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Enzymology

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https://www.readbyqxmd.com/read/28925557/analysis-of-multiple-haloarchaeal-genomes-suggests-that-the-quinone-dependent-respiratory-nitric-oxide-reductase-is-an-important-source-of-nitrous-oxide-in-hypersaline-environments
#1
Javier Torregrosa-Crespo, Pedro González-Torres, Vanesa Bautista, Julia M Esclapez, Carmen Pire, Mónica Camacho, María José Bonete, David J Richardson, Nicholas J Watmough, Rosa María Martínez-Espinosa
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors)...
September 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28925551/clade-ii-nitrous-oxide-respiration-of-wolinella-succinogenes-depends-on-the-nosg-c1-c2-h-electron-transport-module-nosb-and-a-rieske-cytochrome-bc-complex
#2
Sascha Hein, Samantha Witt, Jörg Simon
Microbial reduction of nitrous oxide (N2 O) is an environmentally significant process in the biogeochemical nitrogen cycle. However, it has been recognized only recently that the gene encoding N2 O reductase (nosZ) is organized in varying genetic contexts, thereby defining clade I (or "typical") and clade II (or "atypical") N2 O reductases and nos gene clusters. This study addresses the enzymology of the clade II Nos system from Wolinella succinogenes, a nitrate-ammonifying and N2 O-respiring Epsilonproteobacterium that contains a cytochrome c N2 O reductase (cNosZ)...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28912602/kinetic-adaptation-of-human-myo19-for-active-mitochondrial-transport-to-growing-filopodia-tips
#3
Marko Ušaj, Arnon Henn
Myosins are actin-based molecular motors which are enzymatically adapted for their cellular functions such as transportation and membrane tethering. Human Myo19 affects mitochondrial motility, and promotes their localization to stress-induced filopodia. Therefore, studying Myo19 enzymology is essential to understand how this motor may facilitate mitochondrial motility. Towards this goal, we have purified Myo19 motor domain (Myo19-3IQ) from a human-cell expression system and utilized transient kinetics to study the Myo19-3IQ ATPase cycle...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911782/determining-carbon-kinetic-isotope-effects-using-headspace-analysis-of-evolved-co2
#4
Scott O C Mundle, Barbara Sherwood Lollar, Ronald Kluger
Isotope ratio mass spectrometry (IRMS) provides accurate measurements of relative abundance of isotopes of heavy atoms for reactions that are subject to kinetic isotope effects (KIEs). The recent development of compound-specific isotope analysis (CSIA) allows the use of multiple time points that provide data for a rate plot as well as isotope ratios. Utilizing CSIA in enzymology presents opportunities for obtaining heavy atom KIEs in diverse areas.
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28880538/characterization-of-the-functional-variance-in-mbth-like-protein-interactions-with-a-nonribosomal-peptide-synthetase
#5
Rebecca A Schomer, Michael G Thomas
Many nonribosomal peptide synthetases (NRPSs) require MbtH-like proteins (MLPs) for solubility or for activation of amino acid substrate by the adenylation domain. MLPs are capable of functional crosstalk with noncognate NRPSs at varying levels. Using enterobactin biosynthesis in Escherichia coli as a model MLP-dependent NRPS system, we use in vivo and in vitro techniques to characterize how seven noncognate MLPs influence the function of the enterobactin NRPS EntF when the cognate MLP, YbdZ, is absent. Using a series of in vitro assays to analyze EntF solubility, adenylation, aminoacylation, and in vitro enterobactin production, we show that interactions between MLPs and NRPSs are multifaceted and more complex than previously appreciated...
September 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28873743/inhibition-of-tyrosinase-by-cherimoya-pericarp-proanthocyanidins-structural-characterization-inhibitory-activity-and-mechanism
#6
Wei-Ming Chai, Mei-Zhen Lin, Ying-Xia Wang, Kai-Li Xu, Wen-Yang Huang, Dan-Dan Pan, Zheng-Rong Zou, Yi-Yuan Peng
In this study, the structure of proanthocyanidins purified from cherimoya (Annona squamosa) pericarp was analyzed by ESI-QTOF-MS and HPLC analyses. The result indicated that these compounds were procyanidin-type proanthocyanidins, consisting mainly of (epi)catechin units linked b y B-type interflavan bonds. The analyses of enzymology showed that the activities of monophenolase and diphenolase of tyrosinase could be powerfully inhibited by the proanthocyanidins. Further researches on the inhibition mechanism demonstrated that they were reversible and competitive inhibitors with the KI value of 27...
October 2017: Food Research International
https://www.readbyqxmd.com/read/28855256/from-masochistic-enzymology-to-mechanistic-physiology-and-disease
#7
Dennis E Vance
The pioneering work of Eugene Kennedy in the 1950s established the choline pathway for phosphatidylcholine (PC) biosynthesis. However, the regulation of PC biosynthesis was poorly understood at that time. When I started my lab at the University of British Columbia in the 1970s, this was the focus of my research. This article provides my reflections on these studies that began with enzymology and the use of cultured mammalian cells, and progressed to utilize the techniques of molecular biology and gene targeted mice...
August 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28853735/enzymology-tracking-off-targets
#8
Alison Farrell
No abstract text is available yet for this article.
July 18, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28833969/enzymatic-c-h-oxidation-amidation-cascade-in-the-production-of-natural-and-unnatural-thiotetronate-antibiotics-with-potentiated-bioactivity
#9
Jie Li, Xiaoyu Tang, Takayoshi Awakawa, Bradley S Moore
The selective activation of unreactive hydrocarbons by biosynthetic enzymes has inspired new synthetic methods in C-H bond activation. Herein, we report the unprecedented two-step biosynthetic conversion of thiotetromycin to thiotetroamide C involving the tandem oxidation and amidation of an unreactive ethyl group. We detail the genetic and biochemical basis for the terminal amidation in thiotetroamide C biosynthesis, which involves a uniquely adapted cytochrome P450-amidotransferase enzyme pair and highlights the first oxidation-amidation enzymatic cascade reaction leading to the selective formation of a primary amide group from a chemically inert alkyl group...
August 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28830931/at-the-confluence-of-ribosomally-synthesized-peptide-modification-and-radical-s-adenosylmethionine-sam-enzymology
#10
John A Latham, Ian Barr, Judith P Klinman
Radical SAM (RS) enzymology has emerged as a major biochemical strategy for the homolytic cleavage of unactivated C-H bonds. At the same time, the posttranslational modification of ribosomally encoded peptides is a rapidly expanding area of investigation, already shown to lead to a wide range of natural products that include a redox cofactor, antibiotics, quorum-sensing molecules, growth regulators, and mature proteins. In this mini-review, we discuss the cross-section of these two disciplines, highlighting the recently uncovered importance of protein-protein interactions, in particular, between the ribosomally-encoded peptide substrate and its chaperone, which functions either as a stand-alone protein or as an N-terminal domain to the Radical SAM enzyme in the peptide modification cascade...
August 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28826221/genomic-enzymology-web-tools-for-leveraging-protein-family-sequence-function-space-and-genome-context-to-discover-novel-functions
#11
REVIEW
John A Gerlt
The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis...
August 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28819009/the-aaa-atpase-p97-a-cellular-multitool
#12
REVIEW
Lasse Stach, Paul S Freemont
The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes...
August 17, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28800965/the-crispr-cas9-facilitated-multiplex-pathway-optimization-cfpo-technique-and-its-application-to-improve-the-escherichia-coli-xylose-utilization-pathway
#13
Xinna Zhu, Dongdong Zhao, Huanna Qiu, Feiyu Fan, Shuli Man, Changhao Bi, Xueli Zhang
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome...
August 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28796306/enzyme-activation-with-a-synthetic-catalytic-coenzyme-intermediate-nucleotide-methylation-by-new-flavoenzymes
#14
Charles Bou-Nader, Cornu David, Vincent Guerineau, Marc Fontecave, Djemel Hamdane
To facilitate production of functional enzymes and to study their mechanisms, especially in the complex cases of coenzyme-dependent systems, activation of an inactive apoenzyme preparation with a catalytically competent coenzyme intermediate is an attractive strategy. This is illustrated with the simple chemical synthesis of a flavin-methylene iminium compound previously proposed as a key intermediate in the catalytic cycle of several important flavoenzymes involved in nucleic acids metabolism. Reconstitution of both flavin-dependent RNA methyltransferase and thymidylate synthase apoproteins with this synthetic compound led to active enzymes for the C5-uracil methylation within their respective transfer RNA and dUMP substrate...
August 10, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28763149/three-cases-of-multi-generational-pompe-disease-are-current-practices-missing-diagnostic-and-treatment-opportunities
#15
Paul McIntosh, Stephanie Austin, Jennifer Sullivan, Lauren Bailey, Carrie Bailey, David Viskochil, Priya S Kishnani
Pompe disease (Glycogen storage disease type II, GSDII, or acid maltase deficiency) is an autosomal recessive metabolic myopathy with a broad clinical spectrum, ranging from infantile to late-onset presentations. In 2015, Pompe disease was added as a core condition to the Recommended Uniform Screening Panel for state newborn screening (NBS). The clinical importance of Pompe disease is evolving with the use of NBS, increasing awareness of the disease, and higher than previously reported disease prevalence; however, current practices miss additional diagnostic and potential treatment opportunities in close relatives of the family proband...
August 1, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28757063/atp-competitive-marine-derived-natural-products-that-target-the-dead-box-helicase-eif4a
#16
Joseph Tillotson, Magdalena Kedzior, Larissa Guimarães, Alison B Ross, Tara L Peters, Andrew J Ambrose, Cody J Schmidlin, Donna D Zhang, Letícia V Costa-Lotufo, Abimael D Rodríguez, Jonathan H Schatz, Eli Chapman
Activation of translation initiation is a common trait of cancer cells. Formation of the heterotrimeric eukaryotic initiation factor F (eIF4F) complex is the rate-limiting step in 5' m7GpppN cap-dependent translation. This trimeric complex includes the eIF4E cap binding protein, the eIF4G scaffolding protein, and the DEAD box RNA helicase eIF4A. eIF4A is an ATP-dependent helicase and because it is the only enzyme in the eIF4F complex, it has been shown to be a potential therapeutic target for a variety of malignancies...
September 1, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28755312/mouse-nudt13-is-a-mitochondrial-nudix-hydrolase-with-nad-p-h-pyrophosphohydrolase-activity
#17
Salama R Abdelraheim, David G Spiller, Alexander G McLennan
The mammalian NUDT13 protein possesses a sequence motif characteristic of the NADH pyrophosphohydrolase subfamily of Nudix hydrolases. Due to the persistent insolubility of the recombinant product expressed in Escherichia coli, active mouse Nudt13 was expressed in insect cells from a baculovirus vector as a histidine-tagged recombinant protein. In vitro, it efficiently hydrolysed NADH to NMNH and AMP and NADPH to NMNH and 2',5'-ADP and had a marked preference for the reduced pyridine nucleotides. Much lower activity was obtained with other nucleotide substrates tested...
July 28, 2017: Protein Journal
https://www.readbyqxmd.com/read/28747400/dynamic-disorder-in-simple-enzymatic-reactions-induces-stochastic-amplification-of-substrate
#18
Ankit Gupta, Andreas Milias-Argeitis, Mustafa Khammash
A growing amount of evidence over the last two decades points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon, termed dynamic disorder, has become possible thanks to advances in single-molecule enzymology measurement techniques, through which the catalytic activity of individual enzyme molecules can be tracked in time. The biological role and importance of these fluctuations in a system with a small number of enzymes, such as a living cell, have only recently started being explored...
July 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28720496/substrate-binding-interferes-with-active-site-conformational-dynamics-in-endoglucanase-cel5a-from-thermobifida-fusca
#19
Xukai Jiang, Yuying Wang, Limei Xu, Guanjun Chen, Lushan Wang
The role of protein dynamics in enzyme catalysis is one of the most active areas in current enzymological research. Here, using endoglucanase Cel5A from Thermobifida fusca (TfCel5A) as a model, we applied molecular dynamics simulations to explore the dynamic behavior of the enzyme upon substrate binding. The collective motions of the active site revealed that the mechanism of TfCel5A substrate binding can likely be described by the conformational-selection model; however, we observed that the conformations of active site residues changed differently along with substrate binding...
September 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28719094/discovery-and-characterization-of-a-novel-tryptophan-hydroxylase-1-inhibitor-as-a-prodrug
#20
Hailong Shi, Yaya Cui, Yifei Qin
Serotonin (5-HT) is an important neurotransmitter and paracrine signaling molecule in the gastrointestinal tract. Two distinct tryptophan hydroxylases (TPH), TPH1 and TPH2 are the rate-limiting enzymes in the 5-HT biosynthesis process. TPH1 expression is mainly limited in the enterochromaffin cells and distributed in peripheries such as the skin and gut, while TPH2 is the predominant isoform in the CNS. In this study, mol002291 was screened as a drug-like compound from the TCM database for the inhibitor of TPH...
July 18, 2017: Chemical Biology & Drug Design
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