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https://www.readbyqxmd.com/read/28212821/cloning-and-molecular-characterization-of-the-betaine-aldehyde-dehydrogenase-involved-in-the-biosynthesis-of-glycine-betaine-in-white-shrimp-litopenaeus-vannamei
#1
María F Delgado-Gaytán, Jesús A Rosas-Rodríguez, Gloria Yepiz-Plascencia, Ciria G Figueroa-Soto, Elisa M Valenzuela-Soto
The enzyme betaine aldehyde dehydrogenase (BADH) catalyzes the irreversible oxidation of betaine aldehyde to glycine betaine (GB), a very efficient osmolyte accumulated during osmotic stress. In this study, we determined the nucleotide sequence of the cDNA for the BADH from the white shrimp Litopenaeus vannamei (LvBADH). The cDNA was 1882 bp long, with a complete open reading frame of 1524 bp, encoding 507 amino acids with a predicted molecular mass of 54.15 kDa and a pI of 5.4. The predicted LvBADH amino acid sequence shares a high degree of identity with marine invertebrate BADHs...
February 14, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28212489/direct-single-enzyme-biomineralization-of-catalytically-active-ceria-and-ceria-zirconia-nanocrystals
#2
Christopher D Curran, Li Lu, Yue Jia, Christopher J Kiely, Bryan W Berger, Steven McIntosh
Biomineralization is an intriguing approach to the synthesis of functional inorganic materials for energy applications whereby biological systems are engineered to mineralize inorganic materials and control their structure over multiple length scales under mild reaction conditions. Herein we demonstrate a single enzyme mediated biomineralization route to synthesize crystalline, catalytically active, quantum confined ceria (CeO2-x) and ceria-zirconia (Ce1-yZryO2-x) nanocrystals for application as environmental catalysts...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28209973/structural-basis-for-fragmenting-the-exopolysaccharide-of-acinetobacter-baumannii-by-bacteriophage-%C3%AE-ab6-tailspike-protein
#3
I-Ming Lee, I-Fan Tu, Feng-Ling Yang, Tzu-Ping Ko, Jiahn-Haur Liao, Nien-Tsung Lin, Chung-Yi Wu, Chien-Tai Ren, Andrew H-J Wang, Ching-Ming Chang, Kai-Fa Huang, Shih-Hsiung Wu
With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209966/molecular-interplay-between-the-dimer-interface-and-the-substrate-binding-site-of-human-peptidylarginine-deiminase-4
#4
Chien-Yun Lee, Chu-Cheng Lin, Yi-Liang Liu, Guang-Yaw Liu, Jyung-Hurng Liu, Hui-Chih Hung
Our previous studies suggest that the fully active form of Peptidylarginine deiminase 4 (PAD4) should be a dimer and not a monomer. This paper provides a plausible mechanism for the control of PAD4 catalysis by molecular interplay between its dimer-interface loop (I-loop) and its substrate-binding loop (S-loop). Mutagenesis studies revealed that two hydrophobic residues, W347 and V469, are critical for substrate binding at the active site; mutating these two residues led to a severe reduction in the catalytic activity...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28206761/molecular-cobalt-complexes-with-pendant-amines-for-selective-electrocatalytic-reduction-of-carbon-dioxide-to-formic-acid
#5
Souvik Roy, Bhaskar Sharma, Jacques Pecaut, Philippe Simon, Marc Fontecave, Phong D Tran, Etienne Derat, Vincent Artero
We report here on a new series of CO2-reducing molecular catalysts based on Earth-abundant elements that are very selective for the production of acid formic in DMF/water mixtures (Faradaic efficiency of 90±10%) at moderate overpotentials (500-700 mV in DMF measured at the middle of the catalytic wave). The [CpCo(PR2NR'2)I]+compounds contain diphosphine ligands PR2NR'2 with two pendent amine residues that act as proton relays during CO2 reduction catalysis and tune their activity. Four different PR2NR'2 ligands with cyclohexyl or phenyl substituents on phosphorus and benzyl or phenyl substituents on nitrogen were employed and the compound with the most electron-donating phosphine ligand and the most basic amine functions performs best among the series with turnover frequency >1000 s 1...
February 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28205049/construction-of-potent-recombinant-strain-through-intergeneric-protoplast-fusion-in-endophytic-fungi-for-anticancerous-enzymes-production-using-rice-straw
#6
Mervat Morsy Abbas Ahmed El-Gendy, Salha Hassan Mastour Al-Zahrani, Ahmed Mohamed Ahmed El-Bondkly
Among all fungal endophytes isolates derived from different ethno-medical plants, the hyper-yield L-asparaginase and L-glutaminase wild strains Trichoderma sp. Gen 9 and Cladosporium sp. Gen 20 using rice straw under solid-state fermentation (SSF) were selected. The selected strains were used as parents for the intergeneric protoplast fusion program to construct recombinant strain for prompt improvement production of these enzymes in one recombinant strain. Among 21 fusants obtained, the recombinant strain AYA 20-1, with 2...
February 15, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28203248/structural-determinants-of-the-hyperalgesic-activity-of-myotoxic-lys49-phospholipase%C3%A2-a2
#7
Vanessa Olzon Zambelli, Lucimara Chioato, Vanessa Pacciari Gutierrez, Richard John Ward, Yara Cury
BACKGROUND: Bothropstoxin-I (BthTx-I) is a Lys49-phospholipase A2 (Lys49-PLA2) from the venom of Bothrops jararacussu, which despite of the lack of catalytic activity induces myotoxicity, inflammation and pain. The C-terminal region of the Lys49-PLA2s is important for these effects; however, the amino acid residues that determine hyperalgesia and edema are unknown. The aim of this study was to characterize the structural determinants for the Lys49-PLA2-induced nociception and inflammation...
2017: Journal of Venomous Animals and Toxins Including Tropical Diseases
https://www.readbyqxmd.com/read/28202709/understanding-in-line-probing-experiments-by-modeling-cleavage-of-non-reactive-rna-nucleotides
#8
Vojtech Mlynsky, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i...
February 15, 2017: RNA
https://www.readbyqxmd.com/read/28196869/structural-insights-unravel-the-zymogenic-mechanism-of-the-virulence-factor-gingipain-k-from-porphyromonas-gingivalis-a-causative-agent-of-gum-disease-from-the-human-oral-microbiome
#9
Anja Pomowski, Isabel Uson, Zuzanna M Nowakowska, Florian Veillard, Maryta N Sztukowska, Tibisay Guevara, Theodoros Goulas, Danuta Mizgalska, Magdalena L Nowak, Barbara A Potempa, James A Huntington, Jan Potempa, F Xavier Gomis-Ruth
Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as Porphyromonas gingivalis, the main etiological agent of periodontitis. P. gingivalis secretes proteolytic gingipains (Kgp and RgpA/B) as zymogens inhibited by a pro-domain that is removed during extracellular activation. Unraveling the molecular mechanism of Kgp zymogenicity is essential to design inhibitors blocking its activity. Here, we found that the isolated 209-residue Kgp pro-domain is a boomerang-shaped all-β protein similar to the RgpB pro-domain...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28196865/s-palmitoylation-of-junctional-adhesion-molecule-c-regulates-its-tight-junction-localization-and-cell-migration
#10
Pornpun Aramsangtienchai, Nicole A Spiegelman, Ji Cao, Hening Lin
Junctional Adhesion Molecule C (JAM-C) is an immunoglobulin superfamily protein expressed in epithelial cells, endothelial cells, and leukocytes. JAM-C has been implicated in leukocyte transendothelial migration, angiogenesis, cell-adhesion, cell polarity, spermatogenesis and metastasis. Here, we show that JAM-C undergoes S-palmitoylation on two juxtamembrane cysteine residues, Cys264 and Cys265. We have identified DHHC7 as a JAM-C palmitoylating enzyme by screening all known palmitoyltransferases (PATs or DHHCs)...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28196780/evaluating-the-effectiveness-of-various-biochars-as-porous-media-for-biodiesel-synthesis-via-pseudo-catalytic-transesterification
#11
Jechan Lee, Jong-Min Jung, Jeong-Ik Oh, Yong Sik Ok, Sang-Ryong Lee, Eilhann E Kwon
This study focuses on investigating the optimized chemical composition of biochar used as porous material for biodiesel synthesis via pseudo-catalytic transesterification. To this end, six biochars from different sources were prepared and biodiesel yield obtained from pseudo-catalytic transesterification of waste cooking oil using six biochars were measured. Biodiesel yield and optimal reaction temperature for pseudo-catalytic transesterification were strongly dependent on the raw material of biochar. For example, biochar generated from maize residue exhibited the best performance, which yield was reached ∼90% at 300°C; however, the maximum biodiesel yield with pine cone biochar was 43% at 380°C...
February 3, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28196708/design-synthesis-and-biological-evaluation-of-2-4-disubstituted-oxazole-derivatives-as-potential-pde4-inhibitors
#12
Ya-Sheng Li, De-Kun Hu, Dong-Sheng Zhao, Xing-Yu Liu, Hong-Wei Jin, Gao-Peng Song, Zi-Ning Cui, Lian-Hui Zhang
In this study, a series of pyrazole derivatives containing 4-phenyl-2-oxazole moiety were designed and synthesized in a concise way, some of which exhibited considerable inhibitory activity against PDE4B and blockade of LPS-induced TNF-α release. Compound 4c displayed the strongest inhibition activity (IC50=1.6±0.4μM) and good selectivity against PDE4B. Meanwhile, compound 4c showed good in vivo activity in animal models of asthma/COPD and sepsis induced by LPS. The primary structure-activity relationship study showed the 3,5-dimethylpyrazole residue was essential for the bioactivity, and the substituted group R1 at the benzene ring also affected the activity...
February 3, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28195728/room-temperature-neutron-crystallography-of-drug-resistant-hiv-1-protease-uncovers-limitations-of-x-ray-structural-analysis-at-100k
#13
Oksana O Gerlits, David A Keen, Matthew P Blakeley, John M Louis, Irene T Weber, Andrey Y Kovalevsky
HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/Neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues...
February 14, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28195464/combining-the-martini-and-structure-based-coarse-grained-approaches-for-the-molecular-dynamics-studies-of-conformational-transitions-in-proteins
#14
Adolfo B Poma, Marek Cieplak, Panagiotis E Theodorakis
The application of coarse-grain (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolded protein structures and unfolding processes...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28193843/bound-substrate-in-the-structure-of-cyanobacterial-branching-enzyme-supports-a-new-mechanistic-model
#15
Mari Hayashi, Ryuichiro Suzuki, Christophe Colleoni, Steven G Ball, Naoko Fujita, Eiji Suzuki
Branching enzyme (BE) catalyzes the formation of α-1,6-glucosidic linkages in amylopectin and glycogen. The reaction products are variable depending on the organism sources, and the mechanistic basis for these different outcomes is unclear. Although most cyanobacteria have only one BE isoform belonging to glycoside hydrolase (GH) family 13, Cyanothece sp. ATCC 51142 has three isoforms (BE1, BE2, and BE3) with distinct enzymatic properties, suggesting that investigations of these enzymes might provide unique insights into this system...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193432/biochemical-and-milk-clotting-properties-and-mapping-of-catalytic-subsites-of-an-extracellular-aspartic-peptidase-from-basidiomycete-fungus-phanerochaete-chrysosporium
#16
Ronivaldo Rodrigues da Silva, Lilian Caroline Gonçalves de Oliveira, Maria Aparecida Juliano, Luiz Juliano, Arthur H C de Oliveira, Jose C Rosa, Hamilton Cabral
For a long time, proteolytic enzymes have been employed as key tools of industrial processes, especially in the dairy industry. In the present work, we used Phanerochaete chrysosporium for biochemical characterization and analysis of catalytic specificity of an aspartic peptidase. Our results revealed an aspartic peptidase with molecular mass ∼38kDa, maximal activity at pH 4.5 and 50°C, and stability above 80% in the pH range of 3-8 and temperature up to 55°C for 1h. In a milk-clotting assay, this peptidase showed maximal milk clotting activity at 60-65°C and maintenance of enzymatic activity above 80% in the presence of 20mM CaCl2...
June 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28192428/a-comparative-study-of-cold-and-warm-adapted-endonucleases-a-using-sequence-analyses-and-molecular-dynamics-simulations
#17
Davide Michetti, Bjørn Olav Brandsdal, Davide Bon, Geir Villy Isaksen, Matteo Tiberti, Elena Papaleo
The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale...
2017: PloS One
https://www.readbyqxmd.com/read/28188295/myroilysin-is-a-new-bacterial-member-of-the-m12a-family-of-metzincin-metallopeptidases-and-activated-by-a-cysteine-switch-mechanism
#18
Dongqing Xu, Jiale Zhou, Xiangdi Lou, Jianhua He, Tingting Ran, Weiwu Wang
Proteases play important roles in all living organisms and also have important industrial applications. Family M12A metalloproteases, mainly found throughout the animal kingdom, belong to the metzincin protease family and are synthesized as inactive precursors. So far, only flavastacin and myroilysin, isolated from bacteria, were reported to be M12A proteases, whilst the classification of myroilysin is still conflicting due to the lack of structural information. Here, we report the crystal structures of pro-myroilysin from bacterium Myroides sp...
February 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28186144/engineering-the-residual-side-chains-of-hap-phytases-to-improve-their-pepsin-resistance-and-catalytic-efficiency
#19
Canfang Niu, Peilong Yang, Huiying Luo, Huoqing Huang, Yaru Wang, Bin Yao
Strong resistance to proteolytic attack is important for feed enzymes. Here, we selected three predicted pepsin cleavage sites, L99, L162, and E230 (numbering from the initiator M of premature proteins), in pepsin-sensitive HAP phytases YkAPPA from Yersinia kristensenii and YeAPPA from Y. enterocolitica, which corresponded to L99, V162, and D230 in pepsin-resistant YrAPPA from Y. rohdei. We constructed mutants with different side chain structures at these sites using site-directed mutagenesis and produced all enzymes in Escherichia coli for catalytic and biochemical characterization...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28184005/a-c-terminal-tail-region-in-the-rous-sarcoma-virus-integrase-provides-high-plasticity-of-functional-integrase-oligomerization-during-intasome-assembly
#20
Krishan K Pandey, Sibes Bera, Ke Shi, Hideki Aihara, Duane P Grandgenett
The retrovirus integrase (IN) inserts the viral cDNA into the host DNA genome. Atomic structures of five different retrovirus INs complexed with their respective viral DNA or branched viral/target DNA substrates have indicated these intasomes are composed of IN subunits ranging from tetramers, to octamers or to hexadecamers. IN precursors are monomers, dimers or tetramers in solution. But, how intasome assembly is controlled remains unclear. Therefore, we sought to unravel the functional mechanisms in different intasomes...
February 8, 2017: Journal of Biological Chemistry
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