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Enzymology

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https://www.readbyqxmd.com/read/28644411/on-the-reaction-of-carbonyl-diphosphonic-acid-with-hydroxylamine-and-o-alkylhydroxylamines-unexpected-degradation-of-p-c-p-bridge
#1
Olga A Khomich, Dmitry V Yanvarev, Roman A Novikov, Alexey B Kornev, Elina Puljulla, Jouko Vepsäläinen, Alex R Khomutov, Sergey N Kochetkov
Derivatives of methylenediphosphonic acid possess wide spectra of biological activities and are used in enzymology as research tools as well as in practical medicine. Carbonyl diphosphonic acid is a promising starting building block for synthesis of functionally substituted methylenediphosphonates. Investigation of the interaction of carbonyl diphosphonic acid with hydroxylamine clearly demonstrates that it is impossible to isolate oxime within the pH range 2-12, while only cyanophosphonic and phosphoric acids are the products of the fast proceeding Beckmann-like fragmentation...
June 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28631282/biosynthesis-of-complex-indole-alkaloids-elucidation-of-the-concise-pathway-of-okaramines
#2
Chen-Yu Lai, Hsiao-Ching Lin, I-Wen Lo, Ranuka T Hewage, Yi-Chen Chen, Chien-Ting Chen, Chi-Fang Lee, Steven Lin, Man-Cheng Tang
The okaramines are a class of complex indole alkaloids isolated from Penicillium and Aspergillus species. Their potent insecticidal activity arises from selectively activating glutamate-gated chloride channels (GluCls) in invertebrates, not affecting human ligand-gated anion channels. Okaramines B (1) and D (2) contain a polycyclic skeleton, including an azocine ring and an unprecedented 2-dimethyl-3-methyl-azetidine ring. Due to their complex scaffold, okaramines have inspired many total synthesis efforts, but the enzymology of the okaramine biosynthetic pathway remains unexplored...
June 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28630164/single-molecule-nanopore-enzymology
#3
REVIEW
Kherim Willems, Veerle Van Meervelt, Carsten Wloka, Giovanni Maglia
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28609756/realization-of-microbial-community-stratification-for-single-stage-nitrogen-removal-in-a-sequencing-batch-biofilter-granular-reactor
#4
Na Sun, Chenghao Ge, Hafiz Adeel Ahmad, Baoyu Gao, Shou-Qing Ni
A permanent microbial stratified nitrogen removal system coupling anammox with partial nitrification (SNAP) in a sequencing batch biofilter granular reactor (SBBGR) was successfully constructed for the treatment of ammonia-rich wastewater. With a nitrogen loading rate of 0.1kgNm(-3)·d(-1), the maximal ammonia and total nitrogen removal efficiencies could reach up to 96.08% and 84.86% on day 108, respectively. The pH, DO profiles revealed a switch of functional species (AOB and anammox) at a typical intermittent aeration cycle...
June 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28604895/simultaneous-enzymatic-activity-modulation-and-rapid-determination-of-enzyme-kinetics-by-highly-crystalline-graphite-dots
#5
Rui Shi, Hao Li, Enhui Wu, Lipeng Xiong, Rui Lv, Ruochen Guo, Yang Liu, Guoqiang Xu, Zhenhui Kang, Jian Liu
The research field in enzyme-based biotechnology urgently requires the discovery of new materials and methods with high-performance. Here we report that highly crystalline graphite dots (GDs) can modulate enzyme activities, and simultaneously allow for real-time measurements on enzyme kinetics in combination with mass spectrometry (MS). A well-defined modulation of lipolytic activities from inhibition to enhancement can be realized by selectively coupling lipase enzymes with GDs containing specific functional groups on the surface...
June 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/28601227/trmd-a-methyl-transferase-for-trna-methylation-with-m-1-g37
#6
Ya-Ming Hou, Ryuma Matsubara, Ryuichi Takase, Isao Masuda, Joanna I Sulkowska
TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m(1)G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. Mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m(1)G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis...
2017: Enzymes
https://www.readbyqxmd.com/read/28581740/conformational-selection-as-the-mechanism-of-guest-binding-in-a-flexible-supramolecular-host
#7
Cynthia M Hong, David M Kaphan, Robert G Bergman, Kenneth N Raymond, F Dean Toste
This study offers a detailed mechanistic investigation of host-guest encapsulation behavior in a new enzyme-mimetic metal-ligand host and provides the first observation of a conformational selection mechanism (as opposed to induced fit) in a supramolecular system. The Ga4L4 host described features a C3-symmetric ligand motif with meta-substituted phenyl spacers, which enables the host to initially self-assemble into an S4-symmetric structure and then subsequently isomerize to a T-symmetric tetrahedron for better accommodation of a sufficiently large guest...
June 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28554725/substrate-inhibition-of-17beta-hsd1-in-living-cells-and-regulation-of-17beta-hsd7-by-17beta-hsd1-knockdown
#8
Hui Han, Jean-François Thériault, Guang Chen, Sheng-Xiang Lin
This study addresses first the role of human 17beta-hydroxysteroid dehydrogenase type 1 (17β-HSD1) in breast cancer (BC). The enzyme has a high estrone-activating activity that is subject to strong substrate inhibition as shown by enzyme kinetics at the molecular level. We used BC cells to verify this phenomenon in living cells: estrone concentration increase did reduce the reaction with 0.025 to 4μM substrate. Moreover, 5α-dihydrotestosterone (DHT) demonstrated some inhibition of estrogen activation at both the molecular and cellular level...
May 26, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28546645/fluorination-at-the-4-position-alters-the-substrate-behavior-of-l-glutamine-and-l-glutamate-implications-for-positron-emission-tomography-of-neoplasias
#9
Thomas M Jeitner, Eva Kristoferson, Juan A Azcona, John T Pinto, Clint Stalnecker, Jon W Erickson, Hank F Kung, Jianyong Li, Karl Ploessl, Arthur J L Cooper
Two 4-fluoro-L-glutamine diastereoisomers [(2S,4R)-4-FGln, (2S,4S)-4-FGln] were previously developed for positron emission tomography. Label uptake into two tumor cell types was greater with [(18)F](2S,4R)-4-FGln than with [(18)F](2S,4S)-4-FGln. In the present work we investigated the enzymology of two diastereoisomers of 4-FGln, two diastereoisomers of 4-fluoroglutamate (4-FGlu) (potential metabolites of the 4-FGln diastereoisomers) and another fluoro-derivative of L-glutamine [(2S,4S)-4-(3-fluoropropyl)glutamine (FP-Gln)]...
December 2016: Journal of Fluorine Chemistry
https://www.readbyqxmd.com/read/28543031/in-memoriam-professor-jean-pierre-von-wartburg-1931-to-2017
#10
Helmut K Seitz
No abstract text is available yet for this article.
May 25, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28533982/lid-opening-and-conformational-stability-of-t1-lipase-is-mediated-by-increasing-chain-length-polar-solvents
#11
Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M Normi, Fairolniza Mohd Shariff, Thean Chor Leow
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%...
2017: PeerJ
https://www.readbyqxmd.com/read/28529757/enzyme-activities-and-gene-expression-of-starch-metabolism-provide-insights-into-grape-berry-development
#12
Xudong Zhu, Chaobo Zhang, Weimin Wu, Xiaopeng Li, Chuan Zhang, Jinggui Fang
Grapes are categorized as a non-climacteric type of fruit which its ripening is not associated to important rises in respiration and ethylene synthesis. The starch metabolism shares a certain role in the carbohydrate metabolic pathways during grape berry development, and is regarded as an important transient pool in the pathway of sugar accumulation. However, the comprehensive role of starch and its contribution to the quality and flavor of grape berry have not been explored thoroughly. In this study, the expression levels of genes enzyme activities and carbohydrate concentrations related to starch metabolism, were analyzed to understand the molecular mechanism of starch accumulation during grape berry development...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28526692/understanding-the-interrelationship-between-the-synthesis-of-urea-and-gluconeogenesis-by-formulating-an-overall-balanced-equation
#13
Piero L Ipata, Rossana Pesi
It is well known that a strong metabolic interrelationship exists between ureagenesis and gluconeogenesis. In this paper, we present a detailed, overall equation, describing a possible metabolic link between ureagenesis and gluconeogenesis. We adopted a guided approach in which we strongly suggest that students, when faced with the problem of obtaining the overall equation of a metabolic pathway, carefully account for all atoms and charges of the single reactions, as well as the cellular localizations of the substrates, and the related transport systems...
June 1, 2017: Advances in Physiology Education
https://www.readbyqxmd.com/read/28520920/methylation-of-human-eukaryotic-elongation-factor-alpha-eef1a-by-a-member-of-a-novel-protein-lysine-methyltransferase-family-modulates-mrna-translation
#14
Magnus E Jakobsson, Jedrzej Malecki, Benedikt S Nilges, Anders Moen, Sebastian A Leidel, Pål Ø Falnes
Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific methyltransferase (KMT), remain unknown. Several recently discovered KMTs belong to the so-called seven-β-strand (7BS) class of MTases and we have here investigated an uncharacterized human 7BS MTase currently annotated as part of the endothelin converting enzyme 2, but which should be considered a separate enzyme...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28514423/enzymology-radical-ring-resizing
#15
Caitlin Deane
No abstract text is available yet for this article.
May 17, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28494956/resolution-of-submillisecond-kinetics-of-multiple-reaction-pathways-for-lactate-dehydrogenase
#16
Michael J Reddish, Robert Callender, R Brian Dyer
Enzymes are known to exhibit conformational flexibility. An important consequence of this flexibility is that the same enzyme reaction can occur via multiple reaction pathways on a reaction landscape. A model enzyme for the study of reaction landscapes is lactate dehydrogenase. We have previously used temperature-jump (T-jump) methods to demonstrate that the reaction landscape of lactate dehydrogenase branches at multiple points creating pathways with varied reactivity. A limitation of this previous work is that the T-jump method makes only small perturbations to equilibrium and may not report conclusively on all steps in a reaction...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28490630/understanding-phospholipid-function-why-are-there-so-many-lipids
#17
William Dowhan
In the 1970's phospholipids were still considered mere building blocks of the membrane lipid bilayer, but the subsequent realization that phospholipids could also serve as second messengers brought new interest to the field. My own passion for the unique amphipathic properties of lipids led me to seek other, non-signaling functions for phospholipids, particularly in their interactions with membrane proteins. This seemed the last frontier in protein chemistry and enzymology to be conquered. I was fortunate to find my way to Eugene Kennedy's laboratory where both membrane proteins and phospholipids were foci of study thus providing a jumping-off point for advancing our fundamental understanding of lipid synthesis, membrane protein biosynthesis, phospholipid and membrane protein trafficking and the cellular roles of phospholipids...
May 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28462843/covalent-inhibitors-of-lgtc-a-blueprint-for-the-discovery-of-non-substrate-like-inhibitors-for-bacterial-glycosyltransferases
#18
Yong Xu, Ruth Smith, Mirella Vivoli, Masaki Ema, Niina Goos, Sebastian Gehrke, Nicholas J Harmer, Gerd K Wagner
Non-substrate-like inhibitors of glycosyltransferases are sought after as chemical tools and potential lead compounds for medicinal chemistry, chemical biology and drug discovery. Here, we describe the discovery of a novel small molecular inhibitor chemotype for LgtC, a retaining α-1,4-galactosyltransferase involved in bacterial lipooligosaccharide biosynthesis. The new inhibitors, which are structurally unrelated to both the donor and acceptor of LgtC, have low micromolar inhibitory activity, comparable to the best substrate-based inhibitors...
April 11, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28455407/masochistic-enzymology-dennis-vance-s-work-on-phosphatidylcholine
#19
George Carman, Alexandra Taylor
No abstract text is available yet for this article.
April 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28452355/crystal-structure-of-apobec3a-bound-to-single-stranded-dna-reveals-structural-basis-for-cytidine-deamination-and-specificity
#20
Takahide Kouno, Tania V Silvas, Brendan J Hilbert, Shivender M D Shandilya, Markus F Bohn, Brian A Kelch, William E Royer, Mohan Somasundaran, Nese Kurt Yilmaz, Hiroshi Matsuo, Celia A Schiffer
Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive...
April 28, 2017: Nature Communications
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