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

References

• Till S, Diamantara K, Ladurner AG. PARP: a transferase by any other name. Nat Struct Mol Biol. 2008;15(12):1243–1244.
   PubMed Web of Science ®Google Scholar
• Morales J, Li L, Fattah FJ, et al. Review of poly (ADP-ribose) polymerase (PARP) mechanisms of action and rationale for targeting in cancer and other diseases. Crit Rev Eukaryot Gene Expr. 2014;24(1):15–28.
   PubMed Web of Science ®Google Scholar
• Hottiger MO, Hassa PO, Luscher B, et al. Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem Sci. 2010;35(4):208–219.
   PubMed Web of Science ®Google Scholar
• Otto H, Reche PA, Bazan F, et al. In silico characterization of the family of PARP-like Poly(ADP-ribosyl) transferases (pARTs). BMC Genomics. 2005;6(1):139.
   PubMed Web of Science ®Google Scholar
• Meder VS, Boeglin M, de Murcia G, et al. PARP-1 and PARP-2 interact with nucleophosmin/beta 23 and accumulate in transcriptionally active nucleoli. J Cell Sci. 2005;118(1):211–222.
   PubMed Web of Science ®Google Scholar
• Woodhouse BC, Dianov GL. Poly ADP-ribose polymerase-1: an international molecule of mystery. DNA Repair. 2008;7(7):1077–1086.
   PubMed Web of Science ®Google Scholar
• Xu SW, Bai P, Little PJ, et al. Poly(ADP-ribose) polymerase 1 (PARP1) in atherosclerosis: from molecular mechanisms to therapeutic implications. Med Res Rev. 2014;34(3):644–675.
   PubMed Web of Science ®Google Scholar
• Chugani DC, Rome LH, Kedersha NL. Evidence that vault ribonucleoprotein-particles localize to the nuclear-pore complex. J Cell Sci 1993;106:23–29.
   PubMed Web of Science ®Google Scholar
• Daniel RA, Rozanska AL, Thomas HD, et al. Inhibition of poly (ADP-Ribose) polymerase-1 enhances temozolomide and topotecan activity against childhood neuroblastoma. Clin Cancer Res. 2009;15(4):1241–1249.
   PubMed Web of Science ®Google Scholar
• Opar A. Novel anticancer strategy targets DNA repair. Nat Rev Drug Discov. 2009;8(6):437–438.
   PubMed Web of Science ®Google Scholar
• Mangerich A, Burkle A. How to kill tumor cells with inhibitors of Poly(ADP-ribosyl)ation. Int J Cancer. 2011;128(2):251–265.
   PubMed Web of Science ®Google Scholar
• Peralta-Leal A, Rodriguez-Vargas JM, Aguilar-Quesada R, et al. PARP inhibitors: New partners in the therapy of cancer and inflammatory diseases. Free Radical Bio Med. 2009;47(1):13–26.
   PubMed Web of Science ®Google Scholar
• Jagtap P, Szabo C. Poly(ADP-ribose) polymerase and the therapeutic effects of its inhibitors. Nat Rev Drug Discov. 2005;4(5):421–440.
   PubMed Web of Science ®Google Scholar
• Kickhoefer VA, Siva AC, Kedersha NL, et al. The 193-kD vault protein, VPARP, is a novel Poly(ADP-ribose) polymerase. J Cell Biol. 1999;146(5):917–928.
   PubMed Web of Science ®Google Scholar
• D’Amours D, Desnoyers S, D’Silva I, et al. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J. 1999;342:249–268.
   PubMed Web of Science ®Google Scholar
• Yelamos J, Farres J, Llacuna L, et al. PARP-1 and PARP-2: new players in tumour development. Am J Cancer Res. 2011;1(3):328–346.
   PubMed Web of Science ®Google Scholar
• Yu K, Yau YH, Sinha A, et al. Modulation of the vault protein-protein interaction for tuning of molecular release. Sci Rep. 2017;7(1):1–10.
   PubMed Web of Science ®Google Scholar
• van Zon A, Mossink MH, Schoester M, Houtsmuller AB, et al. The formation of vault-tubes: a dynamic interaction between vaults and vault PARP. J Cell Sci. 2003;116(21):4391–4400.
   PubMed Web of Science ®Google Scholar
• González J, Gálvez A, Morales L, et al. Integrative approach for computationally inferring interactions between the alpha and beta subunits of the calcium-activated potassium channel (BK): a docking study. Bioinform Biol Insights. 2013;7:S10077–S82.
   Google Scholar
• Ünlü A. Computational prediction of actin-actin interaction. Mol Biol Rep. 2014;41(1):355–364.
   PubMed Web of Science ®Google Scholar
• Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–1802.
   PubMed Web of Science ®Google Scholar
• Benkert P, Tosatto SCE, Schwede T. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins. 2009;77(S9):173–180.
   PubMed Web of Science ®Google Scholar
• Rissel D, Peiter E. Poly(ADP-Ribose) polymerases in plants and their human counterparts: parallels and peculiarities. IJMS. 2019;20(7):1638.
   Web of Science ®Google Scholar
• Langelier MF, Planck JL, Roy S, et al. Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity. J Biol Chem. 2011;286(12):10690–10701.
   PubMed Web of Science ®Google Scholar
• Chaitanya GV, Alexander JS, Babu PP. PARP-1 cleavage fragments: signatures of cell-death proteases in neurodegeneration. Cell Commun Signal. 2010;8(1):31.
   PubMed Web of Science ®Google Scholar
• Liu L, Kong M, Gassman NR, et al. PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1. Nucleic Acids Res. 2017;45(22):12834–12847.
   PubMed Web of Science ®Google Scholar
• Chen Q, Kassab MA, Dantzer F, et al. PARP2 mediates branched poly ADP-ribosylation in response to DNA damage. Nat Commun. 2018;9(1):3233.
   PubMed Web of Science ®Google Scholar
• Vyas S, Chang P. New PARP targets for cancer therapy. Nat Rev Cancer. 2014;14(7):502–509.
   PubMed Web of Science ®Google Scholar
• Alemasova EE, Lavrik OI. Poly (ADP-ribosyl) ation by PARP1: reaction mechanism and regulatory proteins. Nucleic acids research. 2019;47(8):3811–3827.
   PubMed Web of Science ®Google Scholar
• Cohen M, Visochek L, Rozensal D, et al. DNA-independent PARP-1 activation by phosphorylated ERK2 increases Elk1 activity: a link to histone acetylation. Mol Cell. 2007;25(2):297–308.
   PubMed Web of Science ®Google Scholar
• Caron M-C, Sharma AK, O’Sullivan J, et al. Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks. Nat Commun. 2019;10(1):2954.
   PubMed Web of Science ®Google Scholar
• Borges HL, Linden R, Wang YJ. DNA damage-induced cell death. Cell Res. 2008;18(1):17–26.
   PubMed Web of Science ®Google Scholar
• Gottschalk AJ, Timinszky G, Kong SE, et al. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. P Natl Acad Sci.2009;106(33):13770–13774.
   PubMed Web of Science ®Google Scholar
• Brown JS, O'Carrigan B, Jackson SP, et al. Targeting DNA repair in cancer: beyond PARP inhibitors. Cancer Discov. 2017;7(1):20–37.
   PubMed Web of Science ®Google Scholar
• Bian C, Zhang C, Luo T, et al. NADP + is an endogenous PARP inhibitor in DNA damage response and tumor suppression. Nat Commun. 2019;10(1):693.
   PubMed Web of Science ®Google Scholar