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Enzymology

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https://www.readbyqxmd.com/read/29772530/deciphering-mechanism-of-conformationally-controlled-electron-transfer-in-nitric-oxide-synthases
#1
Jinghui Li, Huayu Zheng, Changjian Feng
Electron transfer is a fundamental process in life that is very often coupled to catalysis within redox enzymes through a stringent control of protein conformational movements. Mammalian nitric oxide synthase (NOS) proteins are redox flavo-hemoproteins consisting of multiple modular domains. The NOS enzyme is exquisitely regulated in vivo by its partner, the Ca2+ sensing protein calmodulin (CaM), to control production of nitric oxide (NO). The importance of functional domain motion in NOS regulation has been increasingly recognized...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29770675/-enzymology-of-snails-under-treatment-of-molluscicides
#2
Xiong Tao, Zhao Qin-Ping, Liu Rong, Jiang Ming-Sen, Dong Hui-Fen
Studies on the enzymology of snails are important in the study of molluscicidal mechanism. The alteration of activities of enzymes after molluscicidal treatment was reported in large numbers of papers. This paper reviews the progress of studies on the enzymology of snails under the treatment of molluscicides.
February 27, 2018: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29754415/biological-hydropersulfides-and-related-polysulfides-a-new-concept-and-perspective-in-redox-biology
#3
REVIEW
Jon M Fukuto, Louis J Ignarro, Peter Nagy, David A Wink, Christopher G Kevil, Martin Feelisch, Miriam M Cortese-Krott, Christopher L Bianco, Yoshito Kumagai, Adrian J Hobbs, Joseph Lin, Tomoaki Ida, Takaaki Akaike
The chemical biology of thiols (RSH, e.g., cysteine and cysteine containing proteins/peptides) has been a topic of extreme interest for many decades due to their reported roles in protein structure/folding, redox signaling, metal ligation, cellular protection and enzymology. While many of the studies on thiol/sulfur biochemistry have focused on thiols, relatively ignored have been hydropersulfides (RSSH) and higher order polysulfur species (RSSn H, RSSn R, n > 1). Recent and provocative work has alluded to the prevalence and likely physiological importance of RSSH and related RSSn H...
May 12, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29735741/folding-cooperativity-and-allosteric-function-in-the-tandem-repeat-protein-class
#4
REVIEW
Albert Perez-Riba, Marie Synakewicz, Laura S Itzhaki
The term allostery was originally developed to describe structural changes in one binding site induced by the interaction of a partner molecule with a distant binding site, and it has been studied in depth in the field of enzymology. Here, we discuss the concept of action at a distance in relation to the folding and function of the solenoid class of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats. Distantly located repeats fold cooperatively, even though only nearest-neighbour interactions exist in these proteins...
June 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29706671/review-of-methods-in-enzymology-volumes-551-and-552-circadian-rhythms-and-biological-clocks-part-a-and-b-edited-by-amita-sehgal
#5
Brian R Crane
No abstract text is available yet for this article.
June 2017: Quarterly Review of Biology
https://www.readbyqxmd.com/read/29701961/post-translational-tyrosine-geranylation-in-cyanobactin-biosynthesis
#6
Maho Morita, Yue Hao, Jouni K Jokela, Debosmita Sardar, Zhenjian Lin, Kaarina Sivonen, Satish K Nair, Eric W Schmidt
Prenylation is a widespread modification that improves the biological activities of secondary metabolites. This reaction also represents a key modification step in biosyntheses of cyanobactins, a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) produced by cyanobacteria. In cyanobactins, amino acids are commonly isoprenylated by ABBA prenyltransferases that use C5 donors. Notably, mass spectral analysis of piricyclamides from a fresh-water cyanobacterium suggested that they may instead have a C10 geranyl group...
May 1, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29699942/daidzein-reductase-of-eggerthella-sp-yy7918-its-octameric-subunit-structure-containing-fmn-fad-4fe-4s-and-its-enantioselective-production-of-r-dihydroisoflavones
#7
Yuika Kawada, Tomoko Goshima, Rie Sawamura, Shin-Ichiro Yokoyama, Emiko Yanase, Toshio Niwa, Akio Ebihara, Mizuho Inagaki, Keiichi Yamaguchi, Kazuo Kuwata, Yuta Kato, Osamu Sakurada, Tohru Suzuki
S-Equol is a metabolite of daidzein, a type of soy isoflavone, and three reductases are involved in the conversion of daidzein by specific intestinal bacteria. S-Equol is thought to prevent hormone-dependent diseases. We previously identified the equol producing gene cluster (eqlABC) of Eggerthella sp. YY7918. Daidzein reductase (DZNR), encoded by eqlA, catalyzes the reduction of daidzein to dihydrodaidzein (the first step of equol synthesis), which was confirmed using a recombinant enzyme produced in Escherichia coli...
April 23, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29691575/-protective-effects-of-endogenous-carbon-monoxide-against-myocardial-ischemia-reperfusion-injury-in-rats
#8
Zhen Zhou, Shuang Ma, Jie Liu, Qiao-Rong Ji, Cheng-Zhu Cao, Xiao-Na Li, Feng Tang, Wei Zhang
The present study is aimed to explore the effects of endogenous carbon monoxide on the ischemia-reperfusion in rats. Wistar rats were intraperitoneally injected with protoporphyrin cobalt chloride (CoPP, an endogenous carbon monoxide agonist, 5 mg/kg), zinc protoporphyrin (ZnPP, an endogenous carbon monoxide inhibitor, 5 mg/kg) or saline. Twenty-four hours after injection, the myocardial ischemia-reperfusion model was made by Langendorff isolated cardiac perfusion system, and cardiac function parameters were collected...
April 25, 2018: Sheng Li Xue Bao: [Acta Physiologica Sinica]
https://www.readbyqxmd.com/read/29689165/the-taxonomy-of-covalent-inhibitors
#9
Alfred Tuley, Walter Fast
Covalent enzyme inhibitors are widely applied as biochemical tools and therapeutic agents. As a complement to categorization of these inhibitors by reactive group or modification site, we present a categorization by mechanism, which highlights common advantages and disadvantages inherent to each approach. Established categories for reversible and irreversible covalent inhibition are reviewed with representative examples given for each class, including covalent reversible inhibitors, slow substrates, residue-specific reagents, affinity labels (classical, quiescent, and photoaffinity), and mechanism-based inactivators...
April 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29672134/metabolism-and-biodegradation-of-spacecraft-cleaning-reagents-by-strains-of-spacecraft-associated-acinetobacter
#10
Rakesh Mogul, Gregory A Barding, Sidharth Lalla, Sooji Lee, Steve Madrid, Ryan Baki, Mahjabeen Ahmed, Hania Brasali, Ivonne Cepeda, Trevor Gornick, Shawn Gunadi, Nicole Hearn, Chirag Jain, Eun Jin Kim, Thi Nguyen, Vinh Bao Nguyen, Alex Oei, Nicole Perkins, Joseph Rodriguez, Veronica Rodriguez, Gautam Savla, Megan Schmitz, Nicholas Tedjakesuma, Jillian Walker
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions...
April 19, 2018: Astrobiology
https://www.readbyqxmd.com/read/29666216/progress-towards-platform-chemical-production-using-clostridium-autoethanogenum
#11
REVIEW
Rupert O J Norman, Thomas Millat, Klaus Winzer, Nigel P Minton, Charlie Hodgman
Since 2013, there has been an explosion in the number of research articles published on Clostridium autoethanogenum , an acetogen capable of producing platform chemicals such as ethanol and 2,3-butanediol from greenhouse gases. However, no review focusing solely on C. autoethanogenum has appeared in the literature. This review outlines the research conducted into this organism in three broad categories (Enzymology, Genetics, and Systems Biology) and suggestions for future research are offered.
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29620883/an-oxetane-based-polyketide-surrogate-to-probe-substrate-binding-in-a-polyketide-synthase
#12
Bryan Daniel Ellis, Jacob C Milligan, Alexander R White, Vy Duong, Pilar X Altman, Lina Mohammed, Matthew P Crump, John Crosby, Ray Luo, Christopher D Vanderwal, Shiou-Chuan Tsai
Polyketides are a large class of bioactive natural products with a wide range of structures and functions. Polyketides are biosynthesized by large, multi-domain enzyme complexes termed polyketide synthases (PKSs). One of the primary challenges when studying PKSs is the high reactivity of their poly--ketone substrates. This has hampered structural and mechanistic characterization of PKS-polyketide complexes, and, as a result, little is known about how PKSs position the unstable substrates for proper catalysis while displaying high levels of regio- and stereo-specificity...
April 5, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29618298/negative-cooperativity-in-the-interaction-of-prostaglandin-h-synthase-1-with-the-competitive-inhibitor-naproxen-can-be-described-as-the-interaction-of-a-non-competitive-inhibitor-with-heterogeneous-enzyme-preparation
#13
I S Filimonov, A P Berzova, V I Barkhatov, A V Krivoshey, N A Trushkin, P V Vrzheshch
The kinetic mechanism of the interaction of nonsteroidal anti-inflammatory drugs (NSAIDs) with their main pharmacological target, prostaglandin H synthase (PGHS), has not yet been established. We showed that inhibition of PGHS-1 from sheep vesicular glands by naproxen (a representative of NSAIDs) demonstrates a non-competitive character with respect to arachidonic acid and cannot be described within a framework of the commonly used kinetic schemes. However, it can be described by taking into account the negative cooperativity of naproxen binding to the cyclooxygenase active sites of the PGHS-1 homodimer (the first naproxen molecule forms a more stable complex (K1 = 0...
February 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29605646/responses-of-labeo-rohita-fingerlings-to-n-acetyl-p-aminophenol-toxicity
#14
Sivashankar Renuka, Rama Krishnan Poopal, Mathan Ramesh, Frederick Clara-Bindu
The short term (96 h) toxicity of N-acetyl-p-aminophenol (0.58 mg/L - Treatment I and 0.29 mg/L - Treatment II) on certain health indicators (haematology, biochemical, and enzymology) of an Indian major carp Labeo rohita was studied. When compared to control, N-acetyl-p-aminophenol treated fish showed a significant (P < 0.05) decrease in haemoglobin (Hb), haematocrit (Hct), and erythrocyte (RBC) levels throughout the study period. Whereas, a significant (P < 0.05) increase were noted in leucocyte (WBC) counts (except 48 h in Treatment-I), mean corpuscular volume (MCV), and mean corpuscular haemoglobin (MCH) values (except 24 h in Treatment-I)...
March 29, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29604573/design-of-polymer-particle-dispersions-latexes-in-the-course-of-radical-heterophase-polymerization-for-biomedical-applications
#15
REVIEW
A N Generalova, V P Zubov
Dispersions of polymer particle (DPPs) are increasingly being exploited both as biomolecule carriers, and as markers in various DPP biomedical applications related to cell and molecular biology, enzymology, immunology, diagnostics, in vitro and in vivo visualization, bioseparation, etc. Their potential to reduce reaction scales, lower costs, improve the rate, sensitivity, selectivity, stability and reproducibility of assays governs the diversity of their bioapplications. This review focuses on the design of DPPs with innovative special properties in the course of free radical heterophase polymerization that provides careful control of both macromolecular and colloidal properties...
March 26, 2018: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29601864/tmem2-a-missing-link-in-hyaluronan-catabolism-identified
#16
REVIEW
Yu Yamaguchi, Hayato Yamamoto, Yuki Tobisawa, Fumitoshi Irie
Hyaluronan (HA) is a glycosaminoglycan composed of repeating disaccharide units of glucuronic acid and N-acetylglucosamine. HA is an extremely long, unbranched polymer, which often exceeds 106  Da and sometimes reaches 107  Da. A feature that epitomizes HA is its rapid turnover: one-third of the total body HA is turned over daily. The current model of HA catabolism postulates that high-molecular weight HA in the extracellular space is first cleaved into smaller fragments by a hyaluronidase(s) that resides at the cell surface, followed by internalization of fragments and their degradation into monosaccharides in lysosomes...
March 27, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29563907/a-novel-bifunctional-amino-acid-racemase-with-multiple-substrate-specificity-maly-from-lactobacillus-sakei-lt-13-genome-based-identification-and-enzymological-characterization
#17
Shiro Kato, Tadao Oikawa
The Lactobacillus sakei strain LK-145 isolated from Moto, a starter of sake, produces potentially large amounts of three D-amino acids, D-Ala, D-Glu, and D-Asp, in a medium containing amylase-digested rice as a carbon source. The comparison of metabolic pathways deduced from the complete genome sequence of strain LK-145 to the type culture strain of Lactobacillus sakei strain LT-13 showed that the L- and D-amino acid metabolic pathways are similar between the two strains. However, a marked difference was observed in the putative cysteine/methionine metabolic pathways of strain LK-145 and LT-13...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29512390/role-of-zinc-and-magnesium-ions-in-the-modulation-of-phosphoryl-transfer-in-protein-tyrosine-phosphatase-1b
#18
Elisa Bellomo, Asma Abro, Christer Hogstrand, Wolfgang Maret, Carmen Domene
While the majority of phosphatases are metalloenzymes, the prevailing model for the reactions catalyzed by protein tyrosine phosphatases does not involve any metal ion, yet both metal cations and oxoanions affect their enzymatic activity. Mg2+ and Zn2+ activate and inhibit, respectively, protein tyrosine phosphatase 1B (PTP1B). Molecular dynamics simulations, metadynamics, and quantum chemical calculations in combination with experimental investigations demonstrate that Mg2+ and Zn2+ compete for the same binding site in the active site only in the closed conformation of the enzyme in its phosphorylated state...
March 28, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29503433/-enzymological-studies-on-the-mechanisms-of-pathogenesis-of-diabetic-complications
#19
REVIEW
Tsuyoshi Tanimoto
 Aldose reductase (AR) is involved in the pathogenesis of complications in diabetes. In this study, the enzymatic properties of AR isolated from various sources and a recombinant human AR (rh-AR) were analyzed in detail. The sensitivity of different forms of AR to several AR inhibitors (ARIs) was compared. Our findings enabled us to propose that human AR should be used as the target enzyme in the development of ARIs. An enzyme-linked immunosorbent assay (ELISA) for human AR which employed monoclonal antibodies against rh-AR was created, and this method was used to demonstrate the distribution of AR in human tissues...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/29494239/2-oxoglutarate-dependent-oxygenases
#20
Md Saiful Islam, Thomas M Leissing, Rasheduzzaman Chowdhury, Richard J Hopkinson, Christopher J Schofield
2-Oxoglutarate (2OG)-dependent oxygenases (2OGXs) catalyze a remarkably diverse range of oxidative reactions. In animals, these comprise hydroxylations and N-demethylations proceeding via hydroxylation; in plants and microbes, they catalyze a wider range including ring formations, rearrangements, desaturations, and halogenations. The catalytic flexibility of 2OGXs is reflected in their biological functions. After pioneering work identified the roles of 2OGXs in collagen biosynthesis, research indicated they also function in plant and animal development, transcriptional regulation, nucleic acid modification/repair, fatty acid metabolism, and secondary metabolite biosynthesis, including of medicinally important antibiotics...
March 1, 2018: Annual Review of Biochemistry
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