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Enzymology

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https://www.readbyqxmd.com/read/28329912/structural-and-mechanistic-insights-into-homocysteine-degradation-by-a-mutant-of-methionine-%C3%AE-lyase-based-on-substrate-assisted-catalysis
#1
Dan Sato, Tomoo Shiba, Shunsuke Yunoto, Kazuo Furutani, Mitsuki Fukumoto, Daizou Kudou, Takashi Tamura, Kenji Inagaki, Shigeharu Harada
Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28324500/analysis-of-yeast-telomerase-by-primer-extension-assays
#2
Min Hsu, Neal F Lue
Telomeres are specialized nucleoprotein structures located at eukaryotic chromosomal termini, which are required for chromosome stability and are maintained by a reverse transcriptase named telomerase. Budding yeast has served as an extremely useful model system for analyzing telomere maintenance because the organism offers a wide range of genetic and biochemical tools. Several milestones in telomerase research have been reached through investigation of the yeast system. For example, the consequence of telomerase loss was first characterized in the budding yeast Saccharomyces cerevisiae...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28322495/polyketide-synthase-modules-redefined
#3
Adrian T Keatinge-Clay
Modular redefinition: A long-standing paradigm in modular polyketide synthase enzymology, namely the definition of a module, has been challenged by Abe and co-workers in their recent study. With this new understanding has emerged renewed hope for engineering these assembly lines to produce new materials and medicines.
March 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28321407/pten-reduced-uvb-mediated-apoptosis-in-retinal-pigment-epithelium-cells
#4
Jia He, Chongde Long, Zixin Huang, Xin Zhou, Xielan Kuang, Lanying Liu, Huijun Liu, Yan Tang, Yuting Fan, Jie Ning, Xinqi Ma, Qingjiong Zhang, Huangxuan Shen
Age-related macular degeneration (AMD) is a leading cause of blindness and progressive loss of central vision in the elderly population. The important factor of AMD pathogenesis is the degeneration of retinal pigment epithelial (RPE) cells by oxidative stress. Inactivation of PTEN can disrupt intercellular adhesion in the RPE cells, but the mechanism of oxidative stress is less known. Here we presented evidence that UVB-mediated oxidative stress induced apoptosis in ARPE-19 cells. Downregulation of the expression of PTEN in UVB-irradiative RPE cells triggered DNA damage and increased the level of UVB-induced apoptosis by activating p53-dependent pathway...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28321369/developmental-and-loco-like-effects-of-a-swainsonine-induced-inhibition-of-%C3%AE-mannosidase-in-the-honey-bee-apis-mellifera
#5
Laura Wedd, Regan Ashby, Sylvain Foret, Ryszard Maleszka
BACKGROUND: Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. METHODS: We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo...
2017: PeerJ
https://www.readbyqxmd.com/read/28320294/solid-gas-biocatalysis
#6
REVIEW
L M Kulishova, D O Zharkov
Solid/gas biocatalysis is a nontraditional reaction system that employs the ability of some enzymes, being in the solid state, to catalyze reactions of substrates in the gas phase. Manipulation of the reaction parameters (temperature and pressure) in the solid/gas system allows precise control over the thermodynamic activity of water and substrate and creation of a controlled microenvironment for the enzyme, making it an appropriate model for enzymology studies. Owing to such advantages as high stability of dry enzymes and cofactors and easy fractionation of gas mixtures, solid/gas biotechnology has already found several industrial applications...
February 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28320284/apoptotic-endonuclease-endog-inhibits-telomerase-activity-and-induces-malignant-transformation-of-human-cd4-t-cells
#7
D A Vasina, D D Zhdanov, E V Orlova, V S Orlova, M V Pokrovskaya, S S Aleksandrova, N N Sokolov
Telomerase activity is regulated by an alternative splicing of mRNA of the telomerase catalytic subunit hTERT (human telomerase reverse transcriptase). Increased expression of the inactive spliced hTERT results in inhibition of telomerase activity. Little is known about the mechanism of hTERT mRNA alternative splicing. This study was aimed at determining the effect of an apoptotic endonuclease G (EndoG) on alternative splicing of hTERT and telomerase activity in CD4+ human T lymphocytes. Overexpression of EndoG in CD4+ T cells downregulated the expression of the active full-length hTERT variant and upregulated the inactive alternatively spliced variant...
January 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28314776/masochistic-enzymology-dennis-vance-s-work-on-phosphatidylcholine
#8
George Carman, Alexandra Taylor
No abstract text is available yet for this article.
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28295037/a-mutation-in-the-tmem65-gene-results-in-mitochondrial-myopathy-with-severe-neurological-manifestations
#9
Aisha Nazli, Adeel Safdar, Ayesha Saleem, Mahmood Akhtar, Lauren I Brady, Jeremy Schwartzentruber, Mark A Tarnopolsky
Recent research has suggested that transmembrane protein 65 (TMEM65) is localized within the inner mitochondrial membrane. Little else is known about its function. In this study we investigated the location and function of TMEM65. Further, we report the functional consequences of a novel homozygous splice variant (c.472+1G>A) in the TMEM65 gene in a patient with mitochondrial encephalomyopathy. Here we investigated the location of TMEM65 by immunofluorescence staining of the protein and by immunoblotting of the isolated mitochondrial fractions in healthy fibroblasts and those from the patient...
March 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28274732/flavins-as-covalent-catalysts-new-mechanisms-emerge
#10
REVIEW
Valentina Piano, Bruce A Palfey, Andrea Mattevi
With approximately 1% of proteins being flavoproteins, flavins are at the heart of a plethora of redox reactions in all areas of biology. Thanks to a series of fascinating recent discoveries, in addition to redox chemistry, covalent catalysis is now being recognized more frequently as a common strategy in flavoenzymes, with unprecedented mechanisms becoming apparent. Thus, noncanonical covalent reactions by flavins are emerging as a new pervasive concept in basic enzymology and biochemistry. These diverse enzymes are engaged in most biological processes, positioning the knowledge being gained from these new mechanisms to be translated into drugs that function through covalent mechanisms...
March 5, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28263875/molecular-architecture-of-an-n-formyltransferase-from-salmonella-enterica-o60
#11
Colin R Woodford, James B Thoden, Hazel M Holden
N-formylated sugars are found on the lipopolysaccharides of various pathogenic Gram negative bacteria including Campylobacter jejuni 81116, Francisella tularensis, Providencia alcalifaciens O30, and Providencia alcalifaciens O40. The last step in the biosynthetic pathways for these unusual sugars is catalyzed by N-formyltransferases that utilize N(10)-formyltetrahydrofolate as the carbon source. The substrates are dTDP-linked amino sugars with the functional groups installed at either the C-3' or C-4' positions of the pyranosyl rings...
March 2, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28202539/parps-and-adp-ribosylation-recent-advances-linking-molecular-functions-to-biological-outcomes
#12
REVIEW
Rebecca Gupte, Ziying Liu, W Lee Kraus
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28163054/on-the-indirect-relationship-between-protein-dynamics-and-enzyme-activity
#13
REVIEW
Qinyi Zhao
The behaviors of simple thermal systems have been well studied in physical chemistry and the principles obtained from such studies have been applied to complex thermal systems, such as proteins and enzymes. But the simple application of such principles is questionable and may lead to mistakes under some circumstances. In enzymology, the transition state theory of chemical reactions has been accepted as a fundamental theory, but the role of protein dynamics in enzyme catalysis is controversial in the context of transition state theory...
February 3, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28151666/enhanced-catalytic-activity-of-%C3%AE-chymotrypsin-in-cationic-surfactant-solutions-the-component-specificity-revisited
#14
Animesh Patra, Nirnay Samanta, Dipak Kumar Das, Rajib Kumar Mitra
Enhanced catalytic activity (super activity) of enzymes in the presence of surfactants is of key importance in "micellar enzymology"; such super activity is not very trivial, it is highly system specific, and the mechanism behind the activity enhancement is not always well apprehended. We report the catalytic activity of α-chymotrypsin (CHT) on ala-ala-phe-7-amido-4-methylcoumarin (AMC) in the presence of cationic surfactants of different hydrophobic chain lengths: dodecyltrimethylammonium bromide (DTAB), cetyltrimethylammonium bromide (CTAB) and octadecyltrimethylammonium bromide (OTAB)...
February 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28138099/polysaccharide-utilization-loci-fuelling-microbial-communities
#15
Julie M Grondin, Kazune Tamura, Guillaume Déjean, D Wade Abbott, Harry Brumer
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fuelling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species, and are of critical importance in competitive environments...
January 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28126738/discovery-and-characterisation-of-the-automethylation-properties-of-prdm9
#16
Xiaoying Koh-Stenta, Anders Poulsen, Rong Li, John Liang Kuan Wee, Perlyn Zekui Kwek, Sin Yin Chew, Jianhe Peng, Liling Wu, Ernesto Guccione, Joma Joy, Jeffrey Hill
We have previously characterised the histone lysine methyltransferase properties of PRDM9, a member of the PRDM family of putative transcriptional regulators. PRDM9 displays broad substrate recognition and methylates a range of histone substrates including octamers, core histone proteins, and peptides. In this study, we show that PRDM9 performs intramolecular automethylation on multiple lysine residues localised to a lysine-rich region on the post-SET domain. PRDM9 automethylation is abolished by a single active site mutation, C321P, also known to disrupt interactions with SAM...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28122367/enzymology-and-ultrastructure-of-the-in-situ-pellicle-in-caries-active-and-caries-inactive-patients
#17
Jasmin Kirsch, Christian Hannig, Sandra Pötschke, Sabine Basche, William H Bowen, Stefan Rupf, Simone Trautmann, Natalia Umanskaya, Matthias Hannig
AIM: The present study aimed to evaluate the impact of caries activity on the key enzymes and the ultrastructure of the in situ pellicle. METHODS: Pellicle formation was performed on bovine enamel slabs. Intraoral exposure (3, 30, and 120 min) was accomplished by 14 caries-active (DMFS: 22.7 ± 12.1) and 13 caries-inactive (DMFS: 1.5 ± 1.8) individuals. The enzyme activities (lysozyme, peroxidase, α-amylase, glycosyltransferase [GTF]) in the in situ pellicle and resting saliva of all participants were analyzed directly after oral exposure...
2017: Caries Research
https://www.readbyqxmd.com/read/28073471/biochemistry-and-genetics-of-taste-and-odor-producing-cyanobacteria
#18
REVIEW
Susan B Watson, Paul Monis, Peter Baker, Steven Giglio
Cyanobacteria are one of the principal sources of volatile organic compounds (VOCs) which cause offensive taste and odor (T&O) in drinking and recreational water, fish, shellfish and other seafood. Although non-toxic to humans, these T&O compounds severely undermine public trust in these commodities, resulting in substantial costs in treatment, and lost revenue to drinking water, aquaculture, food and beverage and tourist/hospitality industries. Mitigation and control have been hindered by the complexity of the communities and processes which produce and modify T&O events, making it difficult to source-track the major producer(s) and the factors governing VOC production and fate...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28065271/signal-peptidase-enzymology-and-substrate-specificity-profiling
#19
R E Dalbey, D Pei, Ö D Ekici
Signal peptidases are membrane proteases that play crucial roles in the protein transport pathway of bacteria. They cleave off the signal peptide from precursor proteins that are membrane inserted by the SecYEG or Tat translocons. Signal peptide cleavage releases the translocated protein from the inner membrane allowing the protein to be exported to the periplasm, outer membrane, or secreted into the medium. Signal peptidases are very important proteins to study. They are unique serine proteases with a Ser-Lys dyad, catalyze cleavage at the membrane surface, and are promising potential antibacterial drug targets...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28031352/phosphoribosyl-diphosphate-prpp-biosynthesis-enzymology-utilization-and-metabolic-significance
#20
REVIEW
Bjarne Hove-Jensen, Kasper R Andersen, Mogens Kilstrup, Jan Martinussen, Robert L Switzer, Martin Willemoës
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics...
March 2017: Microbiology and Molecular Biology Reviews: MMBR
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