Theoretical study on the degradation of ADP-ribose polymer catalyzed by poly(ADP-ribose) glycohydrolase.
作者： Qianqian Hou , Xin Hu , Xiang Sheng , Yongjun Liu , Chengbu Liu
DOI: 10.1016/J.JMGM.2013.02.010
关键词: Oxocarbenium 、 Poly(ADP-ribose) glycohydrolase 、 Active site 、 Chemistry 、 Glycosidic bond 、 Ribose 、 PARG 、 Stereochemistry 、 Poly ADP ribose polymerase 、 SN2 reaction 、 Organic chemistry
摘要: Abstract Poly(ADP-ribose) glycohydrolase (PARG) is the only enzyme responsible for degradation of ADP-ribose polymers. Very recently, first crystal structure PARG was reported (Dea Slade, et al., Nature 477 (2011) 616), and a possible SN1-type-like mechanism proposed. In this work, we present computational study on hydrolysis glycosidic ribose–ribose bond catalyzed by using hybrid density functional theory (DFT) methods. Based PARG, three models active site were constructed. The calculation results suggest that poly(ADP-ribose) follows an SN2 mechanism, oxocarbenium expected Dea Slade transition state but not intermediate. calculated reaction pathway agrees with proposed mechanism. According to different sizes, roles key residues are elucidated. Our may provide useful information subsequent experimental theoretical studies relationships PARG.
sci-hub.se 参考文章(54)
Ralph G. Meyer, Mirella L. Meyer-Ficca, Elaine L. Jacobson, Myron K. Jacobson, Enzymes in Poly(ADP-Ribose) Metabolism Springer, Boston, MA. pp. 1- 12 ,(2006) , 10.1007/0-387-36005-0_1
Cynthia M.G. Simbulan-Rosenthal, Dean S. Rosenthal, Ruchuang Ding, Joany Jackman, Mark E. Smulson, Depletion of nuclear poly(ADP-ribose) polymerase by antisense RNA expression: influence on genomic stability, chromatin organization, DNA repair, and DNA replication. Progress in Nucleic Acid Research and Molecular Biology. ,vol. 55, pp. 135- 156 ,(1996) , 10.1016/S0079-6603(08)60192-0
F. Simonin, O. Poch, M. Delarue, G. de Murcia, Identification of potential active-site residues in the human poly(ADP-ribose) polymerase. Journal of Biological Chemistry. ,vol. 268, pp. 8529- 8535 ,(1993) , 10.1016/S0021-9258(18)52907-0
K Wielckens, E George, T Pless, H Hilz, Stimulation of poly(ADP-ribosyl)ation during Ehrlich ascites tumor cell "starvation" and suppression of concomitant DNA fragmentation by benzamide. Journal of Biological Chemistry. ,vol. 258, pp. 4098- 4104 ,(1983) , 10.1016/S0021-9258(18)32589-4
X. Yang, S. Wang, Y. Lin, Y. Han, X. Qiu, X. Zhao, L. Cao, X. Wang, Z. Chi, Poly(ADP-ribose) polymerase inhibition protects epileptic hippocampal neurons from apoptosis via suppressing Akt-mediated apoptosis-inducing factor translocation in vitro. Neuroscience. ,vol. 231, pp. 353- 362 ,(2013) , 10.1016/J.NEUROSCIENCE.2012.11.009
Seong-Woon Yu, Hongmin Wang, Marc F Poitras, Carmen Coombs, William J Bowers, Howard J Federoff, Guy G Poirier, Ted M Dawson, Valina L Dawson, Mediation of Poly(ADP-Ribose) Polymerase-1-Dependent Cell Death by Apoptosis-Inducing Factor Science. ,vol. 297, pp. 259- 263 ,(2002) , 10.1126/SCIENCE.1072221
Axel D. Becke, Density-functional thermochemistry. I. The effect of the exchange-only gradient correction Journal of Chemical Physics. ,vol. 96, pp. 2155- 2160 ,(1992) , 10.1063/1.462066
Wensheng Lin, Jean-Christophe Amé, Nasreen Aboul-Ela, Elaine L. Jacobson, Myron K. Jacobson, Isolation and Characterization of the cDNA Encoding Bovine Poly(ADP-ribose) Glycohydrolase Journal of Biological Chemistry. ,vol. 272, pp. 11895- 11901 ,(1997) , 10.1074/JBC.272.18.11895
Mirella L. Meyer-Ficca, Ralph G. Meyer, Elaine L. Jacobson, Myron K. Jacobson, Poly(ADP-ribose) polymerases: managing genome stability The International Journal of Biochemistry & Cell Biology. ,vol. 37, pp. 920- 926 ,(2005) , 10.1016/J.BIOCEL.2004.09.011
Véronique J. Bouchard, Michèle Rouleau, Guy G. Poirier, PARP-1, a determinant of cell survival in response to DNA damage Experimental Hematology. ,vol. 31, pp. 446- 454 ,(2003) , 10.1016/S0301-472X(03)00083-3