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radical sam

Christina M Fitzsimmons, Danica Galonić Fujimori
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets...
2016: PloS One
Christof Martin Jäger, Anna Kristina Croft
Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-Adensosylmethionine (SAM) dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+, identified as a key catalytic component on radical stability and reaction control in 7-Carboxy-7-deazaguanine synthase (QueE). Radical Stabilisation Energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveal Mg2+ as having a directing role in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives...
November 10, 2016: Chemistry: a European Journal
Caitlyn Makins, Soumi Ghosh, Gabriel D Román-Meléndez, Paige A Malec, Robert T Kennedy, E Neil G Marsh
Viperin is an endoplasmic reticulum-associated antiviral responsive protein, which is highly up regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-L-methionine (SAM) enzyme, but it is unknown if viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS)...
November 10, 2016: Journal of Biological Chemistry
Sam Wouters, Tom Hauffman, Marjo C Mittelmeijer-Hazeleger, Gadi Rothenberg, Gert Desmet, Gino V Baron, Sebastiaan Eeltink
Poly(styrene-co-divinylbenzene) monolithic stationary phases with two different domain sizes were synthesized by a thermally initiated free-radical copolymerization in capillary columns. The morphology was investigated at the meso- and macroscopic level using complementary physical characterization techniques aiming at better understanding the effect of column structure on separation performance. Varying the porogenic solvent ratio yielded materials with a mode pore size of 200 nm and 1.5 μm, respectively...
October 5, 2016: Journal of Separation Science
Daseul Park, Hafiz Muhammad Shahbaz, Sun-Hyoung Kim, Mijin Lee, Wooseong Lee, Jong-Won Oh, Dong-Un Lee, Jiyong Park
Human norovirus (HuNoV) is the primary cause of viral gastroenteritis worldwide. Fresh blueberries are among high risk foods associated with norovirus related outbreaks. Therefore, it is important to assess intervention strategies to reduce the risk of foodborne illness. The disinfection efficiency of decontamination methods is difficult to evaluate for fruits and vegetables due to an inconsistent degree of contamination and irregular surface characteristics. The inactivation efficiency and mechanism of murine norovirus 1 (MNV-1, a surrogate for HuNoV) was studied on an experimentally prepared solidified agar matrix (SAM) to simulate blueberries using different wavelengths (A, B, C) of UV light both with and without TiO2 photocatalysis (TP)...
December 5, 2016: International Journal of Food Microbiology
Sophia Taylor, Weyinmi Demeyin, Ann Muls, Catherine Ferguson, Damian J J Farnell, David Cohen, Jervoise Andreyev, John Green, Lesley Smith, Sam Ahmedzai, Sara Pickett, Annmarie Nelson, John Staffurth
INTRODUCTION: Radiotherapy treatment for prostate cancer can cause bowel problems, which may lead to severe difficulties for cancer survivors including limiting travel, work or socialising. These symptoms can appear at any time following radiotherapy. This study focuses on the early identification and protocol-based management of effects known to cause long-term, or even permanent, changes to the well-being of prostate cancer survivors. The rationale of this study is to improve the care offered to men and their families following pelvic radiotherapy for prostate cancer...
October 3, 2016: BMJ Open
Hsin-I Hung, Oliver J Klein, Sam W Peterson, Sarah R Rokosh, Sam Osseiran, Nicholas H Nowell, Conor L Evans
Photodynamic therapy regimens, which use light-activated molecules known as photosensitizers, are highly selective against many malignancies and can bypass certain challenging therapeutic resistance mechanisms. Photosensitizers such as the small cationic molecule EtNBS (5-ethylamino-9-diethyl-aminobenzo[a]phenothiazinium chloride) have proven potent against cancer cells that reside within acidic and hypoxic tumour microenvironments. At higher doses, however, these photosensitizers induce "dark toxicity" through light-independent mechanisms...
September 30, 2016: Scientific Reports
Thibaut Molle, Yohann Moreau, Martin Clemancey, Farhad Forouhar, Jean-Luc Ravanat, Nicolas Duraffourg, Vincent Fourmond, Jean-Marc Latour, Serge Gambarelli, Etienne Mulliez, Mohamed Atta
RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C3 methylthiolation of the D89 residue in the ribosomal S12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS(-) ligand bound to the additional cluster...
October 6, 2016: Biochemistry
Mengmeng Zhang, Hong Zhang, Huixian Li, Furao Lai, Xiaofeng Li, Yuqian Tang, Tian Min, Hui Wu
Betaine (BET) is a native compound widely studied as an antioxidant in agriculture and human health. However, the antioxidant mechanism of BET remains unclear. In this research, radical scavenging assays showed that BET had little free radical scavenging activity. However, the antioxidant activity of BET was confirmed by cellular antioxidant activity (CAA) and erythrocyte hemolysis assays. The results of quantitative PCR (qPCR) and enzyme activity determination kits showed that the antioxidant activity of BET was not due to the gene expression and activity of antioxidases...
October 12, 2016: Journal of Agricultural and Food Chemistry
Kristen R Scarpato, Stephen F Kappa, Kathryn M Goggins, Sam S Chang, Joseph A Smith, Peter E Clark, David F Penson, Matthew J Resnick, Daniel A Barocas, Kamran Idrees, Sunil Kripalani, Kelvin A Moses
Health literacy is the ability to obtain, comprehend, and act on medical information and is an independent predictor of health outcomes in patients with chronic health conditions. However, little has been reported regarding the potential association of health literacy and surgical outcomes. We hypothesized that patient complications after radical cystectomy would be associated with health literacy. In a sample of 368 patients, we found that higher health literacy scores (as determined by the Brief Health Literacy Screen) were associated with decreased odds of developing minor complications (odds ratio = 0...
2016: Journal of Health Communication
Edward A Lilla, Kenichi Yokoyama
Nikkomycins and polyoxins are antifungal peptidylnucleoside antibiotics active against human and plant pathogens. Here we report that during peptidylnucleoside biosynthesis in Streptomyces cacaoi and S. tendae, the C5' extension of the nucleoside essential for downstream structural diversification is catalyzed by a conserved radical S-adenosyl-L-methionine (SAM) enzyme, PolH or NikJ. This is distinct from the nucleophilic mechanism reported for antibacterial nucleosides and represents a new mechanism of nucleoside natural product biosynthesis...
November 2016: Nature Chemical Biology
Robert L Evans, John A Latham, Judith P Klinman, Carrie M Wilmot, Youlin Xia
The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD...
October 2016: Biomolecular NMR Assignments
Shanshan Zhou, Lona M Alkhalaf, Emmanuel Lc de Los Santos, Gregory L Challis
Class B radical S-adenosylmethionine (SAM) methylases are notable for their ability to catalyse methylation reactions in the biosynthesis of a wide variety of natural products, including polyketides, ribosomally biosynthesised and post-translationally modified peptides (RiPPs), nonribosomal peptides (NRPs), aminoglycosides, β-lactams, phosphonates, enediynes, aminocoumarins and terpenes. Here, we discuss the diversity of substrates and catalytic mechanism utilised by such enzymes, highlighting the stereochemical course of methylation reactions at un-activated carbon centres and the ability of some members of the family to catalyse multiple methylations...
September 12, 2016: Current Opinion in Chemical Biology
Yisong Guo, Carlos Echavarri-Erasun, Marie Demuez, Emilio Jiménez-Vicente, Emile L Bominaar, Luis M Rubio
The biological activation of N2 occurs at the FeMo-cofactor, a 7Fe-9S-Mo-C-homocitrate cluster. FeMo-cofactor formation involves assembly of a Fe6-8 -SX -C core precursor, NifB-co, which occurs on the NifB protein. Characterization of NifB-co in NifB is complicated by the dynamic nature of the assembly process and the presence of a permanent [4Fe-4S] cluster associated with the radical SAM chemistry for generating the central carbide. We have used the physiological carrier protein, NifX, which has been proposed to bind NifB-co and deliver it to the NifEN protein, upon which FeMo-cofactor assembly is ultimately completed...
October 4, 2016: Angewandte Chemie
Sebastian W Fuchs, Gerald Lackner, Brandon I Morinaka, Yohei Morishita, Teigo Asai, Sereina Riniker, Jörn Piel
Ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) exhibit diverse structures and bioactivities and are classified into distinct biosynthetic families. A recently reported family is the proteusins, with the prototype members polytheonamides being generated by almost 50 maturation steps, including introduction of d-residues at multiple positions by an unusual radical SAM epimerase. A region in the protein-like N-terminal leader of proteusin precursors is identified that is crucial for epimerization...
September 26, 2016: Angewandte Chemie
Xinjian Ji, Yongzhen Li, Liqi Xie, Haojie Lu, Wei Ding, Qi Zhang
Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety...
September 19, 2016: Angewandte Chemie
Vanja Stojković, Lianet Noda-Garcia, Dan S Tawfik, Danica Galonić Fujimori
Modifications of the bacterial ribosome regulate the function of the ribosome and modulate its susceptibility to antibiotics. By modifying a highly conserved adenosine A2503 in 23S rRNA, methylating enzyme Cfr confers resistance to a range of ribosome-targeting antibiotics. The same adenosine is also methylated by RlmN, an enzyme widely distributed among bacteria. While RlmN modifies C2, Cfr modifies the C8 position of A2503. Shared nucleotide substrate and phylogenetic relationship between RlmN and Cfr prompted us to investigate evolutionary origin of antibiotic resistance in this enzyme family...
October 14, 2016: Nucleic Acids Research
Xin Fu, QiuHong Wang, ZhiBin Wang, HaiXue Kuang, Pinghui Jiang
Danggui-Shaoyao-San (DSS), also called Toki-shakuyaku-san (TJ-23) or Dangguijakyak-san (DJS), is a well-known herbal formula (Angelica sinensis (Oliv.) Diels., Ligusticum chuanxiong Hort., Paeonia lactiflora pall., Poria cocos (Schw.) Wolf, Alisma orientalis (Sam.) Juzep., Atractylodes macrocephala Koidz.), which has been widely used in oriental countries for the treatment of various gynecological diseases. Recent studies show that DSS has an effect on free radical-mediated neurological diseases and exhibits anti-inflammatory and antioxidant activities and reduces cell apoptosis in the hippocampus...
August 2016: Aging and Disease
Xinjian Ji, Wan-Qiu Liu, Shuguang Yuan, Yue Yin, Wei Ding, Qi Zhang
The radical SAM enzyme NosL catalyzes the conversion of l-Trp to 3-methyl-2-indolic acid, and this reaction is initiated by the 5'-deoxyadenosyl (dAdo) radical-mediated hydrogen abstraction from the l-Trp amino group. We demonstrate here that when d-Trp was used in the NosL reaction, hydrogen abstraction occurs promiscuously at both the amino group and Cα of d-Trp. These results inspired us to establish the detailed mechanism of l-Trp amine dehydrogenation catalyzed by a NosL mutant, and to engineer a novel radical SAM-dependent l-Tyr amine dehydrogenase from the thiamine biosynthesis enzyme ThiH...
August 18, 2016: Chemical Communications: Chem Comm
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