keyword
MENU ▼
Read by QxMD icon Read
search

Enzyme kinetics

keyword
https://www.readbyqxmd.com/read/28453854/the-dynamics-of-the-monomeric-restriction-endonuclease-bcni-during-its-interaction-with-dna
#1
Georgij Kostiuk, Jasmina Dikic, Friedrich W Schwarz, Giedrius Sasnauskas, Ralf Seidel, Virginijus Siksnys
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, '/' designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449002/purification-and-biochemical-and-kinetic-properties-of-an-endo-polygalacturonase-from-the-industrial-fungus-aspergillus-sojae
#2
Dante Fratebianchi, Ivana Alejandra Cavello, Sebastián Fernando Cavalitto
An endo-polygalacturonase secreted by Aspergillus sojae was characterized after being purified to homogeneity from submerged cultures with orange peel as the sole carbon source by gel filtration and ion-exchange chromatographies. According to SDS-PAGE and analytical isoelectric focusing analyses, the enzyme presents a molecular weight of 47 kDa and pI value of 4.2. This enzyme exhibits considerable stability under highly acidic to neutral conditions (pH 1.5-6.5) and presents a half-life of 2 h at 50°C. Besides its activity towards pectin and polygalacturonic acid, the enzyme displays pectin-releasing activity, acting best in a pH range of 3...
April 28, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28447456/numerical-modeling-of-electroosmotic-push-pull-perfusion-and-assessment-of-its-application-to-quantitative-determination-of-enzymatic-activity-in-the-extracellular-space-of-mammalian-tissue
#3
Yangguang Ou, Stephen G Weber
Many sampling methods have been developed to measure the extracellular concentrations of solutes in the extracellular space of mammalian tissue. However, few have been used to quantitatively study the various processes, such as enzymatic degradation, that determines the fate of these solutes. For a method to be useful in this pursuit, it must be able to 1) perfuse tissue and collect the perfusate for quantitative analysis of the solutes introduced and reaction products produced, 2) control the average residence time of the active solutes, and 3) have the appropriate spatial resolution for the process of interest...
April 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28446878/computational-model-predicts-the-effects-of-targeting-cellular-metabolism-in-pancreatic-cancer
#4
Mahua Roy, Stacey D Finley
Reprogramming of energy metabolism is a hallmark of cancer that enables the cancer cells to meet the increased energetic requirements due to uncontrolled proliferation. One prominent example is pancreatic ductal adenocarcinoma, an aggressive form of cancer with an overall 5-year survival rate of 5%. The reprogramming mechanism in pancreatic cancer involves deregulated uptake of glucose and glutamine and other opportunistic modes of satisfying energetic demands in a hypoxic and nutrient-poor environment. In the current study, we apply systems biology approaches to enable a better understanding of the dynamics of the distinct metabolic alterations in KRAS-mediated pancreatic cancer, with the goal of impeding early cell proliferation by identifying the optimal metabolic enzymes to target...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28445754/probing-the-dynamics-of-clot-bound-thrombin-at-venous-shear-rates
#5
Laura M Haynes, Thomas Orfeo, Kenneth G Mann, Stephen J Everse, Kathleen E Brummel-Ziedins
In closed system models of fibrin formation, exosite-mediated thrombin binding to fibrin contributes to clot stability and is resistant to inhibition by antithrombin/heparin while still susceptible to small, active-site inhibitors. Each molecule of fibrin can bind ∼1.6 thrombin molecules at low-affinity binding sites (Kd = 2.8 μM) and ∼0.3 molecules of thrombin at high-affinity binding sites (Kd = 0.15 μM). The goal of this study is to assess the stability of fibrin-bound thrombin under venous flow conditions and to determine both its accessibility and susceptibility to inhibition...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445031/importance-of-loop-l1-dynamics-for-substrate-capture-and-catalysis-in-pseudomonas-aeruginosa-d-arginine-dehydrogenase
#6
Daniel Ouedraogo, Michael Souffrant, Sheena Vasquez, Donald Hamelberg, Giovanni Gadda
Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control substrate access to the active site, and to position residues for substrate binding and catalysis. In D-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations of loop L1 on the catalytic function of the enzyme...
April 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28443723/glucuronidation-of-icaritin-by-human-liver-microsomes-human-intestine-microsomes-and-expressed-udp-glucuronosyltransferase-enzymes-identification-of-ugt1a3-1a9-and-2b7-as-the-main-contributing-enzymes
#7
Li Wang, Xiaodan Hong, Zhihong Yao, Yi Dai, Guoping Zhao, Zifei Qin, Baojian Wu, Frank J Gonzalez, Xinsheng Yao
1. Icaritin is a natural flavonoid with anti-osteoporosis activity. This study aimed to characterize icaritin glucuronidation by pooled human liver microsomes (HLM) and pooled human intestine microsomes (HIM), and to determine the contribution of individual UDP-glucuronosyltrans-ferase (UGT) enzyme to icaritin glucuronidation. 2. Glucuronidation rates were determined by incubating icaritin with uridine diphosphate glucuronic acid (UDPGA)-supplemented microsomes. Kinetic parameters were derived by appropriate model fitting...
April 26, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/28442331/non-covalent-conjugation-of-cutinase-from-fusarium-sp-ict-sac1-with-pectin-for-enhanced-stability-process-minutiae-kinetics-thermodynamics-and-structural-study
#8
Abhijeet B Muley, Sandeep A Chaudhari, Rekha S Singhal
Cutinase, a member of α/β-fold hydrolase family possess potentially diverse applications in several industrial processes and products. The present work aims towards thermo-stabilization of cutinase from novel source Fusarium sp. ICT SAC1 via non-covalent interaction with polysaccharides. Although all six polysaccharides chosen for study enhanced the thermal stability, pectin was found to be most promising. The interaction protocol for cutinase with pectin was optimized sequentially with respect to the ratio of enzyme to pectin, solution pH, and buffer strength...
April 22, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28442060/kinetic-effect-of-oestrogen-on-secretion-of-prostaglandins-e2-and-f2%C3%AE-in-bovine-oviduct-epithelial-cells
#9
Zhiheng Dong, Nan Zhang, Wei Mao, Bo Liu, Na Huang, Peifeng Li, Changyou Li, Jinshan Cao
This study aimed to investigate the effect of oestrogen on prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) secretion in bovine oviduct epithelial cells. Bovine oviduct epithelial cells were obtained from the lumen of fresh bovine oviducts. Quantitative real-time polymerase chain reaction and in-cell western assays were used to measure PGE2 and PGF2α synthase activity and enzyme-linked immunosorbent assays were used to detect the concentrations of the two prostaglandins in extracellular fluid. We observed that oestradiol caused a short-term increase in cyclo-oxygenase-2 (COX-2), which stimulated PGE2 and PGF2α secretion, and that a subsequent decrease in COX-2 and an increase in cyclo-oxygenase-1 (COX-1) produced a high PGE2:PGF2α ratio...
March 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28441965/evaluation-of-a-dna-a%C3%AE-42-vaccine-in-adult-rhesus-monkeys-macaca-mulatta-antibody-kinetics-and-immune-profile-after-intradermal-immunization-with-full-length-dna-a%C3%AE-42-trimer
#10
Doris Lambracht-Washington, Min Fu, Pat Frost, Roger N Rosenberg
BACKGROUND: Aggregated amyloid-β peptide 1-42 (Aβ42), derived from the cellular amyloid precursor protein, is one of the pathological hallmarks of Alzheimer's disease (AD). Although active immunization against Aβ42 peptide was successful in AD mouse models and led to removal of plaques and improved memory, a similar clinical trial in humans (Aβ42 peptide immunization with QS-21 adjuvant) was stopped in phase II, when 6% of the treated patients developed encephalitis. Currently ongoing passive immunizations with the injection of preformed monoclonal antibodies against different epitopes within the Aβ1-42 peptide, which do not lead to activation of the immune system, have shown some effects in slowing AD pathology...
April 26, 2017: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28439969/factors-screening-to-statistical-experimental-design-of-racemic-atenolol-kinetic-resolution-via-transesterification-reaction-in-organic-solvent-using-free-pseudomonas-fluorescens-lipase
#11
Joni Agustian, Azlina Harun Kamaruddin, Hassan Y Aboul-Enein
As the (R)-enantiomer of racemic atenolol has no β-blocking activity and no lack of side effects, switching from the racemate to the (S)-atenolol is more favorable. Transesterification of racemic atenolol using free enzymes investigated as a resource to resolve the racemate via this method is limited. Screenings of enzyme, medium, and acetyl donor were conducted first to give Pseudomonas fluorescens lipase, tetrahydrofuran, and vinyl acetate. A statistical design of the experiment was then developed using Central Composite Design on some operational factors, which resulted in the conversions of 11...
April 25, 2017: Chirality
https://www.readbyqxmd.com/read/28438436/effects-of-dextran-sulfate-sodium-induced-experimental-colitis-on-cytochrome-p450-activity-in-rat-liver-kidney-and-intestine
#12
Nan Hu, Yanjuan Huang, Xuejiao Gao, Sai Li, Zhixiang Yan, Bin Wei, Ru Yan
Dextran sulfate sodium (DSS) induced experimental colitis presents a histologic resemblance to human ulcerative colitis (UC). Altered cytochrome P450s (CYPs) have been reported in this model and patients with UC. In this study, six CYPs activities were quantitatively determined in microsomes of liver (RLMs), kidney (RRMs) and intestine (RIMs) from rats with colitis at acute (5% DSS for 7 days, UCA) and remission (7-day DSS treatment followed by 7-day cessation, UCR) phases and compared with normal rats. Generally, CYPs activities varied with isoform, organ, and disease status...
April 21, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28436453/functional-thermodynamics-structural-and-biological-studies-of-in-silico-identified-inhibitors-of-mycobacterium-tuberculosis-enoyl-acp-coa-reductase-enzyme
#13
Leonardo K B Martinelli, Mariane Rotta, Anne D Villela, Valnês S Rodrigues-Junior, Bruno L Abbadi, Rogério V Trindade, Guilherme O Petersen, Giuliano M Danesi, Laura R Nery, Ivani Pauli, Maria M Campos, Carla D Bonan, Osmar Norberto de Souza, Luiz A Basso, Diogenes S Santos
Novel chemotherapeutics agents are needed to kill Mycobacterium tuberculosis, the main causative agent of tuberculosis (TB). The M. tuberculosis 2-trans-enoyl-ACP(CoA) reductase enzyme (MtInhA) is the druggable bona fide target of isoniazid. New chemotypes were previously identified by two in silico approaches as potential ligands to MtInhA. The inhibition mode was determined by steady-state kinetics for seven compounds that inhibited MtInhA activity. Dissociation constant values at different temperatures were determined by protein fluorescence spectroscopy...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28435964/kinetics-of-co2-diffusion-in-human-carbonic-anhydrase-a-study-using-molecular-dynamics-simulations-and-the-markov-state-model
#14
Gong Chen, Xian Kong, Diannan Lu, Jianzhong Wu, Zheng Liu
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28435868/label-free-optical-detection-of-single-enzyme-reactant-reactions-and-associated-conformational-changes
#15
Eugene Kim, Martin D Baaske, Isabel Schuldes, Peter S Wilsch, Frank Vollmer
Monitoring the kinetics and conformational dynamics of single enzymes is crucial to better understand their biological functions because these motions and structural dynamics are usually unsynchronized among the molecules. However, detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single-molecule basis remains as a challenge to established optical techniques because of the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually nontrivial, and the labels themselves might skew the physical properties of the enzyme...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28435098/kinetics-of-chitin-deacetylase-activation-by-the-ionic-liquid-bmim-br
#16
Izabela Aspras, Malgorzata M Jaworska, Andrzej Górak
Chitin deacetylase is the only known enzyme that can deacetylate the N-acetyl-D-glucosamine units in chitin and chitosan to D-glucosamine. Unfortunately, this enzyme, originally obtained from fungi, usually has low activity. Here, we present that it is possible to enhance the activity of chitin deacetylase using the ionic liquid [Bmim][Br]. An increase in activity of up to 160% from the basal chitin deacetylase activity was observed. Kinetic investigations suggest that [Bmim][Br] is a non-essential activator...
April 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28434903/measuring-transcription-dynamics-in-living-cells-using-a-photobleaching-approach
#17
REVIEW
Hodaya Hochberg, Yehuda Brody, Yaron Shav-Tal
The transcriptional kinetics of RNA polymerase II, the enzyme responsible for mRNA transcription in the nucleoplasm, can be modulated by a variety of factors. It is therefore important to establish experimental systems that will enable the readout of transcription kinetics of specific genes as they occur in real time within individual cells. This can be performed by implementing fluorescent tagging of the mRNA under live-cell conditions. This chapter describes how to generate fluorescently tagged genes and mRNA, and how a photobleaching approach can produce information on mRNA transcription kinetics...
April 20, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28433186/characterization-and-thermal-inactivation-kinetics-of-highly-thermostable-ramie-leaf-%C3%AE-amylase
#18
Liqin He, Sung-Hoon Park, Nguyen Dang Hai Dang, Hoa Xo Duong, Thi Phung Cac Duong, Phuong Lan Tran, Jong-Tae Park, Li Ni, Kwan-Hwa Park
We characterized ramie leaf β-amylase, and determined its thermostability and kinetic parameters. The enzyme was purified 53-fold using ammonium sulfate fractionation (40-60% saturation), anion exchange chromatography on DEAE-cellulose and gel permeation chromatography on Superdex-200. The purified enzyme was identified as β-amylase with molecular mass of 42kD. The enzyme displayed Km and kcat values for soluble potato starch of 1.1mg/mL and 7.8s(-1), respectively. The enzyme had a temperature optimum of 65°C, and its activity at 70°C was 92% of that at the optimal temperature after a 15-min incubation...
June 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28432453/the-influence-of-oxo-bridged-binuclear-gold-iii-complexes-on-na-k-atpase-activity-a-joint-experimental-and-theoretical-approach
#19
Aleksandra M Bondžić, Mirjana B Čolović, Goran V Janjić, Božidarka Zarić, Sandra Petrović, Danijela Z Krstić, Tiziano Marzo, Luigi Messori, Vesna M Vasić
The in vitro effects of oxo-bridged binuclear gold(III) complexes, i.e., [(bipy2Me)2Au2(μ-O)2][PF6]2 (Auoxo6), Au2[(bipydmb-H)2(μ-O)][PF6] (Au2bipyC) and [Au2(phen(2Me))2(μ-O)2](PF6)2 (Au2phen) on Na/K-ATPase, purified from the porcine cerebral cortex, were investigated. All three studied gold complexes inhibited the enzyme activity in a concentration-dependent manner achieving IC50 values in the low micromolar range. Kinetic analysis suggested an uncompetitive mode of inhibition for Auoxo6 and Au2bipyC, and a mixed type one for Au2phen...
April 21, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28430241/probing-the-germination-kinetics-of-ethanol-treated-bacillus-thuringiensis-spores
#20
Guiwen Wang, Huanjun Chen, Xiaochun Wang, Lixin Peng, Yuan Peng, Yong-Qing Li
Bacillus thuringiensis (Bt) is the most widely used microbial insecticide. To clarify the mechanism of bacterial resistance to ethanol toxicity, the present study investigated the effects of 70% (v/v) ethanol at a moderate temperature (65°C) on Bt spore germination by single-cell Raman spectroscopy and differential interference contrast microscopy. We found that over 80% of Bt spores were inviable after 30 min of treatment. Moreover, ethanol treatment affected spore germination; the time for initiation of rapid calcium dipicolinate (CaDPA) release (i...
April 20, 2017: Applied Optics
keyword
keyword
104582
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"