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https://www.readbyqxmd.com/read/28538147/structural-and-functional-investigations-of-the-n-terminal-ubiquitin-binding-region-of-usp25
#1
Yuanyuan Yang, Li Shi, Yiluan Ding, Yanhong Shi, Hong-Yu Hu, Yi Wen, Naixia Zhang
Ubiquitin-specific protease 25 (Usp25) is a deubiquitinase that is involved in multiple biological processes. The N-terminal ubiquitin-binding region (UBR) of Usp25 contains one ubiquitin-associated domain, one small ubiquitin-like modifier (SUMO)-interacting motif and two ubiquitin-interacting motifs. Previous studies suggest that the covalent sumoylation in the UBR of Usp25 impairs its enzymatic activity. Here, we raise the hypothesis that non-covalent binding of SUMO, a prerequisite for efficient sumoylation, will impair Usp25's catalytic activity as well...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28533982/lid-opening-and-conformational-stability-of-t1-lipase-is-mediated-by-increasing-chain-length-polar-solvents
#2
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/28533492/anti-tumor-activity-of-anthrax-toxin-variants-that-form-a-functional-translocation-pore-by-intermolecular-complementation
#3
Shihui Liu, Qian Ma, Rasem Fattah, Thomas H Bugge, Stephen H Leppla
Anthrax lethal toxin is a typical A-B type protein toxin secreted by Bacillus anthracis. Lethal factor (LF) is the catalytic A-subunit, a metalloprotease having MEKs as targets. LF relies on the cell-binding B-subunit, protective antigen (PA), to gain entry into the cytosol of target cells. PA binds to cell surface toxin receptors and is activated by furin protease to form an LF-binding-competent oligomer-PA pre-pore, which converts to a functional protein-conductive pore in the acidic endocytic vesicles, allowing translocation of LF into the cytosol...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28533430/heme-thiolate-sulfenylation-of-human-cytochrome-p450-4a11-functions-as-a-redox-switch-for-catalytic-inhibition
#4
Matthew E Albertolle, Donghak Kim, Leslie D Nagy, Chul-Ho Yun, Ambra Pozzi, Uzen Savas, Eric F Johnson, F Peter Guengerich
Cytochrome P450 (P450, CYP) 4A11 is a human fatty acid ω-hydroxylase that catalyzes the oxidation of arachidonic acid to the eicosanoid 20- hydroxyeicosatetraenoic acid (20-HETE), which plays important roles in regulating blood pressure regulation. Variants of P450 4A11 have been associated with high blood pressure and resistance to anti-hypertensive drugs, and 20-HETE has both pro- and antihypertensive properties relating to increased vasoconstriction and natriuresis, respectively. These physiological activities are likely influenced by the redox environment, but the mechanisms are unclear...
May 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28533132/relations-between-the-loop-transposition-of-dna-g-quadruplex-and-the-catalytic-function-of-dnazyme
#5
Mingpan Cheng, Jun Zhou, Guoqing Jia, Xuanjun Ai, Jean-Louis Mergny, Can Li
The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K(+), loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies...
May 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28531656/biodegradation-of-phthalic-acid-esters-paes-and-in-silico-structural-characterization-of-mono-2-ethylhexyl-phthalate-mehp-hydrolase-on-the-basis-of-close-structural-homolog
#6
Neha Singh, Vikram Dalal, Jai Krishna Mahto, Pravindra Kumar
Three bacterial strains capable of degrading phthalates namely Pseudomonas sp. PKDM2, Pseudomonas sp. PKDE1 and Pseudomonas sp. PKDE2 were isolated and characterized for their degradative potential. These strains efficiently degraded 77.4%-84.4% of DMP, 75.0%-75.7% of DEP and 71.7%-74.7% of DEHP, initial amount of each phthalate is 500mgL(-1) of each phthalate, after 44h of incubation. GC-MS results reveal the tentative DEHP degradation pathway, where hydrolases mediate the breakdown of DEHP to phthalic acid (PA) via an intermediate MEHP...
April 25, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28531330/structural-basis-for-substrate-binding-and-catalytic-mechanism-of-a-human-rna-m5c-methyltransferase-nsun6
#7
Ru-Juan Liu, Tao Long, Jing Li, Hao Li, En-Duo Wang
5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m5C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m5C methylation. Here, we have solved the structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28528213/optimal-electrostatic-interactions-between-substrate-and-protein-are-essential-for-radical-chemistry-in-ornithine-4-5-aminomutase
#8
Caitlyn Makins, Douglas A Whitelaw, Michael McGregor, Alix Petit, Robert G Mothersole, Kathleen E Prosser, Kirsten R Wolthers
Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting D-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, D-ornithine...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28526743/systematic-identification-of-functional-residues-of-artemisia-annua-amorpha-4-11-diene-synthase
#9
Xin Fang, Jian-Xu Li, Jin-Quan Huang, You-Li Xiao, Peng Zhang, Xiao-Ya Chen
Terpene synthases (TPSs) are responsible for the extremely diversified and complex structure of terpenoids. Amorpha-4,11-diene synthase (ADS) has a high (90%) fidelity in generating the sesquiterpene precursor for biosynthesis of artemisinin, an antimalarial drug, however, little is known about how active site residues of ADS involved in the carbocation rearrangement and cyclization reactions. Here, we identify seven residues that are key to most of the catalytic steps in ADS. By structural modeling and amino acid sequence alignments of ADS with two functionally relevant sesquiterpene synthases from Artemisia annua, we performed site-directed mutagenesis and found that a single substitution, T296V, impaired the ring closure activity almost completely, and tetra-substitutions (L374Y/L404V/L405I/G439S) led to an enzyme generating 80% monocyclic bisabolyl-type sesquiterpenes, whereas a double mutant (T399L/T447G) showed compromised activity in regioselective deprotonation to yield 34...
May 19, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28523999/molecular-docking-studies-applied-to-a-dataset-of-cruzain-inhibitors
#10
Edeildo Ferreira da Silva-Júnior, Paulo Henrique Barcellos França, Frederico Fávaro Ribeiro, Francisco Jaime Bezerra Mendonça-Júnior, Luciana Scotti, Marcus Tullius Scotti, Thiago Mendonça de Aquino, João Xavier de Araújo-Júnior
BACKGROUND: Chagas' disease is one of the main causes of heart failure in developing countries. The disadvantages of current therapy include the undesirable side-effects, resistance, and therapeutic adhesion. The development of new efficient and safe drugs is, therefore, an issue of extreme importance. OBJECTIVES: In order to gain a better understanding of how the compounds interact with the target, computational methods are essential. METHOD: In this theoretical study, we report a docking protocol applied to a dataset of 173 cruzain inhibitors with IC50 values of less than 10 μM, belonging 16 different chemical classes...
May 18, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28522605/structure-function-analysis-of-human-sucrase-isomaltase-identifies-key-residues-required-for-catalytic-activity
#11
Birthe Gericke, Natalie Schecker, Mahdi Amiri, Hassan Y Naim
Sucrase-isomaltase (SI) is an intestinal membrane-associated α-glucosidase that breaks down di- and oligosaccharides to absorbable monosaccharides. SI has two homologous functional subunits (sucrase and isomaltase) that both belong to the glycoside hydrolase family 31 (GH31) and differ in substrate specificity. All GH31 enzymes share a consensus sequence harboring an aspartic acid residue as a catalytic nucleophile. Moreover, crystallographic structural analysis of isomaltase predicts that another aspartic acid residue functions as a proton donor in hydrolysis...
May 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28522347/functional-analysis-of-tcctlp-5c2-a-chymotrypsin-like-serine-protease-needed-for-molting-in-tribolium-castaneum
#12
Daniel Albaum, Gunnar Broehan, Subbaratnam Muthukrishnan, Hans Merzendorfer
In a previous study, we have characterized a gene family encoding chymotrypsin-like proteases from the red flour beetle, Tribolium castaneum (TcCTLPs). We identified 14 TcCTLP genes that were predominantly expressed in the midgut, where they presumably function in digestion. Two genes (TcCTLP-6C and TcCTLP-5C2), however, additionally showed considerable expression in the carcass, and RNAi studies demonstrated that they are required for molting (Broehan et al., 2010; Insect Biochem. Mol. Biol 40, 274-83). Thus, the enzyme has distinct functions in different physiological environments...
May 15, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28522291/y418-in-410s-loop-is-required-for-high-transglucosylation-activity-and-large-ring-cyclodextrin-production-of-amylomaltase-from-corynebacterium-glutamicum
#13
Suthipapun Tumhom, Kuakarun Krusong, Piamsook Pongsawasdi
Amylomaltase catalyzes α-1,4 glucosyl transfer reaction to yield linear or cyclic oligosaccharide products. The aim of this work is to investigate functional roles of 410s loop unique to amylomaltase from Corynebacterium glutamicum (CgAM). Site-directed mutagenesis of Y418, the residue at the loop tip, was performed. Y418A/S/D/R/W/F - CgAMs were characterized and compared to the wild-type (WT). A significant decrease in starch transglucosylation, disproportionation and cyclization activities was observed. Specificity for G3 substrate in disproportionation reaction was not changed; however, Y418F showed an increase in preference for longer oligosaccharides G5 to G7...
May 15, 2017: Biochemical and Biophysical Research Communications
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/28516206/identification-expression-and-characterization-of-an-r-%C3%AF-transaminase-from-capronia-semiimmersa
#15
César Iglesias, Paola Panizza, Sonia Rodriguez Giordano
Chiral amines are essential precursors in the production of biologically active compounds, including several important drugs. Among the biocatalytic strategies that have been developed for their synthesis, the use of ω-transaminases (ω-TA) appears as an attractive alternative allowing the stereoselective amination of prochiral ketones. However, the problems associated with narrow substrate specificity, unfavourable reaction equilibrium and expensive amine donors still hamper its industrial application. The search for novel enzymes from nature can contribute to expand the catalytic repertoire of ω-TA and help to circumvent some of these problems...
May 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28512318/structure-based-prediction-and-identification-of-4-epimerization-activity-of-phosphate-sugars-in-class-ii-aldolases
#16
Seon-Hwa Lee, Seung-Hye Hong, Jung-Ung An, Kyoung-Rok Kim, Dong-Eun Kim, Lin-Woo Kang, Deok-Kun Oh
Sugar 4-epimerization reactions are important for the production of rare sugars and their derivatives, which have various potential industrial applications. For example, the production of tagatose, a functional sweetener, from fructose by sugar 4-epimerization is currently constrained because a fructose 4-epimerase does not exist in nature. We found that class II D-fructose-1,6-bisphosphate aldolase (FbaA) catalyzed the 4-epimerization of D-fructose-6-phosphate (F6P) to D-tagatose-6-phosphate (T6P) based on the prediction via structural comparisons with epimerase and molecular docking and the identification of the condensed products of C3 sugars...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28512128/refined-topology-model-of-the-stt3-sttp3-protein-subunit-of-the-oligosaccharyl-transferase-complex
#17
Patricia Lara, Karin Öjemalm, Johannes Reithinger, Aurora Holgado, You Maojun, Abdessalem Hammed, Daniel Mattle, Hyun Kim, IngMarie Nilsson
The oligosaccharyl transferase (OST) complex, localized in the endoplasmic reticulum (ER) of eukaryotic cells, is responsible for the N-linked glycosylation of numerous protein substrates. The membrane protein STT3 is a highly conserved part of the OST, and likely contains the active site of the complex. However, understanding the catalytic determinants of this system has been challenging, in part because of a discrepancy in the structural topology of the bacterial vs eukaryotic proteins and incomplete information about the mechanism of membrane integration...
May 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28511016/structural-and-biochemical-insights-into-dimethylsulfoniopropionate-cleavage-by-cofactor-bound-dddk-from-the-prolific-marine-bacterium-pelagibacter
#18
Nicholas J Schnicker, Saumya M De Silva, Jonathan D Todd, Mishtu Dey
Enormous amounts of the organic osmolyte dimethylsulfoniopropionate (DMSP) are produced in marine environments where bacterial DMSP lyases cleave it yielding acrylate and the climate-active gas dimethylsulfide (DMS). SAR11 bacteria are the most abundant clade of heterotrophic bacteria in the oceans and they play a key role in DMSP catabolism. An important environmental factor affecting DMS generation via DMSP lyases is the availability of metal ions since they are essential cofactors for many of these enzymes...
May 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28511011/iron-hydroperoxide-intermediate-in-superoxide-reductase-protonation-or-dissociation-first-mm-dynamics-and-qm-mm-metadynamics-study
#19
Rolf David, Helene Jamet, Vincent Niviere, Yohann Moreau, Anne Milet
Superoxide reductase is a mononuclear iron enzyme involved in superoxide radical detoxification in some bacteria. Its catalytic mechanism is associated with the remarkable formation of a ferric hydroperoxide Fe3+-OOH intermediate, which is specifically protonated on its proximal oxygen to generate the reaction product H2O2. Here we present a computational study of the protonation mechanism of the Fe3+ OOH intermediate, at different level of theory. This was performed on the whole system (solvated protein) using well-tempered metadynamics at the QM/MM (B3LYP/AmberFF99SB) level...
May 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28508424/computational-site-directed-mutagenesis-studies-of-the-role-of-the-hydrophobic-triad-on-substrate-binding-in-cholesterol-oxidase
#20
Laith Hisham Harb, Mahreen Arooj, Alice Vrielink, Ricardo L Mancera
Cholesterol oxidase (ChOx) is a flavoenzyme that oxidises and isomerises cholesterol (CHL) to form cholest-4-en-3-one. Molecular docking and molecular dynamics simulations were conducted to predict the binding interactions of CHL in the active site. Several key interactions (E361-CHL, N485-FAD and H447-CHL) were identified and which are likely to determine the correct positioning of CHL relative to flavin-adenine dinucleotide (FAD). Binding of CHL also induced changes in key residues of the active site leading to the closure of the oxygen channel...
May 15, 2017: Proteins
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