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Enzymology

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https://www.readbyqxmd.com/read/28425708/revealing-multiple-pathways-in-t4-lysozyme-sub-step-conformational-motions-by-single-molecule-enzymology-and-modeling
#1
Maolin Lu, H Peter Lu
Enzyme conformational dynamics play crucial roles in catalytic functions. Obtaining molecular level insights into the conformational transition dynamics of enzyme-substrate complex from the inactive state to the active state is fundamental for understanding enzymatic function and dynamics. Here, we report our progress on the real-time conformational transition dynamics of T4 lysozyme under enzymatic reactions using single-molecule fluorescence resonance energy transfer. The time duration in forming the active enzyme-substrate complex state (ES*) show distinctive Poisson and Non-Poisson statistics, including exponential and non-exponential, convoluted Poisson distributions and Gaussian-like distributions...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28425208/nitrogenase-cofactor-inspiration-for-model-chemistry
#2
Ivana Djurdjevic, Oliver Einsle, Laure Decamps
The cofactor of nitrogenase is the largest and most intricate metal cluster known in nature. Its reactivity, mode of action and even the precise binding site of substrate remain a matter of debate. For decades, synthetic chemists have taken inspiration from the exceptional structural, electronic and catalytic features of the cofactor and have tried to either mimic the unique topology of the entire site, or to extract its functional principles and build them into novel catalysts that achieve the same - or very similar - astounding transformations...
April 20, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28411647/nanoarmored-enzymes-for-organic-enzymology-synthesis-and-characterization-of-poly-2-alkyloxazoline-enzyme-conjugates
#3
Melanie Leurs, Joerg C Tiller
The properties of enzymes can be altered significantly by modification with polymers. Numerous different methods are known to obtain such polymer-enzyme conjugates (PECs). However, there is no universal method to render enzymes into PECs that are fully soluble in organic solvents. Here, we present a method, which achieves such high degree of modification of proteins that the majority of modified enzymes will be soluble in organic solvents. This is achieved by preparing poly(2-alkyloxazoline)s (POx) with an NH2 end group and coupling this functional polymer via pyromellitic acid dianhydride onto the amino groups of the respective protein...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28394118/the-uncommon-enzymology-of-cis-acyltransferase-assembly-lines
#4
Adrian T Keatinge-Clay
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered...
April 10, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28389555/targeting-of-microbe-derived-metabolites-to-improve-human-health-the-next-frontier-for-drug-discovery
#5
J Mark Brown, Stanley L Hazen
Recent advances in metabolomic and genome mining approaches have uncovered a poorly understood metabolome that originates solely or in part from bacterial enzyme sources. Whether living on exposed surfaces or within our intestinal tract, our microbial inhabitants produce a remarkably diverse set of natural products and small molecule metabolites that can impact human health and disease. Highlighted here, the gut microbe-derived metabolite trimethylamine N-oxide (TMAO) has been causally linked to the development of cardiovascular diseases...
April 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28380376/sirt4-is-a-lysine-deacylase-that-controls-leucine-metabolism-and-insulin-secretion
#6
Kristin A Anderson, Frank K Huynh, Kelsey Fisher-Wellman, J Darren Stuart, Brett S Peterson, Jonathan D Douros, Gregory R Wagner, J Will Thompson, Andreas S Madsen, Michelle F Green, R Michael Sivley, Olga R Ilkayeva, Robert D Stevens, Donald S Backos, John A Capra, Christian A Olsen, Jonathan E Campbell, Deborah M Muoio, Paul A Grimsrud, Matthew D Hirschey
Sirtuins are NAD(+)-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine...
April 4, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28380256/investigation-of-the-mycobacterial-enzyme-hsad-as-a-potential-novel-target-for-anti-tubercular-agents-using-a-fragment-based-drug-design-approach
#7
Ali Ryan, Elena Polycarpou, Nathan A Lack, Dimitrios Evangelopoulos, Christian Sieg, Alice Halman, Sanjib Bhakta, Olga Eleftheriadou, Timothy D McHugh, Sebastian Keany, Edward D Lowe, Romain Ballet, Areej Abuhammad, William R Jacobs, Alessio Ciulli, Edith Sim
BACKGROUND AND PURPOSE: With the emergence of extensively drug-resistant tuberculosis there is a need for new anti-tubercular drugs that work through novel mechanisms of action. The meta cleavage product hydrolase, HsaD, has been demonstrated to be critical to the survival of Mycobacterium tuberculosis in macrophages and is encoded in an operon involved in cholesterol catabolism, which is identical in M. tuberculosis and M. bovis BCG. EXPERIMENTAL APPROACH: We generated a mutant strain of M...
April 5, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28377529/catabolism-of-the-last-two-steroid-rings-in-mycobacterium-tuberculosis-and-other-bacteria
#8
Adam M Crowe, Israël Casabon, Kirstin L Brown, Jie Liu, Jennifer Lian, Jason C Rogalski, Timothy E Hurst, Victor Snieckus, Leonard J Foster, Lindsay D Eltis
Most mycolic acid-containing actinobacteria and some proteobacteria use steroids as growth substrates, but the catabolism of the last two steroid rings has yet to be elucidated. In Mycobacterium tuberculosis, this pathway includes virulence determinants and has been proposed to be encoded by the KstR2-regulated genes, which include a predicted coenzyme A (CoA) transferase gene (ipdAB) and an acyl-CoA reductase gene (ipdC). In the presence of cholesterol, ΔipdC and ΔipdAB mutants of either M. tuberculosis or Rhodococcus jostii strain RHA1 accumulated previously undescribed metabolites: 3aα-H-4α(carboxyl-CoA)-5-hydroxy-7aβ-methylhexahydro-1-indanone (5-OH HIC-CoA) and (R)-2-(2-carboxyethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA), respectively...
April 4, 2017: MBio
https://www.readbyqxmd.com/read/28375734/high-dimensional-mutant-and-modular-thermodynamic-cycles-molecular-switching-and-free-energy-transduction
#9
Charles W Carter
Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion...
March 24, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28369120/fatty-acid-dsf-binds-and-allosterically-activates-histidine-kinase-rpfc-of-phytopathogenic-bacterium-xanthomonas-campestris-pv-campestris-to-regulate-quorum-sensing-and-virulence
#10
Zhen Cai, Zhi-Hui Yuan, Huan Zhang, Yue Pan, Yao Wu, Xiu-Qi Tian, Fang-Fang Wang, Li Wang, Wei Qian
As well as their importance to nutrition, fatty acids (FA) represent a unique group of quorum sensing chemicals that modulate the behavior of bacterial population in virulence. However, the way in which full-length, membrane-bound receptors biochemically detect FA remains unclear. Here, we provide genetic, enzymological and biophysical evidences to demonstrate that in the phytopathogenic bacterium Xanthomonas campestris pv. campestris, a medium-chain FA diffusible signal factor (DSF) binds directly to the N-terminal, 22 amino acid-length sensor region of a receptor histidine kinase (HK), RpfC...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28358347/the-enzymology-of-2-hydroxyglutarate-2-hydroxyglutaramate-and-2-hydroxysuccinamate-and-their-relationship-to-oncometabolites
#11
Vivek A Hariharan, Travis T Denton, Sarah Paraszcszak, Kyle McEvoy, Thomas M Jeitner, Boris F Krasnikov, Arthur J L Cooper
Many enzymes make "mistakes". Consequently, repair enzymes have evolved to correct these mistakes. For example, lactate dehydrogenase (LDH) and mitochondrial malate dehydrogenase (mMDH) slowly catalyze the reduction of 2-oxoglutarate (2-OG) to the oncometabolite l-2-hydroxyglutarate (l-2-HG). l-2-HG dehydrogenase corrects this error by converting l-2-HG to 2-OG. LDH also catalyzes the reduction of the oxo group of 2-oxoglutaramate (2-OGM; transamination product of l-glutamine). We show here that human glutamine synthetase (GS) catalyzes the amidation of the terminal carboxyl of both the l- and d- isomers of 2-HG...
March 30, 2017: Biology
https://www.readbyqxmd.com/read/28358161/post-translational-modifications-involved-in-the-biosynthesis-of-thiopeptide-antibiotics
#12
REVIEW
Qingfei Zheng, Hui Fang, Wen Liu
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins...
April 18, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28351529/analysis-of-the-regulation-of-surfactant-phosphatidylcholine-metabolism-using-stable-isotopes
#13
REVIEW
Joost Brandsma, Anthony D Postle
The pathways and mechanisms that regulate pulmonary surfactant synthesis, processing, secretion and catabolism have been extensively characterised using classical biochemical and analytical approaches. These have constructed a model, largely in experimental animals, for surfactant phospholipid metabolism in the alveolar epithelial cell whereby phospholipid synthesised on the endoplasmic reticulum is selectively transported to lamellar body storage vesicles, where it is subsequently processed before secretion into the alveolus...
March 25, 2017: Annals of Anatomy, Anatomischer Anzeiger: Official Organ of the Anatomische Gesellschaft
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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