Investigation of the three-dimensional structure and interaction mechanism of poly (ADP-ribose) polymerase 4

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dc.authoridDinc, Bircan/0000-0002-9717-6410
dc.authoridunlu, ayhan/0000-0001-6033-7148
dc.authorwosidDinc, Bircan/ADG-4955-2022
dc.authorwosidunlu, ayhan/Q-1843-2016
dc.contributor.authorUnlu, Ayhan
dc.contributor.authorDinc, Bircan
dc.date.accessioned2024-06-12T10:50:47Z
dc.date.available2024-06-12T10:50:47Z
dc.date.issued2020
dc.departmentTrakya Üniversitesien_US
dc.description.abstractPoly ADP-ribose polymerases (PARPs) are family of proteins that use nicotinamide adenine dinucleotide (NAD) as substrate. Seventeen putative PARP sequences were determined in the human genome. Although PARPs show a variety of functions and low sequence identities, they share common structural and functional properties. In our study, PARP1 and PARP2 and PARP4 sequences in different species were compared; it was found that active sites of PARP1 for human, rat and mouse have highly conserved sequence. Overall folding of PARP1, PARP2 and PARP4 confirms similarity in catalytic domains but can differ in substrate proteins. The three-dimensional structure of PARP4 was interacted with NAD using the molecular docking method and the interaction sites were determined. When we modeled the three-dimensional structure of PARP4 using MODELLER v9.22 algorithm and examined the interaction with Autodock v4.2 in computer environment, we observed that the enzyme is connected with a common motif similar to PARP1 and PARP2. When PARP1 and PARP2 interact with this common motif with NAD, we experimentally observed that these structures interact directly with NAD in order to undergo catalytic reactions by Thermal-Shift assay. The PARP4-NAD complex with the binding energy -26.73 kJ/mol was further used for molecular dynamics analysis. Root mean square deviation (RMSD) for all backbone atoms, electrostatic energy, van der Waals energy of PARP4-NAD complex were studied in the form of molecular dynamics trajectories to throw light on the medically important PARP family of enzymes.en_US
dc.identifier.doi10.1080/13102818.2020.1726208
dc.identifier.endpage202en_US
dc.identifier.issn1310-2818
dc.identifier.issn1314-3530
dc.identifier.issue1en_US
dc.identifier.scopus2-s2.0-85082530344en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.startpage191en_US
dc.identifier.urihttps://doi.org/10.1080/13102818.2020.1726208
dc.identifier.urihttps://hdl.handle.net/20.500.14551/18126
dc.identifier.volume34en_US
dc.identifier.wosWOS:000521043400001en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherTaylor & Francis Ltden_US
dc.relation.ispartofBiotechnology & Biotechnological Equipmenten_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectADP-Ribosylating Toxinsen_US
dc.subjectPoly ADP-Ribose Polymerasesen_US
dc.subjectNicotinamide Adenine Dinucleotide (NAD)en_US
dc.subjectProtein-Ligand Interactionen_US
dc.subjectPoly(Adp-Ribose) Polymeraseen_US
dc.subjectParpen_US
dc.subjectCanceren_US
dc.subjectActivationen_US
dc.subjectTargetsen_US
dc.titleInvestigation of the three-dimensional structure and interaction mechanism of poly (ADP-ribose) polymerase 4en_US
dc.typeArticleen_US

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