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Tomić A, Tomić S. Demystifying DPP III Catalyzed Peptide Hydrolysis-Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis. Int J Mol Sci 2022; 23:1858. [PMID: 35163780 PMCID: PMC8836397 DOI: 10.3390/ijms23031858] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Dipeptidyl peptides III (DPP III) is a dual-domain zinc exopeptidase that hydrolyzes peptides of varying sequence and size. Despite attempts to elucidate and narrow down the broad substrate-specificity of DPP III, there is no explanation as to why some of them, such as tynorphin (VVYPW), the truncated form of the endogenous heptapeptide spinorphin, are the slow-reacting substrates of DPP III compared to others, such as Leu-enkephalin. Using quantum molecular mechanics calculations followed by various molecular dynamics techniques, we describe for the first time the entire catalytic cycle of human DPP III, providing theoretical insight into the inhibitory mechanism of tynorphin. The chemical step of peptide bond hydrolysis and the substrate binding to the active site of the enzyme and release of the product were described for DPP III in complex with tynorphin and Leu-enkephalin and their products. We found that tynorphin is cleaved by the same reaction mechanism determined for Leu-enkephalin. More importantly, we showed that the product stabilization and regeneration of the enzyme, but not the nucleophilic attack of the catalytic water molecule and inversion at the nitrogen atom of the cleavable peptide bond, correspond to the rate-determining steps of the overall catalytic cycle of the enzyme.
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Affiliation(s)
- Antonija Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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Matić S, Kekez I, Tomin M, Bogár F, Šupljika F, Kazazić S, Hanić M, Jha S, Brkić H, Bourgeois B, Madl T, Gruber K, Macheroux P, Matković-Čalogović D, Matovina M, Tomić S. Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process. J Biomol Struct Dyn 2020; 39:6870-6881. [PMID: 32811353 DOI: 10.1080/07391102.2020.1804455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This work is about synergy of theory and experiment in revealing mechanism of binding of dipeptidyl peptidase III (DPP III) and Kelch-like ECH-associated protein 1 (KEAP1), the main cellular sensor of oxidative stress. The NRF2 ̶ KEAP1 signaling pathway is important for cell protection, but it is also impaired in many cancer cells where NRF2 target gene expression leads to resistance to chemotherapeutic drugs. DPP III competitively binds to KEAP1 in the conditions of oxidative stress and induces release of NRF2 and its translocation into nucleus. The binding is established mainly through the ETGE motif of DPP III and the Kelch domain of KEAP1. However, although part of a flexible loop, ETGE itself is firmly attached to the DPP III surface by strong hydrogen bonds. Using combined computational and experimental study, we found that DPP III ̶ Kelch binding is a two-step process comprising the endergonic loop detachment and exergonic DPP III ̶ Kelch interaction. Substitution of arginines, which keep the ETGE motif attached, decreases the work needed for its release and increases DPP III ̶ Kelch binding affinity. Interestingly, mutations of one of these arginine residues have been reported in cBioPortal for cancer genomics, implicating its possible involvement in cancer development. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sara Matić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Tomin
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ferenc Bogár
- Department of Medical Chemistry, MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Szeged, Hungary
| | - Filip Šupljika
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Saša Kazazić
- Divison of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Hanić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Hrvoje Brkić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & BiocBioTechMed-Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & BiocBioTechMed-Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | | | - Mihaela Matovina
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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Tomić A, Horvat G, Ramek M, Agić D, Brkić H, Tomić S. New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. J Chem Inf Model 2019; 59:3437-3453. [PMID: 31274304 DOI: 10.1021/acs.jcim.9b00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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 proved to be robust enough to enable reliable modeling not only of 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 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.
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Affiliation(s)
- Antonija Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia.,Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102A , 10 000 Zagreb , Croatia
| | - Michael Ramek
- Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek , Josip Juraj Strossmayer University of Osijek , Petra Svačića 1d , 31 000 Osijek , Croatia
| | - Hrvoje Brkić
- Faculty of Medicine , Josip Juraj Strossmayer University of Osijek , J. Huttlera 4 , 31 000 Osijek , Croatia.,Faculty of Dental Medicine and Health , Josip Juraj Strossmayer University of Osijek , Crkvena 21 , 31 000 Osijek , Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia
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