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https://www.readbyqxmd.com/read/28646405/revealing-the-importance-of-linkers-in-k-series-oxime-reactivators-for-tabun-inhibited-ache-using-quantum-chemical-docking-and-smd-studies
#1
Shibaji Ghosh, Nellore Bhanu Chandar, Kalyanashis Jana, Bishwajit Ganguly
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules...
June 23, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28646214/structural-and-biochemical-studies-of-sulphotransferase-18-from-arabidopsis-thaliana-explain-its-substrate-specificity-and-reaction-mechanism
#2
Felix Hirschmann, Florian Krause, Petra Baruch, Igor Chizhov, Jonathan Wolf Mueller, Dietmar J Manstein, Jutta Papenbrock, Roman Fedorov
Sulphotransferases are a diverse group of enzymes catalysing the transfer of a sulfuryl group from 3'-phosphoadenosine 5'-phosphosulphate (PAPS) to a broad range of secondary metabolites. They exist in all kingdoms of life. In Arabidopsis thaliana (L.) Heynh. twenty-two sulphotransferase (SOT) isoforms were identified. Three of those are involved in glucosinolate (Gl) biosynthesis, glycosylated sulphur-containing aldoximes containing chemically different side chains, whose break-down products are involved in stress response against herbivores, pathogens, and abiotic stress...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28643349/a-qm-mm-study-of-the-catalytic-mechanism-of-sam-methyltransferase-rlmn-from-escherichia-coli
#3
Chenxiao Zhao, Lihua Dong, Yongjun Liu
RlmN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C2 methylation of adenosine 2503 (A2503) in 23S rRNA and adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNA). The catalytic reaction of RlmN is distinctly different from that of typical SAM-dependent methyltransferases that employs an SN 2 mechanism, but follows a ping-pong mechanism which involves the intermediate methylation of a conserved cysteine residue. Recently, the x-ray structure of a key intermediate in the RlmN reaction has been reported, allowing us to perform combined quantum mechanics and molecular mechanics (QM/MM) calculations to delineate the reaction details of RlmN at atomic level...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28643343/alpha-beta-hydrolases-a-unique-structural-motif-coordinates-catalytic-acid-residue-in-40-protein-fold-families
#4
Polytimi S Dimitriou, Alexander Denesyuk, Seiji Takahashi, Satoshi Yamashita, Mark S Johnson, Toru Nakayama, Konstantin Denessiouk
The alpha/beta-hydrolases (ABH) are a family of acid-base-nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28640742/identification-of-amino-acids-within-norovirus-polymerase-involved-in-rna-binding-and-viral-replication
#5
Kang Rok Han, Bader Y Alhatlani, Sunyoung Cho, Ji-Hye Lee, Myra Hosmillo, Ian G Goodfellow, Kyung Hyun Kim, Jai Myung Yang
Until recently, molecular studies on human norovirus (HuNoV), a major causative agent of gastroenteritis, have been hampered by the lack of an efficient cell culture system. Murine norovirus-1 (MNV-1) has served as a surrogate model system for norovirus research, due to the availability of robust cell culture systems and reverse genetics. To identify amino acids involved in RNA synthesis by the viral RNA-dependent RNA polymerase (NS7), we constructed NS7 mutants in which basic amino acids surrounding the catalytic site were substituted with alanine...
June 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28640638/enzyme-mediated-conversion-of-fad-to-8-formyl-fad-in-formate-oxidase-results-in-modified-cofactor-with-enhanced-catalytic-properties
#6
John M Robbins, Michael G Souffrant, Donald Hamelberg, Giovanni Gadda, Andreas S Bommarius
Flavins, including flavin adenine dinucleotide (FAD), are fundamental catalytic cofactors responsible for the redox functionality of a diverse set of proteins. Alternatively, modified flavin analogues are rarely found in nature as their incorporation typically results in inactivation of flavoproteins, thus leading to the disruption of important cellular pathways. Here, we report that the fungal flavoenzyme formate oxidase (FOX) catalyzes the slow conversion of non-covalently bound FAD to 8-formyl FAD (8-fFAD), and that this conversion results in a nearly 10-fold increase in formate oxidase activity...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640623/reactions-of-sulfur-containing-organic-compounds-and-peptides-in-1-ethyl-3-methyl-imidazolium-acetate
#7
Andreas C Baumruck, Daniel Tietze, Annegret Stark, Alesia A Tietze
The neat ionic liquid (IL) [C2mim][OAc] is not just capable of dissolving thiol- and disulfide-containing compounds, but is able to chemically react with them without addition of any catalytic reagent. Through the analysis of four small organic molecules and a cysteine-containing peptide we could postulate a general reaction mechanism. Here, the imidazolium-carbenes preferentially react with the disulfide bond, but not thiol group. Moreover, the imidazole moiety was found to abstract the sulfur atom from the cysteine residue, providing an alternative way to transform Cys residues, which were artificially inserted into a peptide sequence in order to perform native chemical ligation (NCL) of two peptide fragments...
June 22, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28640600/horse-liver-alcohol-dehydrogenase-zinc-coordination-and-catalysis
#8
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/28640323/lys-42-43-44-and-arg-12-of-thrombin-activable-fibrinolysis-inhibitor-comprise-a-thrombomodulin-exosite-essential-for-its-antifibrinolytic-potential
#9
Chengliang Wu, Alan R Stafford, James C Fredenburgh, Jeffrey I Weitz, Ann Gils, Paul J Declerck, Paul Y Kim
The thrombin-thrombomodulin (TM) complex activates thrombin-activable fibrinolysis inhibitor (TAFI) more efficiently than thrombin alone. The exosite on TAFI required for its TM-dependent activation by thrombin has not been identified. Based on previous work by us and others, we generated TAFI variants with one or more of residues Lys 42, Lys 43, Lys 44 and Arg 12 within the activation peptide mutated to alanine. Mutation of one, two, or three Lys residues or the Arg residue alone decreased the catalytic efficiency of TAFI activation by thrombin-TM by 2...
June 22, 2017: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/28640218/studies-on-the-two-thymine-residues-in-the-catalytic-core-of-10-23-dnazyme-the-impact-on-the-catalysis-of-their-5-substituted-functional-groups
#10
Pengyu Li, Shanshan Du, Yang Li, Junlin He
In the 15-mer catalytic core of 10-23 DNAzyme, each residue contributes to the catalytic conformation differently. Here, the critically conserved T4 and the least conserved T8 were modified on their 5-position with hydroxyl, imidazolyl, and amino groups with a hydrogen-bonding ability. These external functional groups induced new interactions within the catalytic core, resulting in both negative and positive effects on the catalytic activity of 10-23 DNAzyme, and the different linkages could be used to modulate the effect of the functional groups...
June 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28638321/membrane-guanylate-cyclase-catalytic-subdomain-structure-and-linkage-with-calcium-sensors-and-bicarbonate
#11
Sarangan Ravichandran, Teresa Duda, Alexandre Pertzev, Rameshwar K Sharma
Membrane guanylate cyclase (MGC) is a ubiquitous multi-switching cyclic GMP generating signaling machine linked with countless physiological processes. In mammals it is encoded by seven distinct homologous genes. It is a single transmembrane spanning multi-modular protein; composed of integrated blocks and existing in homo-dimeric form. Its core catalytic domain (CCD) module is a common transduction center where all incoming signals are translated into the production of cyclic GMP, a cellular signal second messenger...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28637443/trichoderma-virens-%C3%AE-glucosidase-i-bgli-gene-expression-in-saccharomyces-cerevisiae-including-docking-and-molecular-dynamics-studies
#12
Gammadde Hewa Ishan Maduka Wickramasinghe, Pilimathalawe Panditharathna Attanayake Mudiyanselage Samith Indika Rathnayake, Naduviladath Vishvanath Chandrasekharan, Mahindagoda Siril Samantha Weerasinghe, Ravindra Lakshman Chundananda Wijesundera, Wijepurage Sandhya Sulochana Wijesundera
BACKGROUND: Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions...
June 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28636006/copper-ion-interaction-with-the-rnase-catalytic-site-fragment-of-the-angiogenin-protein-an-experimental-and-theoretical-investigation
#13
Antonio Magrì, Giovanni Tabbì, Raffaella Breglia, Luca De Gioia, Piercarlo Fantucci, Maurizio Bruschi, Raffaele P Bonomo, Diego La Mendola
The angiogenin protein (Ang) is a member of the vertebrate-specific secreted ribonucleases and one of the most potent angiogenic factors known. Ang is a normal constituent of human plasma and its concentration increases under some physiological and pathological conditions to promote neovascularization. Ang was originally identified as an angiogenic tumour factor, but its biological activity has been found to extend from inducing angiogenesis to promoting cell survival in different neurodegenerative diseases...
June 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28635254/sudoku-like-lab-on-paper-cyto-device-with-dual-enhancement-of-electrochemiluminescence-intermediates-strategy
#14
Hongmei Yang, Yan Zhang, Li Li, Lina Zhang, Feifei Lan, Jinghua Yu
This paper describes the design and construction of sudoku-like lab-on-paper platform, in which dual enhancement of reaction intermediates strategy was incorporated for multiplexed competitive electrochemiluminescence (ECL) cyto-assay. Benefit from the sudoku-like structure, integrated multifunction were obtained on such elaborately devised platform, including specific reagents storage, multiple samples immobilization, residual automatic washing, and signal collection. By utilizing semicarbazide (SE) and silver nanoparticles (AgNPs) as dual enhancers, more ECL intermediates could be obtained in the graphene quantum dots (GQDs) and peroxydisulfate system, resulting in the production of more excited state GQDs to emit light...
June 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28634712/site-directed-mutagenesis-under-the-direction-of-in-silico-protein-docking-modeling-reveals-the-active-site-residues-of-3-ketosteroid-%C3%AE-1-dehydrogenase-from-mycobacterium-neoaurum
#15
Ning Qin, Yanbing Shen, Xu Yang, Liqiu Su, Rui Tang, Wei Li, Min Wang
3-Ketosteroid-Δ(1)-dehydrogenases (KsdD) from Mycobacterium neoaurum could transform androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione. This reaction has a significant effect on the product of pharmaceutical steroid. The crystal structure and active site residues information of KsdD from Mycobacterium is not yet available, which result in the engineering of KsdD is tedious. In this study, by the way of protein modeling and site-directed mutagenesis, we find that, Y122, Y125, S138, E140 and Y541 from the FAD-binding domain and Y365 from the catalytic domain play a key role in this transformation...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28634178/ascorbate-protects-the-di-heme-enzyme-maug-against-self-inflicted-oxidative-damage-by-an-unusual-antioxidant-mechanism
#16
Zhongxin Ma, Victor L Davidson
Ascorbate protects MauG from self-inactivation that occurs during the autoreduction of the reactive bis -Fe(IV) state of its diheme cofactor. The mechanism of protection does not involve direct reaction with reactive oxygen species in solution. Instead it binds to MauG and mitigates oxidative damage that occurs via internal transfer of electrons from amino acid residues within the protein to the high-valent hemes. The presence of ascorbate does not inhibit the natural catalytic reaction of MauG which catalyzes oxidative posttranslational modifications of a substrate protein that binds to the surface of MauG, and is oxidized by the high-valent hemes via long range electron transfer...
June 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28630929/splitting-of-the-o-o-bond-at-the-heme-copper-catalytic-site-of-respiratory-oxidases
#17
Federica Poiana, Christoph von Ballmoos, Nathalie Gonska, Margareta R A Blomberg, Pia Ädelroth, Peter Brzezinski
Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR ; Fe(4+)=O(2-), CuB(2+)-OH(-)). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O-O bond...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630323/role-of-the-cbp-catalytic-core-in-intramolecular-sumoylation-and-control-of-histone-h3-acetylation
#18
Sangho Park, Robyn L Stanfield, Maria A Martinez-Yamout, H Jane Dyson, Ian A Wilson, Peter E Wright
The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28628666/the-effector-avrrxo1-phosphorylates-nad-in-planta
#19
Teja Shidore, Corey D Broeckling, Jay S Kirkwood, John J Long, Jiamin Miao, Bingyu Zhao, Jan E Leach, Lindsay R Triplett
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways...
June 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28627879/the-%C3%AE-1-%C3%AE-2-motif-of-the-rnase-h-domain-of-hiv-1-rt-is-responsible-for-conferring-open-conformation-to-p66-subunit-by-displacing-the-connection-domain-from-the-polymerase-cleft
#20
Ashutosh K Pandey, Updesh Dixit, Vladyslav Kholodovych, Thomas W Comollo, Virendra N Pandey
Heterodimeric HIV-1 RT is composed of p66 and p51 subunits. While in the p51 subunit, the connection domain is tucked in the polymerase cleft,; it is effectively displaced from the cleft of the catalytically active p66 subunit. How is the connection domain relocated from the polymerase cleft of p66? Does RNase H domain have any role in this process? To answer this question, we extended the C-terminal region of p51 by stepwise addition of N-terminal motifs of RNase H domain to generate p54, p57, p60, and p63 derivatives...
June 19, 2017: Biochemistry
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