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https://www.readbyqxmd.com/read/28640600/horse-liver-alcohol-dehydrogenase-zinc-coordination-and-catalysis
#1
Bryce V Plapp, Baskar Raj Savarimuthu, Daniel J Ferraro, Jon K Rubach, Eric N Brown, Subramanian Ramaswamy
: During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism may involve a pentacoordinated zinc or a double displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1 and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. Apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174 and a water molecule...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28634238/electron-transport-chain-is-biochemically-linked-to-pilus-assembly-required-for-polymicrobial-interactions-and-biofilm-formation-in-the-gram-positive-actinobacterium-actinomyces-oris
#2
Belkys C Sanchez, Chungyu Chang, Chenggang Wu, Bryan Tran, Hung Ton-That
The Gram-positive actinobacteria Actinomyces spp. are key colonizers in the development of oral biofilms due to the inherent ability of Actinomyces to adhere to receptor polysaccharides on the surface of oral streptococci and host cells. This receptor-dependent bacterial interaction, or coaggregation, requires a unique sortase-catalyzed pilus consisting of the pilus shaft FimA and the coaggregation factor CafA forming the pilus tip. While the essential role of the sortase machine SrtC2 in pilus assembly, biofilm formation, and coaggregation has been established, little is known about trans-acting factors contributing to these processes...
June 20, 2017: MBio
https://www.readbyqxmd.com/read/28631861/renewable-molecular-flasks-with-nadh-models-combination-of-light-driven-proton-reduction-and-biomimetic-hydrogenation-of-benzoxazinones
#3
Liang Zhao, Jianwei Wei, Junhua Lu, Cheng He, Chunying Duan
Using small molecules with defined pockets to catalyze chemical transformations resulted in attractive catalytic syntheses that echo the remarkable properties of enzymes. By modulating the active site of a nicotinamide adenine dinucleotide (NADH) model in a redox-active molecular flask, we combined biomimetic hydrogenation with in situ regeneration of the active site in a one-pot transformation using light as a clean energy source. This molecular flask facilitates the encapsulation of benzoxazinones for biomimetic hydrogenation of the substrates within the inner space of the flask using the active sites of the NADH models...
June 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28631845/mild-metabolic-perturbations-alter-succinylation-of-mitochondrial-proteins
#4
Huanlian Chen, Hui Xu, Samuel Potash, Anatoly Starkov, Vsevolod V Belousov, Dmitry S Bilan, Travis T Denton, Gary E Gibson
Succinylation of proteins is widespread, modifies both the charge and size of the molecules, and can alter their function. For example, liver mitochondrial proteins have 1,190 unique succinylation sites representing multiple metabolic pathways. Succinylation is sensitive to both increases and decreases of the NAD(+) -dependent desuccinylase, SIRT5. Although the succinyl group for succinylation is derived from metabolism, the effects of systematic variation of metabolism on mitochondrial succinylation are not known...
June 20, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28631380/a-highly-sensitive-enzymatic-catalysis-system-for-trace-detection-of-arsenic-in-water
#5
Yuanli Liu, Chuanbai Yu, Zhixin Cao, Daniel Shvarts, William C Trogler
Arsenic (As) is an extremely toxic element that exists in the environment in different chemical forms. The detection of arsenic in potable water remains a challenging task. This study presents a highly sensitive enzymatic catalysis system for trace sensing of inorganic arsenic in water. This is the first enzyme-catalyzed fluorescence assay capable of detecting arsenic at concentrations below the allowable level adopted by the World Health Organization (10 ppb in drinking water). The enzyme catalytically produces fluorescent NADH in the presence of arsenate, which enables facile detection of arsenate at concentrations in the 0 - 200 ppb range...
June 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28630648/comparative-metabolic-profiling-of-the-lipid-producing-green-microalga-chlorella-reveals-that-nitrogen-and-carbon-metabolic-pathways-contribute-to-lipid-metabolism
#6
Hui Chen, Yanli Zheng, Jiao Zhan, Chenliu He, Qiang Wang
Microalgae are a promising feedstock for biofuel production. Microalgal metabolic pathways are heavily influenced by environmental factors. For instance, lipid metabolism can be induced by nitrogen-limiting conditions. However, the underlying mechanisms of lipid biosynthesis are unclear. In this study, we analyzed the global metabolic profiles of three genetically closely related Chlorella strains (C1, C2, and C3) with significant differences in lipid productivity to identify the contributions of key metabolic pathways to lipid metabolism...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28630487/multicolor-two-photon-imaging-of-endogenous-fluorophores-in-living-tissues-by-wavelength-mixing
#7
Chiara Stringari, Lamiae Abdeladim, Guy Malkinson, Pierre Mahou, Xavier Solinas, Isabelle Lamarre, Sébastien Brizion, Jean-Baptiste Galey, Willy Supatto, Renaud Legouis, Ana-Maria Pena, Emmanuel Beaurepaire
Two-photon imaging of endogenous fluorescence can provide physiological and metabolic information from intact tissues. However, simultaneous imaging of multiple intrinsic fluorophores, such as nicotinamide adenine dinucleotide(phosphate) (NAD(P)H), flavin adenine dinucleotide (FAD) and retinoids in living systems is generally hampered by sequential multi-wavelength excitation resulting in motion artifacts. Here, we report on efficient and simultaneous multicolor two-photon excitation of endogenous fluorophores with absorption spectra spanning the 750-1040 nm range, using wavelength mixing...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630126/a-key-enzyme-of-the-nad-salvage-pathway-in-thermus-thermophilus-characterization-of-nicotinamidase-and-the-impact-of-its-gene-deletion-at-high-temperatures
#8
Hironori Taniguchi, Sathidaphorn Sungwallek, Phatcharin Chotchuang, Kenji Okano, Kohsuke Honda
Nicotinamide adenine dinucleotide (NAD(+)) is a cofactor related to many cellular processes. This cofactor is known to be unstable, especially at high temperatures, where it chemically decomposes to nicotinamide and ADP-ribose. Bacteria, yeast, and higher organisms possess the salvage pathway for reconstructing NAD(+) from these decomposition products; however, the importance of the salvage pathway for survival is not well elucidated, except for in pathogens lacking the NAD(+)de novo synthesis pathway. Herein, we report the importance of the NAD(+) salvage pathway in the thermophilic bacterium Thermus thermophilus HB8 at high temperatures...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28629859/s-adenosyl-l-homocysteine-hydrolase-from-a-hyperthermophile-thermotoga-maritima-is-expressed-in-escherichia-coli-in-inactive-form-biochemical-and-structural-studies
#9
Krzysztof Brzezinski, Justyna Czyrko, Joanna Sliwiak, Edyta Nalewajko-Sieliwoniuk, Mariusz Jaskolski, Boguslaw Nocek, Zbigniew Dauter
Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity...
June 16, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28629697/increase-in-furfural-tolerance-by-combinatorial-overexpression-of-nad-salvage-pathway-enzymes-in-engineered-isobutanol-producing-e-coli
#10
Hun-Suk Song, Jong-Min Jeon, Hyun-Joong Kim, Shashi Kant Bhatia, Ganesan Sathiyanarayanan, Junyoung Kim, Ju Won Hong, Yoon Gi Hong, Kwon Young Choi, Yun-Gon Kim, Wooseong Kim, Yung-Hun Yang
To reduce the furfural toxicity for biochemical production in E. coli, a new strategy was successfully applied by supplying NAD(P)H through the nicotine amide salvage pathway. To alleviate the toxicity, nicotinamide salvage pathway genes were overexpressed in recombinant, isobutanol-producing E. coli. Gene expression of pncB and nadE respectively showed increased tolerance to furfural among these pathways. The combined expression of pncB and nadE was the most effective in increasing the tolerance of the cells to toxic aldehydes...
June 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28625912/isolation-of-recombinant-human-untagged-glyceraldehyde-3-phosphate-dehydrogenase-from-e-coli-producer-strain
#11
K V Barinova, M A Eldarov, E V Khomyakova, V I Muronetz, E V Schmalhausen
The goal of the present work was expression of human glyceraldehyde-3-phosphate dehydrogenase (hGAPDH) without additional tag constructions in E. coli cells and elaboration of the procedure for purification of untagged hGAPDH from the extract of the producer cells. We present a simple method for purification of untagged hGAPDH including ammonium sulfate fractionation and gel filtration on a G-100 Sephadex column. The method allows isolation of 2 mg of pure hGAPDH from 600 ml of cell culture (7 g of the cell biomass)...
June 15, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28625911/white-shrimp-litopenaeus-vannamei-recombinant-lactate-dehydrogenase-biochemical-and-kinetic-characterization
#12
Ambar A Fregoso-Peñuñuri, Elisa M Valenzuela-Soto, Ciria G Figueroa-Soto, Alma B Peregrino-Uriarte, Manuel Ochoa-Valdez, Lilia Leyva-Carrillo, Gloria Yepiz-Plascencia
Shrimp lactate dehydrogenase (LDH) is induced in response to environmental hypoxia. Two protein subunits deduced from different transcripts of the LDH gene from the shrimp Litopenaeus vannamei (LDHvan-1 and LDHvan-2) were identified. These subunits are expressed by alternative splicing. Since both subunits are expressed in most tissues, the purification of the enzyme from the shrimp will likely produce hetero LDH containing both subunits. Therefore, the aim of this study was to overexpress, purify and characterize only one subunit as a recombinant protein, the LDHvan-2...
June 15, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28622642/highly-sensitive-electrochemical-thrombin-aptasensor-based-on-peptide-enhanced-electrocatalysis-of-hemin-g-quadruplex-and-nanocomposite-as-nanocarrier
#13
Yongmei Wu, Lina Zou, Sheng Lei, Qian Yu, Baoxian Ye
In this work, we first conjugated a short peptide to thrombin binding aptamer (TBA) and bond hemin to the hybrid, effectively rendering hemin/G4-peptide more active over the original hemin/G4, so that a highly sensitive electrochemical thrombin (TB) aptasensor was developed based on it and PtNTs@rGO nanocomposite. It was the first report on the application of hemin/G4-peptide in electrochemical aptasensor. PtNTs@rGO with large surface area served as excellent nanocarrier for high loading of hemin/G4-peptide hybrids, resulting in the formation of hemin/G4-peptide-PtNTs@rGO bioconjugate as the secondary aptamer and further signal enhancement...
June 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28621940/on-the-solvation-and-proton-coupled-electron-transfer-reduction-potential-of-2-no-%C3%A2-to-1-hno-in-aqueous-solution-a-theoretical-investigation
#14
Mateus F Venancio, Fabio Doctorovich, Willian Ricardo Rocha
In this work quantum mechanical calculations and Monte Carlo statistical mechanical simulations were carried out to investigate the solvation properties of HNO in aqueous solution and to evaluate the proton coupled one electron reduction potential of 2NO to 1HNO, which are essential missing information to understand the fate of 2NO in the biological medium. Our results showed that the 1HNO molecule acts mainly as hydrogen bond donor in aqueous solution with an average energy of -5.5  1.3 kcal/mol. The solvation free energy of 1HNO in aqueous solution, computed using three approaches based on the Liner Response Theory revealed that the current prediction of the hydration free energy of HNO is, at least, two times underestimated...
June 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28621879/bactericidal-peptidoglycan-recognition-protein-induces-oxidative-stress-in-escherichia-coli-through-a-block-in-respiratory-chain-and-increase-in-central-carbon-catabolism
#15
Des R Kashyap, Marcin Kuzma, Dominik A Kowalczyk, Dipika Gupta, Roman Dziarski
Mammalian Peptidoglycan Recognition Proteins (PGRPs) kill both Gram-positive and Gram-negative bacteria through simultaneous induction of oxidative, thiol, and metal stress responses in bacteria. However, metabolic pathways through which PGRPs induce these bactericidal stress responses are unknown. We screened Keio collection of Escherichia coli deletion mutants and revealed that deleting genes for respiratory chain flavoproteins or for tricarboxylic acid (TCA) cycle resulted in increased resistance of E. coli to PGRP killing...
June 16, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28621566/glutamate-dehydrogenase-is-essential-to-sustain-neuronal-oxidative-energy-metabolism-during-stimulation
#16
Michaela C Hohnholt, Vibe H Andersen, Jens V Andersen, Sofie K Christensen, Melis Karaca, Pierre Maechler, Helle S Waagepetersen
The enzyme glutamate dehydrogenase (GDH; Glud1) catalyzes the (reversible) oxidative deamination of glutamate to α-ketoglutarate accompanied by a reduction of NAD(+) to NADH. GDH connects amino acid, carbohydrate, neurotransmitter and oxidative energy metabolism. Glutamine is a neurotransmitter precursor used by neurons to sustain the pool of glutamate, but glutamine is also vividly oxidized for support of energy metabolism. This study investigates the role of GDH in neuronal metabolism by employing the Cns- Glud1(-/-) mouse, lacking GDH in the brain (GDH KO) and metabolic mapping using (13)C-labelled glutamine and glucose...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28619386/a-novel-17%C3%AE-hydroxysteroid-dehydrogenase-in-rhodococcus-sp-p14-for-transforming-17%C3%AE-estradiol-to-estrone
#17
Xueying Ye, Hui Wang, Jie Kan, Jin Li, Tongwang Huang, Guangming Xiong, Zhong Hu
17β-hydroxysteroid dehydrogenases (17β-HSD) are a group of oxidoreductase enzymes that exhibit high specificity for 17C reduction/oxidation. However, the mechanism of 17β-HSD in oxidizing steroid hormone 17β-estradiol to estrone in bacterium is still unclear. In this work, a functional bacterium Rhodococcus sp. P14 was identified having rapid ability to oxidize estradiol into estrone in mineral salt medium (MSM) within 6 h. The functional genes encoding NADH-dependent oxidoreductase were successfully detected with the help of bioinformatics, and it was identified that it contained two consensus regions affiliated to the short-chain dehydrogenase/reductase (SDR) superfamily...
June 12, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28617502/bioelectrocatalytic-nad-nadh-inter-conversion-transformation-of-an-enzymatic-fuel-cell-into-an-enzymatic-redox-flow-battery
#18
Timothy Quah, Ross D Milton, Sofiene Abdellaoui, Shelley D Minteer
Diaphorase and a benzylpropylviologen redox polymer were combined to create a bioelectrode that can both oxidize NADH and reduce NAD(+). We demonstrate how bioelectrocatalytic NAD(+)/NADH inter-conversion can transform a glucose/O2 enzymatic fuel cell (EFC) with an open circuit potential (OCP) of 1.1 V into an enzymatic redox flow battery (ERFB), which can be rapidly recharged by operation as an EFC.
June 15, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28615457/deconvoluting-amp-dependent-kinase-ampk-adenine-nucleotide-binding-and-sensing
#19
Xin Gu, Yan Yan, Scott J Novick, Amanda Kovich, Devrishi Goswami, Jiyuan Ke, M H Eileen Tan, Lili Wang, Xiaodan Li, Parker de Waal, Martin R Webb, Patrick R Griffin, H Eric Xu, Karsten Melcher
AMP-activated protein kinase (AMPK) is a central cellular energy sensor that adapts metabolism and growth to the energy state of the cell. AMPK senses the ratio of adenine nucleotides (adenylate energy charge) by competitive binding of AMP, ADP, and ATP to three sites (CBS1, CBS3, and CBS4) in its γ-subunit. Since these three binding sites are functionally interconnected, it remains unclear how nucleotides bind to individual sites, which nucleotides occupy each site under physiological conditions, and how binding to one site affects binding to the other sites...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28615449/equilibrium-and-ultrafast-kinetic-studies-manipulating-electron-transfer-a-short-lived-flavin-semiquinone-is-not-sufficient-for-electron-bifurcation
#20
John P Hoben, Carolyn E Lubner, Michael W Ratzloff, Gerrit J Schut, Diep M N Nguyen, Karl W Hempel, Michael W W Adams, Paul W King, Anne-Frances Miller
Flavin-based electron transfer bifurcation is emerging as a fundamental and powerful mechanism for conservation and deployment of electrochemical energy in enzymatic systems. In this process, a pair of electrons is acquired at intermediate reduction potential (i.e. intermediate reducing power) and each electron is passed to a different acceptor, one with lower and the other with higher reducing power, leading to 'bifurcation'. It is believed that a strongly reducing semiquinone species is essential for this process, and it is expected that this species should be kinetically short-lived...
June 14, 2017: Journal of Biological Chemistry
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