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https://www.readbyqxmd.com/read/28708394/human-viperin-causes-radical-sam-dependent-elongation-of-escherichia-coli-hinting-at-its-physiological-role
#1
Micah T Nelp, Anthony P Young, Branden M Stepanski, Vahe Bandarian
Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible) is a widely distributed protein that is expressed in response to infection and causes antiviral effects against a broad spectrum of viruses. Viperin is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. Though the specific reaction catalyzed by viperin remains unknown, it has been shown that expression of viperin causes an increase in the fluidity of lipid membranes, which impedes the budding of nascent viral particles from the membrane inhibiting propagation of the infection...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28704777/preinvasive-disease-of-the-airway
#2
REVIEW
Ricky M Thakrar, Adam Pennycuick, Elaine Borg, Sam M Janes
Squamous cell carcinoma of the lung arises from preinvasive progenitors in the central airways. The archetypal model appears to be a stepwise morphological progression until there is invasion of the basement membrane. However, not every lesion appears to follow this course and many individuals can have stable disease, or indeed regress to normal epithelium. From our increased understanding of the molecular pathology it is becoming apparent that the respiratory epithelium accumulates progressive genetic and epigenetic insults in response to carcinogens...
July 10, 2017: Cancer Treatment Reviews
https://www.readbyqxmd.com/read/28704043/structural-insights-into-thioether-bond-formation-in-the-biosynthesis-of-sactipeptides
#3
Tyler L Grove, Paul Michael Himes, Sungwon Hwang, Hayretin Yumerefendi, Jeffrey B Bonanno, Brian Kuhlman, Steven C Almo, Albert A Bowers
Sactipeptides are ribsomally-produced peptides that contain a characteristic thioether bridge (sactionine bond) that is installed posttranslationally and is absolutely required for their antibiotic activity. Sactipeptide biosynthesis requires a unique class of radical SAM enzymes that contain multiple [4Fe-4S] clusters to form the requisite thioether bridge between a cysteine and the α-carbon of an opposing amino acid through radical chemistry. Here we present the structure of the sactionine bond forming enzyme CteB, from Clostridium thermocellum ATCC 27405, with both SAM and an N-terminal fragment of it's peptidyl-substrate at 2...
July 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28701039/aminofutalosine-synthase-evidence-for-captodative-and-aryl-radical-intermediates-using-beta-scission-and-srn1-trapping-reactions
#4
Sumedh Joshi, Nilkamal Mahanta, Dmytro Fedoseyenko, Howard J Williams, Tadhg P Begley
Aminofutalosine synthase (MqnE) is a radical SAM enzyme involved in the menaquinone biosynthetic pathway. In this communication, we propose a novel mechanism for this reaction involving the addition of the adenosyl radical to the substrate double bond to form a captodative radical followed by rearrangement and decarboxylation to form an aryl radical anion which is then oxidized by the [4Fe-4S]+2 cluster. Consistent with this proposal, we describe the trapping of the captodative radical and the aryl radical anion using radical triggered C-Br fragmentation reactions...
July 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28678474/methylcobalamin-dependent-radical-sam-c-methyltransferase-fom3-recognizes-cytidylyl-2-hydroxyethylphosphonate-and-catalyzes-the-nonstereoselective-c-methylation-in-fosfomycin-biosynthesis
#5
Shusuke Sato, Fumitaka Kudo, Seung-Young Kim, Tomohisa Kuzuyama, Tadashi Eguchi
A methylcobalamin (MeCbl)-dependent radical S-adenosyl-l-methionine (SAM) methyltransferase Fom3 was found to catalyze the C-methylation of cytidylyl-2-hydroxyethylphosphonate (HEP-CMP) to give cytidylyl-2-hydroxypropylphosphonate (HPP-CMP), although it was originally proposed to catalyze the C-methylation of 2-hydroxyethylphosphonate to give 2-hydroxypropylphosphonate in the biosynthesis of a unique C-P bond containing antibiotic fosfomycin in Streptomyces. Unexpectedly, the Fom3 reaction product from HEP-CMP was almost a 1:1 diastereomeric mixture of HPP-CMP, indicating that the C-methylation is not stereoselective...
July 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28671210/a-mechanistic-study-of-the-non-oxidative-decarboxylation-catalyzed-by-the-radical-s-adenosyl-l-methionine-enzyme-blse-involved-in-blasticidin-s-biosynthesis
#6
Lei Liu, Xinjian Ji, Yongzhen Li, Wenjuan Ji, Tianlu Mo, Wei Ding, Qi Zhang
Decarboxylation is a fundamentally important reaction in biology and involves highly diverse mechanisms. Here we report a mechanistic study of the non-oxidative decarboxylation catalyzed by BlsE, a radical S-adenosyl-l-methionine (SAM) enzyme involved in blasticidin S biosynthesis. Through a series of biochemical analysis with isotopically labeled reagents, we show that the BlsE-catalyzed reaction is initiated by the 5'-deoxyadenosyl (dAdo) radical-mediated hydrogen abstraction from a sugar carbon of the substrate cytosylglucuronic acid (CGA), and does not involve a carboxyl radical as has been proposed for 4-hydroxyphenylacetate decarboxylase (HPAD)...
July 3, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28644475/post-translational-modification-of-ribosomally-synthesized-peptides-by-a-radical-sam-epimerase-in-bacillus-subtilis
#7
Alhosna Benjdia, Alain Guillot, Pauline Ruffié, Jérôme Leprince, Olivier Berteau
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28643349/a-qm-mm-study-of-the-catalytic-mechanism-of-sam-methyltransferase-rlmn-from-escherichia-coli
#8
Chenxiao Zhao, Lihua Dong, Yongjun Liu
RlmN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C2 methylation of adenosine 2503 (A2503) in 23S rRNA and adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNA). The catalytic reaction of RlmN is distinctly different from that of typical SAM-dependent methyltransferases that employs an SN 2 mechanism, but follows a ping-pong mechanism which involves the intermediate methylation of a conserved cysteine residue. Recently, the x-ray structure of a key intermediate in the RlmN reaction has been reported, allowing us to perform combined quantum mechanics and molecular mechanics (QM/MM) calculations to delineate the reaction details of RlmN at atomic level...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28640310/spectroscopic-evidence-for-cofactor-substrate-interaction-in-the-radical-sam-enzyme-tyw1
#9
Velavan Kathirvelu, Phanélie Perche-Letuvée, Jean-Marc Latour, Mohamed Atta, Farhad Forouhar, Serge Gambarelli, Ricardo Garcia-Serres
TYW1 is a metalloenzyme involved in the modifications of guanosine 37 of Phe-tRNA of Eukaryota and Archaea. It catalyzes the second step of Wybutosine biosynthesis, which consists of the formation of the tricyclic compound imG-14 from m(1)G using pyruvate and SAM (S-adenosyl-methionine) as co-substrates. Two [4Fe-4S] clusters are needed in the catalytic process. One effects the reductive binding of SAM, which initiates the radical reaction that inserts a C-C moiety into m(1)G. The other [4Fe-4S] cluster binds the pyruvate molecule that provides the C-C motif...
June 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28617585/solution-phase-photochemical-nanopatterning-enabled-by-high-refractive-index-beam-pen-arrays
#10
Zhuang Xie, Pavlo Gordiichuk, Qing-Yuan Lin, Brian Meckes, Peng-Cheng Chen, Lin Sun, Jingshan S Du, Jinghan Zhu, Yuan Liu, Vinayak P Dravid, Chad A Mirkin
A high-throughput, solution-based, scanning-probe photochemical nanopatterning approach, which does not require the use of probes with subwavelength apertures, is reported. Specifically, pyramid arrays made from high-refractive-index polymeric materials were constructed and studied as patterning tools in a conventional liquid-phase beam pen lithography experiment. Two versions of the arrays were explored with either metal-coated or metal-free tips. Importantly, light can be channeled through both types of tips and the appropriate solution phase (e...
June 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/28615450/cellular-requirements-for-iron-sulfur-cluster-insertion-into-the-antiviral-radical-sam-protein-viperin
#11
Arunkumar S Upadhyay, Oliver Stehling, Christakis Panayiotou, Ralf Rösser, Roland Lill, Anna K Överby
Viperin (RSAD2) is an interferon-stimulated antiviral protein that belongs to the radical S-adenosyl methionine (SAM) enzyme family. Viperin's iron-sulfur (Fe/S) cluster is critical for its antiviral activity against many different viruses. CIA1 (CIAO1), an essential component of the cytosolic iron-sulfur protein assembly (CIA) machinery, is crucial for Fe/S cluster insertion into viperin and hence for viperin's antiviral activity. In the CIA pathway, CIA1 cooperates with CIA2A, CIA2B, and MMS19 targeting factors to form various complexes that mediate the dedicated maturation of specific Fe/S recipient proteins...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28607080/structural-studies-of-viperin-an-antiviral-radical-sam-enzyme
#12
Michael K Fenwick, Yue Li, Peter Cresswell, Yorgo Modis, Steven E Ealick
Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure...
June 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28585831/characterization-of-self-assembled-monolayers-on-a-ruthenium-surface
#13
A Shaheen, J M Sturm, R Ricciardi, J Huskens, C J Lee, F Bijkerk
We have modified and stabilized the ruthenium surface by depositing a self-assembled monolayer (SAM) of 1-hexadecanethiol on a polycrystalline ruthenium thin film. The growth mechanism, dynamics, and stability of these monolayers were studied. SAMs, deposited under ambient conditions, on piranha-cleaned and piranha + H2SO4 cleaned substrates were compared to monolayers formed on H-radical-cleaned Ru surfaces. We found that alkanethiols on H-radical-cleaned Ru formed densely packed monolayers that remained stable when kept in a nitrogen atmosphere...
June 27, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28579687/therapeutic-ultrasound-and-prostate-cancer
#14
REVIEW
Karthik M Sundaram, Sam S Chang, David F Penson, Sandeep Arora
Therapeutic ultrasound approaches including high-intensity focused ultrasound (HIFU) are emerging as popular minimally invasive alternative treatments for localized, low-to-intermediate risk prostate cancer. FDA approval was recently granted for two ultrasound-guided HIFU devices. Clinical trials for devices using MRI guidance are ongoing. The current level of evidence for whole-gland ultrasound ablation suggests that its clinical efficacy and adverse event rates including erectile dysfunction and urinary incontinence are similar to current definitive therapies such as radical prostatectomy and external-beam radiotherapy...
June 2017: Seminars in Interventional Radiology
https://www.readbyqxmd.com/read/28553520/watasemycin-biosynthesis-in-streptomyces-venezuelae-thiazoline-c-methylation-by-a-type-b-radical-sam-methylase-homologue
#15
Yuki Inahashi, Shanshan Zhou, Maureen J Bibb, Lijiang Song, Mahmoud M Al-Bassam, Mervyn J Bibb, Gregory L Challis
2-Hydroxyphenylthiazolines are a family of iron-chelating nonribosomal peptide natural products that function as virulence-conferring siderophores in various Gram-negative bacteria. They have also been reported as metabolites of Gram-positive Streptomyces species. Transcriptional analyses of Streptomyces venezuelae ATCC 10712 revealed that its genome contains a putative 2-hydroxyphenylthiazoline biosynthetic gene cluster. Heterologous expression of the gene cluster in Streptomyces coelicolor M1152 showed that the mono- and dimethylated derivatives, thiazostatin and watasemycin, respectively, of the 2-hydroxyphenylthiazoline enantiopyochelin are two of its metabolic products...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28533006/association-between-preoperative-albumin-levels-and-length-of-stay-after-radical-cystectomy
#16
Rohan G Bhalla, Li Wang, Sam S Chang, Mark D Tyson
PURPOSE: Using contemporary population-based epidemiologic data, we measured the relationship between preoperative serum albumin level and hospital length of stay (LOS) after cystectomy and urinary diversion. MATERIALS & METHODS: Data was acquired from the 2014-2015 National Surgical Quality Improvement Program (NSQIP) database. We identified 1,582 adult patients who underwent a cystectomy between January 1st 2014 and December 31st 2015 and had a documented preoperative serum albumin level...
May 19, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28505894/re-the-prognostic-significance-of-the-early-postoperative-neutrophil-to-lymphocyte-ratio-in-patients-with-urothelial-carcinoma%C3%A2-of%C3%A2-the%C3%A2-bladder-undergoing-radical-cystectomy
#17
https://www.readbyqxmd.com/read/28487403/cluster-assembly-in-nitrogenase
#18
REVIEW
Nathaniel S Sickerman, Lee A Rettberg, Chi Chung Lee, Yilin Hu, Markus W Ribbe
The versatile enzyme system nitrogenase accomplishes the challenging reduction of N2and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe8S7]-core P-cluster and a [MoFe7S9C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N2, and both originate from [Fe4S4] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe4S4] clusters on NifDK called the P*-cluster...
May 9, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28476884/insights-into-the-catalysis-of-a-lysine-tryptophan-bond-in-bacterial-peptides-by-a-spasm-domain-radical-s-adenosylmethionine-sam-peptide-cyclase
#19
Alhosna Benjdia, Laure Decamps, Alain Guillot, Xavier Kubiak, Pauline Ruffié, Corine Sandström, Olivier Berteau
Radical S-adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to Cα atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus, and a reaction mechanism has been proposed...
June 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28455341/lack-of-methylated-hopanoids-renders-the-cyanobacterium-nostoc-punctiforme-sensitive-to-osmotic-and-ph-stress
#20
Tamsyn J Garby, Emily D Matys, Sarah E Ongley, Anya Salih, Anthony W D Larkum, Malcolm R Walter, Roger E Summons, Brett A Neilan
To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S-adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting ΔhpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the ΔhpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions...
July 1, 2017: Applied and Environmental Microbiology
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