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https://www.readbyqxmd.com/read/29156123/a-nanopore-based-label-free-and-real-time-monitoring-assay-for-dna-methyltransferase-activity-and-inhibition
#1
Sana Rauf, Ling Zhang, Asghar Ali, Jalal Ahmad, Yang Liu, Jinghong Li
DNA methylation catalyzed by DNA methyltransferase plays an important role in many biological processes. However, conventional assays proposed for DNA methyltransferase activity are laborious and discontinuous. We describe a novel method for real-time monitoring of the activity and kinetics of Escherichia coli DNA adenine methyltransferase (Dam), using nanopore technique coupled with enzyme-linkage reactions. A double-stranded DNA probe AB having a recognition sequence 5'-GATC-3' for both Dam and MboI restriction endonuclease was prepared...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155974/transcript-profiling-of-a-bitter-variety-of-narrow-leafed-lupin-to-discover-alkaloid-biosynthetic-genes
#2
Ting Yang, Istvan Nagy, Davide Mancinotti, Sophie Lisa Otterbach, Trine Bundgaard Andersen, Mohammed Saddik Motawia, Torben Asp, Fernando Geu-Flores
Lupins (Lupinus spp.) are nitrogen-fixing legumes that accumulate toxic alkaloids in their protein-rich beans. These anti-nutritional compounds belong to the family of quinolizidine alkaloids (QAs), which are of interest to the pharmaceutical and chemical industries. To unleash the potential of lupins as protein crops and as sources of QAs, a thorough understanding of the QA pathway is needed. However, only the first enzyme in the pathway, lysine decarboxylase (LDC), is known. Here, we report the transcriptome of a high-QA variety of narrow-leafed lupin (L...
November 16, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29153699/characterization-of-d-succinylase-from-cupriavidus-sp-p4-10-c-and-its-application-in-d-amino-acid-synthesis
#3
Yosuke Sumida, Sachio Iwai, Yoshiaki Nishiya, Shinya Kumagai, Toshihide Yamada, Masayuki Azuma
d-Amino acids are important building blocks for various compounds, such as pharmaceuticals and agrochemicals. A more cost-effective enzymatic method for d-amino acid production is needed in the industry. We improved a one-pot enzymatic method for d-amino acid production by the dynamic kinetic resolution of N-succinyl amino acids using two enzymes: d-succinylase (DSA) from Cupriavidus sp. P4-10-C, which hydrolyzes N-succinyl-d-amino acids enantioselectively to their corresponding d-amino acid, and N-succinyl amino acid racemase (NSAR, EC...
November 15, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29153644/propionic-acid-production-from-soy-molasses-by-propionibacterium-acidipropionici-fermentation-kinetics-and-economic-analysis
#4
Hopen Yang, Zhongqiang Wang, Meng Lin, Shang-Tian Yang
Propionic acid (PA) is a specialty chemical; its calcium salt is widely used as food preservative. Soy molasses (SM), a low-value byproduct from soybean refinery, contains sucrose and raffinose-family oligosaccharides (RFO), which are difficult to digest for most animals and industrial microorganisms. The feasibility of using SM for PA production by P. acidipropionici, which has genes encoding enzymes necessary for RFO hydrolysis, was studied. With corn steep liquor as the nitrogen source, stable long-term PA production from SM was demonstrated in sequential batch fermentations, achieving PA productivity of >0...
November 8, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29153530/physicochemical-and-sensory-properties-of-yogurts-containing-sacha-inchi-plukenetia-volubilis-l-seeds-and-%C3%AE-glucans-from-ganoderma-lucidum
#5
Ana-Milena Vanegas-Azuero, Luis-Felipe Gutiérrez
Dairy products have been widely used for adding various biomolecules with the aim of improving their functional properties and health benefits. In this study, the physicochemical properties and sensory acceptance of yogurts enriched with sacha inchi (Plukenetia volubilis) seeds (SIS) and β-glucans from Ganoderma lucidum (BGGL) were investigated. The angiotensin-converting enzyme-inhibitory activity of some yogurt samples was also evaluated. Yogurts were produced from reconstituted skim milk powder, and SIS (4% wt/wt) and BGGL were added at different concentrations (0-1...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29152096/the-non-canonical-ubiquitin-activating-enzyme-uba6-suppresses-epithelial-mesenchymal-transition-of-mammary-epithelial-cells
#6
Xianpeng Liu, Limin Sun, Demirkan B Gursel, Chonghui Cheng, Sui Huang, Alfred W Rademaker, Seema A Khan, Jun Yin, Hiroaki Kiyokawa
Ubiquitination plays critical roles in the regulation of oncoproteins and tumor suppressors during carcinogenesis. The two ubiquitin activating enzymes (E1) in human genome, UBA1 and UBA6, initiate ubiquitination by ATP-dependent activation of ubiquitin. Recent evidence suggests that UBA1 and UBA6 play partially overlapped yet distinct roles in controlling the proteome. Here we demonstrate that ubiquitination pathways initiated specifically by UBA6 set a suppressive barrier against critical steps of mammary carcinogenesis such as loss of polarity, anoikis resistance and epithelial-mesenchymal transition (EMT)...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151159/enhanced-catalytic-efficiency-and-enantioselectivity-of-epoxide-hydrolase-from-agrobacterium-radiobacter-ad1-by-iterative-saturation-mutagenesis-for-r-epichlorohydrin-synthesis
#7
Shu-Ping Zou, Yu-Guo Zheng, Qun Wu, Zhi-Cai Wang, Ya-Ping Xue, Zhi-Qiang Liu
Enantioselective hydrolysis of epoxides by epoxide hydrolase (EH) is one of the most attractive approaches for the synthesis of chiral epoxides. So far, attempts to develop an efficient epoxide hydrolase -mediated biotransformation have been limited by either the low activity or insufficient enantioselectivity of epoxide hydrolase. In this study, iterative saturation mutagenesis (ISM) of epoxide hydrolase from Agrobacterium radiobacter AD1 (ArEH) was performed for efficient production of (R)-epichlorohydrin...
November 18, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29149203/alc1-chd1l-a-chromatin-remodeling-enzyme-is-required-for-efficient-base-excision-repair
#8
Masataka Tsuda, Kosai Cho, Masato Ooka, Naoto Shimizu, Reiko Watanabe, Akira Yasui, Yuka Nakazawa, Tomoo Ogi, Hiroshi Harada, Keli Agama, Jun Nakamura, Ryuta Asada, Haruna Fujiike, Tetsushi Sakuma, Takashi Yamamoto, Junko Murai, Masahiro Hiraoka, Kaoru Koike, Yves Pommier, Shunichi Takeda, Kouji Hirota
ALC1/CHD1L is a member of the SNF2 superfamily of ATPases carrying a macrodomain that binds poly(ADP-ribose). Poly(ADP-ribose) polymerase (PARP) 1 and 2 synthesize poly(ADP-ribose) at DNA-strand cleavage sites, promoting base excision repair (BER). Although depletion of ALC1 causes increased sensitivity to various DNA-damaging agents (H2O2, UV, and phleomycin), the role played by ALC1 in BER has not yet been established. To explore this role, as well as the role of ALC1's ATPase activity in BER, we disrupted the ALC1 gene and inserted the ATPase-dead (E165Q) mutation into the ALC1 gene in chicken DT40 cells, which do not express PARP2...
2017: PloS One
https://www.readbyqxmd.com/read/29148053/effective-inactivation-of-a-wide-range-of-viruses-by-pasteurization
#9
Albrecht Gröner, Connie Broumis, Randel Fang, Thomas Nowak, Birgit Popp, Wolfram Schäfer, Nathan J Roth
BACKGROUND: Careful selection and testing of plasma reduces the risk of blood-borne viruses in the starting material for plasma-derived products. Furthermore, effective measures such as pasteurization at 60°C for 10 hours have been implemented in the manufacturing process of therapeutic plasma proteins such as human albumin, coagulation factors, immunoglobulins, and enzyme inhibitors to inactivate blood-borne viruses of concern. A comprehensive compilation of the virus reduction capacity of pasteurization is presented including the effect of stabilizers used to protect the therapeutic protein from modifications during heat treatment...
November 16, 2017: Transfusion
https://www.readbyqxmd.com/read/29146530/identification-of-the-glucosamine-kinase-in-the-chitinolytic-pathway-of-thermococcus-kodakarensis
#10
Mehwish Aslam, Naoya Takahashi, Kohei Matsubara, Tadayuki Imanaka, Tamotsu Kanai, Haruyuki Atomi
Although the chitinolytic pathway of the hyperthermophilic archaeon Thermococcus kodakarensis is well-studied, the genome does not contain genes homologous to previously identified glucosamine kinase genes. As some ADP-dependent glucokinases in the order Thermococcales exhibit phosphorylation activities for both glucose and glucosamine in vitro, the homolog in T. kodakarensis, encoded by TK1110, was selected as a candidate for the missing glucosamine kinase gene. The purified, recombinant TK1110 enzyme exhibited phosphorylation activities for not only glucose but also glucosamine and N-acetylglucosamine...
November 13, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29145241/the-prognostic-value-of-the-serum-neuron-specific-enolase-and-lactate-dehydrogenase-in-small-cell-lung-cancer-patients-receiving-first-line-platinum-based-chemotherapy
#11
Xiaofan Liu, Weiming Zhang, Wen Yin, Yang Xiao, Changzhi Zhou, Yi Hu, Shuang Geng
The aim of this study was to investigate the associations of serum levels of neuron-specific enolase (NSE), pro-gastrin releasing peptide (ProGRP), and lactate dehydrogenase (LDH) with clinical response and survival in small cell lung cancer (SCLC) patients receiving first-line platinum-based chemotherapy.One hundred thirty-six patients with SCLC were recruited in this study. All the patients received first-line platinum-based chemotherapy. Clinical efficacy was assessed according to Response Evaluation Criteria in Solid Tumors v1...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29143302/convergent-selection-pressures-drive-the-evolution-of-rhodopsin-kinetics-at-high-altitudes-via-non-parallel-mechanisms
#12
Gianni M Castiglione, Ryan K Schott, Frances E Hauser, Belinda S W Chang
Convergent evolution in response to similar selective pressures is a well-known phenomenon in evolutionary biology. Less well understood is how selection drives convergence in protein function, and the underlying mechanisms by which this can be achieved. Here we investigate functional convergence in the visual system of two distantly related lineages of high-altitude adapted Andean and Himalayan catfishes. Statistical analyses revealed in the two high-altitude lineages, a parallel acceleration of evolutionary rates in rhodopsin, the dim-light visual pigment...
November 16, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29142780/molecular-mechanism-of-enzymatic-chlorite-detoxification-insights-from-structural-and-kinetic-studies
#13
Irene Schaffner, Georg Mlynek, Nicola Flego, Dominic Pühringer, Julian Libiseller-Egger, Leighton Coates, Stefan Hofbauer, Marzia Bellei, Paul G Furtmüller, Gianantonio Battistuzzi, Giulietta Smulevich, Kristina Djinović-Carugo, Christian Obinger
The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Although structure and steady-state kinetics of Clds have been elucidated, many questions remain (e.g., the mechanism of chlorite cleavage and the pH dependence of the reaction). Here, we present high-resolution X-ray crystal structures of a dimeric Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and the neutron structure at pH 9.0 together with the pH dependence of the Fe(III)/Fe(II) couple, and the UV-vis and resonance Raman spectral features...
November 3, 2017: ACS Catalysis
https://www.readbyqxmd.com/read/29142591/a-novel-highly-efficient-%C3%AE-glucosidase-with-a-cellulose-binding-domain-characterization-and-properties-of-native-and-recombinant-proteins
#14
J A Méndez-Líter, J Gil-Muñoz, M Nieto-Domínguez, J Barriuso, L I de Eugenio, M J Martínez
Background: Cellulose, the most abundant biopolymer on earth, is an alternative for fossil fuels as a renewable feedstock for the production of second-generation biofuels and other chemicals. The discovery of novel, highly efficient β-glucosidases remains as one of the major bottlenecks for cellulose degradation. In this context, the ascomycete Talaromyces amestolkiae, isolated from cereal samples, has been studied as a promising source for these enzymes. Results: BGL-2 is the major β-glucosidase secreted by this fungus in the presence of cellulosic inductors...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29142210/millisecond-dynamics-of-btk-reveal-kinome-wide-conformational-plasticity-within-the-apo-kinase-domain
#15
Mohammad M Sultan, Rajiah Aldrin Denny, Ray Unwalla, Frank Lovering, Vijay S Pande
Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinase's solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTK's kinase domain...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29140092/determinants-and-expansion-of-specificity-in-a-trichothecene-udp-glucosyltransferase-from-oryza-sativa
#16
Karl M Wetterhorn, Kaitlyn Gabardi, Herbert Michlmayr, Alexandra Malachova, Mark Busman, Susan Patricia McCormick, Franz Berthiller, Gerhard Adam, Ivan Rayment
Family 1 UDP-glycosyltransferases in plants (UGTs) primarily form glucose conjugates of small molecules and, besides other functions, play a role in detoxification of xenobiotics. Indeed, overexpression of a barley UGT in wheat has been shown to control Fusarium head blight, where this is a plant disease of global significance that leads to reduced crop yields and contamination with trichothecene mycotoxins such as deoxynivalenol (DON), T-2 toxin and many other structural variants. The UGT Os79 from rice has emerged as a promising candidate for inactivation of mycotoxins on account of its ability to glycosylate DON, nivalenol and hydrolyzed T-2 toxin (HT-2)...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29140090/qm-mm-simulations-identify-the-ring-opening-mechanism-of-creatininase
#17
Jitrayut Jitonnom, Joni Mujika, Marc W van der Kamp, Adrian J Mulholland
Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water-addition followed by ring-opening. Water-addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring-opening is still under debate. The proton donor in this step is either His178, or a water molecule bound to one of metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29140084/characterization-of-a-ugt84-family-glycosyltransferase-provides-new-insights-into-substrate-binding-and-reactivity-of-galloylglucose-ester-forming-ugts
#18
Alexander E Wilson, Xiaoxue Feng, Nadia N Ono, Doron Holland, Rachel Amir, Li Tian
Galloylated plant specialized metabolites play important roles in plant-environment interactions as well as the promotion of human and animal health. The galloylation reactions are mediated by the formation of galloylglucose esters from gallic acid and UDP-glucose, catalyzed by the plant UGT84 family glycosyltransferases. To explore and exploit the structural determinants of UGT84 activities, we performed homology modeling and substrate docking of PgUGT84A23, a galloylglucose ester-forming family 84 UGT, as well as sequence comparisons of PgUGT84A23 with other functionally characterized plant UGTs...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29139594/a-multi-perspective-approach-to-solvent-regulation-of-enzymatic-activity-hmg-coa-reductase
#19
Frank Schulz, Michael Dirkmann, Javier Iglesias, Victor Muñoz, Pandian Sokkar, Christoph Rumancev, Andreas von Gundlach, Oktavian Krenczyk, Tobias Vöpel, Julia Nowack, Martin A Schroer, Simon Ebbinghaus, Christian Herrmann, Axel Rosenhahn, Elsa Sanchez-Garcia
HMG-CoA reductase was investigated in different organic co-solvents using kinetic and calorimetric measurements, molecular dynamics simulations and small-angle x-ray scattering. The combined experimental and theoretical techniques were essential to complement each other's limitations in the investigation of the complex interaction pattern between the enzyme and the different solvent types and concentrations. In this way, we could elucidate the underlying mechanisms for the loss of enzyme activity in different water-miscible solvents...
November 15, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29138643/interactions-of-desmethoxyyangonin-a-secondary-metabolite-from-renealmia-alpinia-with-human-monoamine-oxidase-a-and-oxidase-b
#20
Narayan D Chaurasiya, Francisco León, Yuanqing Ding, Isabel Gómez-Betancur, Dora Benjumea, Larry A Walker, Stephen J Cutler, Babu L Tekwani
Renealmia alpinia (Zingiberaceae), a medicinal plant of tropical rainforests, is used to treat snakebites and other injuries and also as a febrifuge, analgesic, antiemetic, antiulcer, and anticonvulsant. The dichloromethane extract of R. alpinia leaves showed potent inhibition of human monoamine oxidases- (MAOs-) A and B. Phytochemical studies yielded six known compounds, including pinostrobin 1, 4'-methyl ether sakuranetin 2, sakuranetin 3, pinostrobin chalcone 4, yashabushidiol A 5, and desmethoxyyangonin 6...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
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