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Enzyme kinetics

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https://www.readbyqxmd.com/read/29334428/development-of-potent-inhibitors-of-the-mycobacterium-tuberculosis-virulence-factor-zmp1-and-evaluation-of-their-effect-on-mycobacterial-survival-inside-macrophages
#1
Marco Paolino, Margherita Brindisi, Alessandra Vallone, Stefania Butini, Giusepp Campiani, Chiara Nannicini, Germano Giuliani, Maurizio Anzini, Stefania Lamponi, Gianluca Giorgi, Diego Sbardella, Davide M Ferraris, Stefano Marini, Massimo Coletta, Ivana Palucci, Mariachiara Minerva, Giovanni Delogu, Ilaria Pepponi, Delia Goletti, Andrea Cappelli, Sandra Gemma, Simone Brogi
The enzyme Zmp1 is a zinc-peptidase having a critical role in M. tuberculosis pathogenicity. Here we describe the identification of a small set of Zmp1 inhibitors based on a novel 8-hydroxyquinoline-2-hydroxamate scaffold. Among the synthesized compounds, 1c was the most potent Zmp1 inhibitor known to date, and its binding mode was analysed both through kinetic studies and molecular modelling, identifying critical interactions of 1c with the zinc-ion and residues in the active site. Effect of 1c on intracellular Mycobacterium survival was assayed in J774 murine macrophages infected with M...
January 15, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29332979/standardized-maximim-d-optimal-designs-for-enzyme-kinetic-inhibition-models
#2
Ping-Yang Chen, Ray-Bing Chen, Heng-Chin Tung, Weng Kee Wong
Locally optimal designs for nonlinear models require a single set of nominal values for the unknown parameters. An alternative is the maximin approach that allows the user to specify a range of values for each parameter of interest. However, the maximin approach is difficult because we first have to determine the locally optimal design for each set of nominal values before maximin types of optimal designs can be found via a nested optimization process. We show that particle swarm optimization (PSO) techniques can solve such complex optimization problems effectively...
October 15, 2017: Chemometrics and Intelligent Laboratory Systems
https://www.readbyqxmd.com/read/29332816/comparative-enzymatic-studies-using-ion-selective-electrodes-the-case-of-cholinesterases
#3
Maria Cuartero, Soraya Pérez, Maria S García, Francisco García-Cánovas, Joaquín A Ortuño
The application of traditional ion-selective electrodes for comparative enzymatic analysis was demonstrated for the first time in this study. A kinetic-potentiometric method based on the monitoring of the concentration of the ionic substrate involved in the enzymatic reaction catalyzed by different cholinesterases is used for this purpose. A comparative study was performed comprising both enzymatic assays using different ionic substrates and the corresponding inhibited reactions in presence of neostigmine (a synthetic anticholinesterase)...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29332049/free-heme-and-amyloid-%C3%AE-a-fatal-liaison-in-alzheimer-s-disease
#4
Elisabeth Chiziane, Henriette Telemann, Martin Krueger, Juliane Adler, Jürgen Arnhold, A Alia, Jörg Flemmig
While the etiology of Alzheimer's disease (AD) is still unknown, an increased formation of amyloid-β (Aβ) peptide and oxidative processes are major pathological mechanism of the disease. The interaction of Aβ with free heme leads to the formation of peroxidase-active Aβ-heme complexes. However, enzyme-kinetic data and systematic mutational studies are still missing. These aspects were addressed in this study to evaluate the role of Aβ-heme complexes in AD. The enzyme-kinetic measurements showed peroxidase-specific pH- and H2O2-dependencies...
2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29331521/increased-transcript-levels-and-kinetic-function-of-pyruvate-kinase-during-severe-dehydration-in-aestivating-african-clawed-frogs-xenopus-laevis
#5
Neal J Dawson, Yulia Biggar, Amal I Malik, Kenneth B Storey
The African clawed frog, Xenopus laevis, can withstand extremely arid conditions through aestivation, resulting in dehydration and urea accumulation. Aestivating X. laevis reduce their metabolic rate, and rely on anaerobic glycolysis to meet reduced ATP demands. The present study investigated how severe dehydration affected the transcript levels, kinetic profile, and phosphorylation state of the key glycolytic enzyme pyruvate kinase (PK) in the liver and skeletal muscle of X. laevis. Compared to control frogs, severely dehydrated frogs showed an increase in the transcript abundance of both liver and muscle isoforms of PK...
January 10, 2018: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29330906/generating-retinoic-acid-gradients-by-local-degradation-during-craniofacial-development-one-cell-s-cue-is-another-cell-s-poison
#6
REVIEW
Aditi Dubey, Rebecca E Rose, Drew R Jones, Jean-Pierre Saint-Jeannet
Retinoic acid (RA) is a vital morphogen for early patterning and organogenesis in the developing embryo. RA is a diffusible, lipophilic molecule that signals via nuclear RA receptor heterodimeric units that regulate gene expression by interacting with RA response elements in promoters of a significant number of genes. For precise RA signaling, a robust gradient of the morphogen is required. The developing embryo contains regions that produce RA, and specific intracellular concentrations of RA are created through local degradation mediated by Cyp26 enzymes...
January 13, 2018: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/29330786/kinetic-analysis-of-hif-prolyl-hydroxylases
#7
Peppi Koivunen, Johanna Myllyharju
Kinetic analyses of HIF prolyl 4-hydroxylases (HIF-P4Hs) allow determination of substrate, cosubstrate and cofactor requirements, analysis of the reaction rate, and inhibitory properties of the isoenzymes in vitro. Here we describe an assay measuring the substrate hydroxylation-coupled decarboxylation of radioactive 2-oxoglutarate to radioactive carbon dioxide as a fast, efficient, and diverse method to analyze the enzyme kinetics of HIF-P4Hs.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29329854/enzymatic-preparation-of-functional-oil-rich-in-feruloylated-structured-lipids-with-solvent-free-ultrasound-pretreatment
#8
Haiping Zhang, Mingming Zheng, Jie Shi, Hu Tang, Qianchun Deng, Fenghong Huang, Dan Luo
In this study, a series of functional oils rich in feruloylated structured lipids (FSLs) was prepared by enzymatic transesterification of ethyl ferulate (EF) with triglycerides under ultrasound pretreatment. A conversion of more than 92.7% and controllable FSLs (3.1%-26.3%) can be obtained under the following conditions: 16% enzyme, substrate ratio 1:5 (oil/EF, mol/mol), 85 °C, ultrasound 1 h, pulse mode 3 s/3s (working/waiting), and 17.0 W/mL. Compared to conventional mechanical stirring, the activation energy decreased from 50...
May 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29329804/a-rapid-and-sensitive-fluorometric-method-for-determination-of-aldehyde-oxidase-activity
#9
Nancy Apenova, Hui Peng, Markus Hecker, Markus Brinkmann
Previous research has characterized the important role of aldehyde oxidases (AOX) in biotransformation of N-heterocyclic therapeutic drugs and environmental contaminants in mammals. Research pertaining to AOX activity in non-mammalian vertebrates, however, is scarce, despite its biological role as a potentially important metabolic pathway for xenobiotics. One of the limiting factors of research on AOX is that available photometric methods are relatively insensitive, limited in throughput, and prone to cross-reactivity from other enzymes...
January 9, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29327812/hyper-acetylation-contributes-to-the-sensitivity-of-chemo-resistant-prostate-cancer-cells-to-histone-deacetylase-inhibitor-trichostatin-a
#10
Qingqing Xu, Xiaofei Liu, Shiqin Zhu, Xuelei Hu, Huanmin Niu, Xiulei Zhang, Deyu Zhu, Effat Un Nesa, Keli Tian, Huiqing Yuan
Therapeutic agents are urgently needed for treating metastatic castration-refractory prostate cancer (mCRPC) that is unresponsive to androgen deprivation and chemotherapy. Our screening assays demonstrated that chemotherapy-resistant prostate cancer (PCa) cells are more sensitive to HDAC inhibitors than paired sensitive PCa cells, as demonstrated by cell proliferation and apoptosis in vitro and in vivo. Kinetic study revealed that TSA-induced apoptosis was significantly dependent on enhanced transcription and protein synthesis in an early stage, which subsequently caused ER stress and apoptosis...
January 12, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29324781/neuraminidase-inhibitor-susceptibility-and-neuraminidase-enzyme-kinetics-of-human-influenza-a-and-b-viruses-circulating-in-thailand-in-2010-2015
#11
Nipaporn Tewawong, Bindumadhav M Marathe, Yong Poovorawan, Sompong Vongpunsawad, Richard J Webby, Elena A Govorkova
Amino acid substitutions within or near the active site of the viral neuraminidase (NA) may affect influenza virus fitness. In influenza A(H3N2) and B viruses circulating in Thailand between 2010 and 2015, we identified several NA substitutions that were previously reported to be associated with reduced inhibition by NA inhibitors (NAIs). To study the effect of these substitutions on the enzymatic properties of NA and on virus characteristics, we generated recombinant influenza viruses possessing either a wild type (WT) NA or an NA with a single I222V, S331G, or S331R substitution [in influenza A(H3N2) viruses] or a single D342S, A395T, A395V, or A395D NA substitution (in influenza B viruses)...
2018: PloS One
https://www.readbyqxmd.com/read/29324352/administration-of-exercise-conditioned-plasma-alters-muscle-catalase-kinetics-in-rat-an-argument-for-in-vivo-like-km-instead-of-in-vitro-like-vmax
#12
Aristidis S Veskoukis, Vassilis Paschalis, Antonios Kyparos, Michalis G Nikolaidis
Maximal velocity (Vmax) is a well established biomarker for the assessment of tissue redox status. There is scarce evidence, though, that it does not probably reflect sufficiently in vivo tissue redox profile. Instead, the Michaelis constant (Km) could more adequately image tissue oxidative stress and, thus, be a more physiologically relevant redox biomarker. Therefore, the aim of the present study was to side-by-side compare Vmax and Km of an antioxidant enzyme after implementing an in vivo set up that induces alterations in tissue redox status...
January 3, 2018: Redox Biology
https://www.readbyqxmd.com/read/29324350/formation-of-phosphatidylethanol-from-endogenous-phosphatidylcholines-in-animal-tissues-from-pig-calf-and-goat
#13
Marc Luginbühl, Sytske Willem, Stefan Schürch, Wolfgang Weinmann
In the presence of alcohol, phosphatidylcholine (PC) is transformed to the direct alcohol biomarker phosphatidylethanol (PEth). This reaction is catalyzed by the enzyme phospholipase D (PLD) and dependent on substrate availability. As recent methods have solely focused on the determination of PEth, information about the PC composition was generally missing. To address this issue and monitor PC (16:0/18:1 and 16:0/18:2) and PEth (16:0/18:1 and 16:0/18:2) simultaneously, a reversed phase LC-MS/MS method based on a C8 core-shell column, coupled to a Sciex 5500 QTrap instrument was developed...
December 24, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29323490/activity-related-microsecond-dynamics-revealed-by-temperature-jump-f%C3%A3-rster-resonance-energy-transfer-measurements-on-thermophilic-alcohol-dehydrogenase
#14
Morgan B Vaughn, Jianyu Zhang, Thomas G Spiro, R Brian Dyer, Judith P Klinman
Previous studies of a thermophilic alcohol dehydrogenase (ht-ADH) demonstrated a range of discontinuous transitions at 30 °C that include catalysis, kinetic isotope effects, protein hydrogen-deuterium exchange rates, and intrinsic fluorescence properties. Using the Förster resonance energy transfer response from a Trp-NADH donor-acceptor pair in T-jump studies of ht-ADH, we now report microsecond protein motions that can be directly related to active site chemistry. Two distinctive transients are observed: a slow, kinetic process lacking a temperature break, together with a faster transient that is only detectable above 30 °C...
January 11, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29322601/temperature-sensitivities-of-extracellular-enzyme-vmax-and-km-across-thermal-environments
#15
Steven D Allison, Adriana L Romero-Olivares, Ying Lu, John W Taylor, Kathleen K Treseder
The magnitude and direction of carbon cycle feedbacks under climate warming remain uncertain due to insufficient knowledge about the temperature sensitivities of soil microbial processes. Enzymatic rates could increase at higher temperatures, but this response could change over time if soil microbes adapt to warming. We used the Arrhenius relationship, biochemical transition state theory, and thermal physiology theory to predict the responses of extracellular enzyme Vmax and Km to temperature. Based on these concepts, we hypothesized that Vmax and Km would correlate positively with each other and show positive temperature sensitivities...
January 11, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29320733/dna-unwinding-is-the-primary-determinant-of-crispr-cas9-activity
#16
Shanzhong Gong, Helen Hong Yu, Kenneth A Johnson, David W Taylor
Bacterial adaptive immunity utilizes RNA-guided surveillance complexes comprising Cas proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single-guide RNA that base pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and the RuvC nuclease domains cleave opposing strands. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge...
January 9, 2018: Cell Reports
https://www.readbyqxmd.com/read/29320490/the-glutamine-synthetase-of-trypanosoma-cruzi-is-required-for-its-resistance-to-ammonium-accumulation-and-evasion-of-the-parasitophorous-vacuole-during-host-cell-infection
#17
Marcell Crispim, Flávia Silva Damasceno, Agustín Hernández, María Julia Barisón, Ismael Pretto Sauter, Raphael Souza Pavani, Alexandre Santos Moura, Elizabeth Mieko Furusho Pral, Mauro Cortez, Maria Carolina Elias, Ariel Mariano Silber
Trypanosoma cruzi, the etiological agent of Chagas disease, consumes glucose and amino acids depending on the environmental availability of each nutrient during its complex life cycle. For example, amino acids are the major energy and carbon sources in the intracellular stages of the T. cruzi parasite, but their consumption produces an accumulation of NH4+ in the environment, which is toxic. These parasites do not have a functional urea cycle to secrete excess nitrogen as low-toxicity waste. Glutamine synthetase (GS) plays a central role in regulating the carbon/nitrogen balance in the metabolism of most living organisms...
January 10, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29320163/reaction-intermediates-of-nitric-oxide-synthase-from-deinococcus-radiodurans-as-revealed-by-pulse-radiolysis-evidence-for-intramo-lecular-electron-transfer-from-biopterin-to-feii-o2-complex
#18
Yuko Tsutsui, Kazuo Kobayashi, Fusako Takeuchi, Motonari Tsubaki, Takahiro Kozawa
Nitric oxide synthase (NOS) is a cytochrome P450-type mono-oxygenase that catalyzes the oxidation of L-arginine (Arg) to nitric oxide (NO) through a reaction intermediate N-hydroxy-L-arginine (NHA). The mechanism underlying the reaction catalyzed by NOS from Deinococcus radiodurans was investigated using pulse radiolysis. Radiolytically-generated hydrated electrons reduced the heme iron of NOS within 2 μs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediated with a second-order rate constant of 2...
January 10, 2018: Biochemistry
https://www.readbyqxmd.com/read/29318252/spatial-requirement-for-pamo-for-transformation-of-non-native-linear-substrates
#19
Alexandra T P Carvalho, Daniel F A R Dourado, Timofey Skvortsov, Miguel de Abreu, Lyndsey J Ferguson, Derek J Quinn, Thomas S Moody, Meilan Huang
Phenylacetone monooxygenase is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenases family, and therefore it is an ideal candidate for the synthesis of industrially relevant ester or lactone compounds. However, its limited substrate scope has largely limited its industrial applications. Linear substrates are interesting from an industrial point of view, it is thus necessary to identify the essential spatial requirement for achieving high conversions for non-native linear substrates...
January 10, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29317499/the-oligomerization-state-of-bacterial-enzyme-i-ei-determines-ei-s-allosteric-stimulation-or-competitive-inhibition-by-%C3%AE-ketoglutarate
#20
Trang Truc Nguyen, Rodolfo Ghirlando, Vincenzo Venditti
The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by phosphorylation of enzyme I (EI) by phosphoenolpyruvate (PEP). The EI phosphorylation state determines the phosphorylation states of all other PTS components and is thought to play a central role in the regulation of several metabolic pathways and to control the biology of bacterial cells at multiple levels, for example, affecting virulence and biofilm formation...
January 9, 2018: Journal of Biological Chemistry
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