Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Multiple Sequence Alignment of PARPs 1–16
2.2. Modeling of PARPs with Known Structures
2.3. Modeling of PARPs with Unknown Structures
3. Discussion
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
7-MG | 7-methylguanine |
MD | molecular dynamics |
NA | nicotinamide |
NAD+ | nicotinamide adenine dinucleotide |
PARP | poly(ADP-ribose)polymerase |
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PARP | Activity | Function |
---|---|---|
1 | poly 1 | DNA repair enzymes regulating transcription and eliminating single- and double-strand breaks of DNA [13,14,15,16,17] |
2 | poly | |
3 | mono 2 | DNA repair [18,19] |
4 | mono | poorly studied |
5a | poly | tankyrase enzymes regulating the Wnt signaling pathway and controlling cellular proliferation and differentiation [20,21,22,23] |
5b | poly | |
6 | mono | tumor suppressor regulating Survivin expression [24] |
7 | mono | poorly studied |
8 | mono | poorly studied |
9 | inactive | poorly studied |
10 | mono | regulates Aurora A and suppresses tumor metastasis [25] |
11 | mono | poorly studied |
12 | mono | suppresses Zika virus infection [26] |
13 | inactive | regulates the cellular response to stress [27] |
14 | mono | suppresses kinase-mediated apoptosis [28] |
15 | mono | poorly studied |
16 | mono | poorly studied |
PARP | Residues of the NA Site | PDB ID 1 | |||
---|---|---|---|---|---|
1 | Gly863 | Ala898 | Ser904 | Tyr907 | 4zzz [54] |
2 | Gly429 | Ala464 | Ser470 | Tyr473 | 4zzx [54] |
3 | Gly385 | Ala416 | Ser422 | Tyr425 | 4gv2 [55] |
4 | Gly439 | Ser479 | Ser485 | Tyr488 | - |
5a | Gly1185 | Ala1215 | Ser1221 | Tyr1224 | 4w6e/4msg [56,57] |
5b | Gly1032 | Ala1062 | Ser1068 | Tyr1071 | 5nwg [58] |
6 | Gly474 | Ser510 | Ser516 | Tyr519 | - |
7 | Gly533 | Ala566 | Ser572 | Phe575 | - |
8 | Gly698 | Ser734 | Ser740 | Tyr743 | - |
9 | Gln706 | Thr739 | Leu745 | Lys750 | - |
10 | Gly888 | Ala921 | Ser927 | Tyr932 | 5lx6 [59] |
11 | Gly205 | Ala238 | Ser244 | Phe247 | - |
12 | Gly565 | Ala598 | Ser604 | Tyr607 | 2pqf [60] |
13 | Ala788 | Ala821 | Ser827 | Asn830 | 2x5y [60] |
14 | Gly1602 | Ala1635 | Ser1641 | Tyr1646 | 3smj [37] |
15 | Gly538 | Ala571 | Ser577 | Tyr582 | 4f0e [61] |
16 | Gly153 | Thr184 | Ala190 | Tyr193 | 4f0d [62] |
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Manasaryan, G.; Suplatov, D.; Pushkarev, S.; Drobot, V.; Kuimov, A.; Švedas, V.; Nilov, D. Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers 2021, 13, 1201. https://doi.org/10.3390/cancers13061201
Manasaryan G, Suplatov D, Pushkarev S, Drobot V, Kuimov A, Švedas V, Nilov D. Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers. 2021; 13(6):1201. https://doi.org/10.3390/cancers13061201
Chicago/Turabian StyleManasaryan, Garri, Dmitry Suplatov, Sergey Pushkarev, Viktor Drobot, Alexander Kuimov, Vytas Švedas, and Dmitry Nilov. 2021. "Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins" Cancers 13, no. 6: 1201. https://doi.org/10.3390/cancers13061201
APA StyleManasaryan, G., Suplatov, D., Pushkarev, S., Drobot, V., Kuimov, A., Švedas, V., & Nilov, D. (2021). Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers, 13(6), 1201. https://doi.org/10.3390/cancers13061201