Results 31 to 40 of about 3,982 (151)

Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq

Scientific Reports, 2021
Plastic waste management has become a global issue. Polyethylene (PE) is the most abundant synthetic plastic worldwide, and one of the most resistant to biodegradation. Indeed, few bacteria can degrade polyethylene.
Jessica Zampolli, Alessandro Orro, Andrea Manconi, Diletta Ami, Antonino Natalello, Patrizia Di Gennaro   +5 more
doaj   +1 more source

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes [PDF]

Chemistry – A European Journal, 2013
AbstractAlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics
Quesne, Matthew G., Latifi, Reza, Gonzalez Ovalle, Luis, Kumar, Devesh, De Visser, Sam P.; id_orcid 0000-0002-2620-8788   +4 more
openaire   +2 more sources

Glutamine deficiency induces DNA alkylation damage and sensitizes cancer cells to alkylating agents through inhibition of ALKBH enzymes. [PDF]

PLoS Biology, 2017
Driven by oncogenic signaling, glutamine addiction exhibited by cancer cells often leads to severe glutamine depletion in solid tumors. Despite this nutritional environment that tumor cells often experience, the effect of glutamine deficiency on cellular
Thai Q Tran, Mari B Ishak Gabra, Xazmin H Lowman, Ying Yang, Michael A Reid, Min Pan, Timothy R O'Connor, Mei Kong   +7 more
doaj   +1 more source

Adaptive Response Enzyme AlkB Preferentially Repairs 1-Methylguanine and 3-Methylthymine Adducts in Double-Stranded DNA [PDF]

Chemical Research in Toxicology, 2016
The AlkB protein is a repair enzyme that uses an α-ketoglutarate/Fe(II)-dependent mechanism to repair alkyl DNA adducts. AlkB has been reported to repair highly susceptible substrates, such as 1-methyladenine and 3-methylcytosine, more efficiently in ss-DNA than in ds-DNA.
Chen, Fangyi, Tang, Qi, Bian, Ke, Humulock, Zachary T., Yang, Xuedong, Li, Deyu, Jost, Marco, Drennan, Catherine L., Essigmann, John M.   +8 more
openaire   +4 more sources

Protein Dynamics Control the Progression and Efficiency of the Catalytic Reaction Cycle of the Escherichia coli DNA-Repair Enzyme AlkB [PDF]

Journal of Biological Chemistry, 2014
A central goal of enzymology is to understand the physicochemical mechanisms that enable proteins to catalyze complex chemical reactions with high efficiency. Recent methodological advances enable the contribution of protein dynamics to enzyme efficiency to be explored more deeply.
Burçe, Ergel, Michelle L, Gill, Lewis, Brown, Bomina, Yu, Arthur G, Palmer, John F, Hunt   +5 more
openaire   +2 more sources

Anaerobic fixed-target serial crystallography

IUCrJ, 2020
Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitrogen cryo-stream at 100 K) enable, is data collection of dioxygen-
Patrick Rabe, John H. Beale, Agata Butryn, Pierre Aller, Anna Dirr, Pauline A. Lang, Danny N. Axford, Stephen B. Carr, Thomas M. Leissing, Michael A. McDonough, Bradley Davy, Ali Ebrahim, Julien Orlans, Selina L. S. Storm, Allen M. Orville, Christopher J. Schofield, Robin L. Owen   +16 more
doaj   +1 more source

Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy

Molecules, 2022
Elucidation of physicochemical mechanisms of enzymatic processes is one of the main tasks of modern biology. High efficiency and selectivity of enzymatic catalysis are mostly ensured by conformational dynamics of enzymes and substrates.
Lyubov Yu. Kanazhevskaya, Denis A. Smyshliaev, Nadezhda A. Timofeyeva, Alexander A. Ishchenko, Murat Saparbaev, Nikita A. Kuznetsov, Olga S. Fedorova   +6 more
doaj   +1 more source

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

BMC Genomics, 2022
Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has ...
Maryam Rezaei Somee, Mohammad Ali Amoozegar, Seyed Mohammad Mehdi Dastgheib, Mahmoud Shavandi, Leila Ghanbari Maman, Stefan Bertilsson, Maliheh Mehrshad   +6 more
doaj   +1 more source

Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions [PDF]

Chemical Research in Toxicology, 2017
Cancer-associated mutations often lead to perturbed cellular energy metabolism and accumulation of potentially harmful oncometabolites. One example is the chiral molecule 2-hydroxyglutarate (2HG); its two stereoisomers (d- and l-2HG) have been found at abnormally high concentrations in tumors featuring anomalous metabolic pathways.
Fangyi Chen, Ke Bian, Qi Tang, Bogdan I. Fedeles, Vipender Singh, Zachary T. Humulock, John M. Essigmann, Deyu Li   +7 more
openaire   +4 more sources

DNA Methylation on N6-Adenine Regulates the Hyphal Development during Dimorphism in the Early-Diverging Fungus Mucor lusitanicus

Journal of Fungi, 2021
The epigenetic modifications control the pathogenicity of human pathogenic fungi, which have been poorly studied in Mucorales, causative agents of mucormycosis.
Macario Osorio-Concepción, Carlos Lax, Eusebio Navarro, Francisco E. Nicolás, Victoriano Garre   +4 more
doaj   +1 more source