scholarly journals Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways

2020 ◽  
Vol 49 (14) ◽  
pp. 4266-4276
Author(s):  
Reza Latifi ◽  
Jennifer L. Minnick ◽  
Matthew G. Quesne ◽  
Sam P. de Visser ◽  
Laleh Tahsini

A detailed QM/MM and DFT study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases is reported. In particular, we investigate the aliphatic hydroxylation and CC epoxidation mechanisms of the enzymes by a high-valent iron(iv)–oxo intermediate.

Antioxidants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 97
Author(s):  
Leila Rashki Ghaleno ◽  
AliReza Alizadeh ◽  
Joël R. Drevet ◽  
Abdolhossein Shahverdi ◽  
Mojtaba Rezazadeh Valojerdi

One important reason for male infertility is oxidative stress and its destructive effects on sperm structures and functions. The particular composition of the sperm membrane, rich in polyunsaturated fatty acids, and the easy access of sperm DNA to oxidative damage due to sperm cell specific cytologic and metabolic features (no cytoplasm left and cells unable to mount stress responses) make it the cell type in metazoans most susceptible to oxidative damage. In particular, oxidative damage to the spermatozoa genome is an important issue and a cause of male infertility, usually associated with single- or double-strand paternal DNA breaks. Various methods of detecting sperm DNA fragmentation have become important diagnostic tools in the prognosis of male infertility and such assays are available in research laboratories and andrology clinics. However, to date, there is not a clear consensus in the community as to their respective prognostic value. Nevertheless, it is important to understand that the effects of oxidative stress on the sperm genome go well beyond DNA fragmentation alone. Oxidation of paternal DNA bases, particularly guanine and adenosine residues, the most sensitive residues to oxidative alteration, is the starting point for DNA damage in spermatozoa but is also a danger for the integrity of the embryo genetic material independently of sperm DNA fragmentation. Due to the lack of a spermatozoa DNA repair system and, if the egg is unable to correct the sperm oxidized bases, the risk of de novo mutation transmission to the embryo exists. These will be carried on to every cell of the future individual and its progeny. Thus, in addition to affecting the viability of the pregnancy itself, oxidation of the DNA bases in sperm could be associated with the development of conditions in young and future adults. Despite these important issues, sperm DNA base oxidation has not attracted much interest among clinicians due to the lack of simple, reliable, rapid and consensual methods of assessing this type of damage to the paternal genome. In addition to these technical issues, another reason explaining why the measurement of sperm DNA oxidation is not included in male fertility is likely to be due to the lack of strong evidence for its role in pregnancy outcome. It is, however, becoming clear that the assessment of DNA base oxidation could improve the efficiency of assisted reproductive technologies and provide important information on embryonic developmental failures and pathologies encountered in the offspring. The objective of this work is to review relevant research that has been carried out in the field of sperm DNA base oxidation and its associated genetic and epigenetic consequences.


2005 ◽  
Vol 109 (46) ◽  
pp. 22045-22052 ◽  
Author(s):  
R. E. A. Kelly ◽  
Y. J. Lee ◽  
L. N. Kantorovich
Keyword(s):  

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 206
Author(s):  
Guillaume Brysbaert ◽  
Jérôme de Ruyck ◽  
Marc Aumercier ◽  
Marc F. Lensink

The transcription factor Ets-1 (ETS proto-oncogene 1) shows low expression levels except in specific biological processes like haematopoiesis or angiogenesis. Elevated levels of expression are observed in tumor progression, resulting in Ets-1 being named an oncoprotein. It has recently been shown that Ets-1 interacts with two DNA repair enzymes, PARP-1 (poly(ADP-ribose) polymerase 1) and DNA-PK (DNA-dependent protein kinase), through two different domains and that these interactions play a role in cancer. Considering that Ets-1 can bind to distinctly different domains of two DNA repair enzymes, we hypothesized that the interaction can be transposed onto homologs of the respective domains. We have searched for sequence and structure homologs of the interacting ETS(Ets-1), BRCT(PARP-1) and SAP(DNA-PK) domains, and have identified several candidate binding pairs that are currently not annotated as such. Many of the Ets-1 partners are associated to DNA repair mechanisms. We have applied protein-protein docking to establish putative interaction poses and investigated these using centrality analyses at the protein residue level. Most of the identified poses are virtually similar to our recently established interaction model for Ets-1/PARP-1 and Ets-1/DNA-PK. Our work illustrates the potentially high number of interactors of Ets-1, in particular involved in DNA repair mechanisms, which shows the oncoprotein as a potential important regulator of the mechanism.


2014 ◽  
Vol 16 (41) ◽  
pp. 22611-22622 ◽  
Author(s):  
Baharan Karamzadeh ◽  
Devendra Singh ◽  
Wonwoo Nam ◽  
Devesh Kumar ◽  
Sam P. de Visser

Computational studies show that the perceived nonheme iron(v)–oxo is actually an iron(iv)–oxo ligand cation radical species.


ChemInform ◽  
2010 ◽  
Vol 33 (1) ◽  
pp. no-no
Author(s):  
James P. Collman ◽  
LeGrande M. Slaughter ◽  
Todd A. Eberspacher ◽  
Thomas Strassner ◽  
John I. Brauman

2003 ◽  
Vol 115 (48) ◽  
pp. 6155-6159 ◽  
Author(s):  
Jacob S. Lai ◽  
Jin Qu ◽  
Eric T. Kool

2013 ◽  
Vol 04 (03) ◽  
pp. 442-451 ◽  
Author(s):  
Eisuke Shimizu ◽  
Ryota Hoshino ◽  
Kazuya Nomura ◽  
Victor I. Danilov ◽  
Noriyuki Kurita

2017 ◽  
Vol 15 (2) ◽  
pp. 426-434 ◽  
Author(s):  
Gabriela G. Gerosa ◽  
Nicolás Grimblat ◽  
Rolando A. Spanevello ◽  
Alejandra G. Suárez ◽  
Ariel M. Sarotti

The mechanism of the acid-catalyzed isomerization of polysubstituted pyrrolidines was unravelled by a combination of experimental, spectroscopic and computational studies.


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