; Ramek, Michael; Agić, Dejan; Brkić, Hrvoje; Tomić, Sanja (2019) New zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases. Journal of Chemical Information and Modeling, 59 (8). pp. 3437-3453. ISSN 1549-9596

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Abstract

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.

Item Type:	Article
Additional Information:	Authors A.T., D.A., H.B., and S.T. received funding from Croatian Science Foundation under the project IP-2018-01-2936.
Uncontrolled Keywords:	metallo-peptidase ; human dipeptidyl peptidase III ; thermolysin ; neprilysin ; aminopeptidase N ; molecular dynamic simulations ; quantum mechanics – molecular mechanics ; nonbonded model ; hybrid bonded/nonbonded model ; cationic dummy atom model ; polarizable potential ; zinc ion parameters ; zinc ion coordination ; second metal ion coordination sphere
Subjects:	NATURAL SCIENCES > Chemistry > Physical Chemistry
Divisions:	Division of Organic Chemistry and Biochemistry
Projects:	Project title Project leader Project code Project type Biološka važnost dipeptidil peptidaze III i njezin utjecaj na zdravlje čovjeka-DPP3BioRe Sanja Tomić IP-2018-01-2936 HRZZ
Depositing User:	Antonija Tomić
Date Deposited:	07 May 2020 09:05
URI:	http://fulir.irb.hr/id/eprint/5730
DOI:	10.1021/acs.jcim.9b00235

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