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Chembiochem: a European Journal of Chemical Biology

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https://www.readbyqxmd.com/read/28741300/the-hotdog-fold-thioesterase-pa1618-catalytic-mechanism-revealed-by-x-ray-structure-determination-of-the-substrate-oxygen-ester-analog-complex
#1
John A Latham, Tianyang Ji, Kaila Matthews, Patrick Mariano, Karen N Allen, Debra Dunaway-Mariano
Thioesterase activity (hydrolysis of thioester bonds) accounts for the majority of the activities in the hotdog-fold superfamily. The structure and mechanism of catalysis for many hotdog enzymes have been elucidated by X-ray crystallography and kinetics to probe the specific substrate usage and cellular functions. However, structures of hotdog thioesterases in complex with substrate analogs reported to date utilize ligands that comprise either truncations of the substrate or include additional atoms to prevent the hydrolysis...
July 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28741290/biochemical-characterization-of-lysine-acetylation-of-tyrosyl-trna-synthetase-in-escherichia-coli
#2
Sumana Venkat, Caroline Gregory, Qinglei Gan, Chenguang Fan
Aminoacyl-tRNA synthetases (AARSs) play essential roles in protein synthesis. As a member of the AARS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown to be acetylated at multiple lysine residues by proteomic studies. However, these putative acetylation targets have not been biochemically characterized yet. In this study, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyl-L-lysine into selected positions of TyrRS for in vitro characterization...
July 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28722796/extended-catalytic-scope-of-a-well-known-enzyme-asymmetric-reduction-of-iminium-substrates-by-glucose-dehydrogenase
#3
Sebastian Roth, Andreas Präg, Cindy Wechsler, Marija Marolt, Sascha Ferlaino, Steffen Lüdeke, Nicolas Sandon, Dennis Wetzl, Hans Iding, Beat Wirz, Michael Müller
NADP(H)-dependent imine reductases (IREDs) are of interest in biocatalytic research due to their ability to generate chiral amines from imine/iminium substrates. In reaction protocols involving IREDs, glucose dehydrogenase (GDH) is generally used to regenerate the expensive cofactor NADPH by oxidation of d-glucose to gluconolactone. We have characterized different IREDs with regard to reduction of a set of bicyclic iminium compounds and have utilized (1) H NMR and GC analyses to determine degree of substrate conversion and product enantiomeric excess (ee)...
July 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28722776/esterified-trehalose-analogs-protect-mammalian-cells-from-heat-shock
#4
Jack T Bragg, Hannah K D'Ambrosio, Timothy J Smith, Caroline A Gorka, Faraz A Khan, Joshua T Rose, Andrew J Rouff, Terence S Fu, Brittany J Bisnett, Michael Boyce, Sudhir Khetan, Margot G Paulick
Trehalose is a disaccharide that is produced by many organisms to better enable them to survive environmental stresses, including heat, cold, desiccation, and reactive oxygen species. Mammalian cells do not naturally biosynthesize trehalose; however, when introduced into mammalian cells, trehalose provides protection from the damages associated with freezing and drying. One of the major difficulties in using trehalose as a cellular protectant for mammalian cells is the delivery of this disaccharide into the intracellular environment; mammalian cell membranes are impermeable to the hydrophilic sugar trehalose...
July 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28722191/a-chemoproteomics-approach-to-investigate-phosphopantetheine-transferase-activity-at-the-cellular-level
#5
Sho Konno, Fumihiro Ishikawa, Takehiro Suzuki, Naoshi Dohmae, Hideaki Kakeya, Genzoh Tanabe
Phosphopantetheinylation is an essential post-translational protein modification to primary and secondary metabolic pathways that ensures bacterial cell viability and virulence, and it is used in the production of many pharmaceuticals. Traditional methods have not provided a comprehensive understanding of these modifications. Using chemical proteomic probes for adenylation and thiolation domains in nonribosomal peptide synthetases (NRPSs), we applied chemoproteomics to survey and validate the cellular activity of 4-(3-chloro-5-(trifluoromethyl)pyridin-2-yl)-N-(4-methoxypyridin-2-yl)piperazine-1-carbothioamide (ML267), a potent and selective small molecule 4'-phosphopantetheinyl transferase (PPTase) inhibitor, which attenuates secondary metabolism and viability of bacterial cells...
July 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28719729/synthesis-of-c-glucosylated-octaketide-anthraquinones-in-n-benthamiana-using-a-multispecies-based-biosynthetic-pathway
#6
Johan Andersen-Ranberg, Kenneth Thermann Kongstad, Majse Nafisi, Dan Staerk, Finn Okkels, Uffe Hasbro Mortensen, Birger Lindberg Møller, Rasmus John Normand Frandsen, Rubini Kannangara
Carminic acid is a C-glucosylated octaketide anthraquinone and the main constituent of the natural dye carmine (E120) possessing unique coloring, stability and solubility properties. Despite being used since ancient times, longstanding efforts to elucidate its route of biosynthesis have been unsuccessful. Herein is reported a novel combination of enzymes derived from a plant (Aloe arborescens, Aa), a bacterium (Streptomyces sp R1128, St), and an insect (Dactylopius coccus, Dc) that allows for the biosynthesis of the C-glucosylated anthraquinone, dcII, a precursor for carminic acid...
July 18, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28715110/irreversible-protein-labeling-via-paal-knorr-conjugation
#7
Ramesh Dasari, James J La Clair, Alexander Kornienko
The application of new chemical reactions in a biological context has advanced bioconjugation methods for both fundamental research and commercial arenas. Recent adaptations of reactions such as Huisgen 1,3-dipolar or Diels-Alder cycloadditions have enabled the labeling of specific residues in biomolecules by the attachment of molecules carrying azides, alkynes, or strained alkenes. Although these are fundamental tools, there is a need for the discovery of reactions that can label native proteins. We now report on the adaptation of the Paal-Knorr reaction to label lysine-residues in proteins via pyrrole linkages...
July 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28714559/how-we-make-dna-origami
#8
Klaus F Wagenbauer, Floris A S Engelhardt, Evi K Stahl, Vera K Hechtl, Pierre Stömmer, Fabian Seebacher, Letizia Meregalli, Philip Ketterer, Thomas Gerling, Hendrik Dietz
DNA ORIGAMI has attracted substantial attention since its invention ten years ago due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. While the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality, and preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge...
July 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28704573/modulation-of-mitochondriotropic-properties-of-cyanine-dyes-by-in-organello-copper-free-click-reaction
#9
Inka Negwer, Markus Hirsch, Stefka Kaloyanova, Tom Brown, Kalina Peneva, Hans-Jürgen Butt, Kaloian Koynov, Mark Helm
Cyanine dyes show a general propensity to localize to polarized mitochondria. This mitochondriotropism was used to perform a copper-free click reaction in the mitochondria of living cells. The in organello reaction of a Cy3 and Cy5 dye led to a product that was easily traceable by Förster resonance energy transfer (FRET). As determined by confocal laser scanning microscopy, the Cy3-Cy5 conjugate showed enhanced retention in mitochondria as compared to the starting compounds. This enhancement of a favorable property can be achieved by synthesis in organello but not outside mitochondria...
July 13, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28703362/in-vivo-delivery-and-activation-of-masked-fluorogenic-hydrolase-substrates-by-endogenous-hydrolases-in-c-elegans
#10
Shataakshi Dube, Hitesh Dube, Nicole B Green, Erik M Larsen, Alex White, R Jeremy Johnson, Jennifer Kowalski
Protein expression and localization are often studied in vivo by tagging molecules with green fluorescent protein (GFP), yet subtle changes in protein levels are not easily detected. To develop a sensitive in vivo method to amplify fluorescence signals and allow cell-specific quantification of protein abundance changes, we sought to apply an enzyme-activated cellular fluorescence system in vivo by delivering ester-masked fluorophores to Caenorhabditis elegans neurons expressing porcine liver esterase (PLE)...
July 12, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28696509/an-l-rna-aptamer-with-expanded-chemical-functionality-that-inhibits-microrna-biogenesis
#11
Adam Michael Kabza, Jonathan Thomas Sczepanski
In order to facilitate isolation of L-aptamers with novel RNA-binding properties, we have employed a cationic nucleotide, 5-aminoallyl-uridine, during the mirror image in vitro selection process. In this effort, we identified a modified L-RNA aptamer (MLRA) capable of binding oncogenic pre-miR-19a with exceptional affinity, and we show that the cationic modification is absolutely critical for binding. Furthermore, formation of the MLRA-pre-miR-19a complex inhibits Dicer-mediated cleavage of the pre-miR, thus blocking formation of the mature functional microRNA...
July 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28681411/new-fluorescent-nanoparticles-for-ultrasensitive-detection-of-nucleic-acids-by-optical-methods
#12
Mads Westergaard Mulberg, Maria Taskova, Rasmus P Thomsen, Anders H Okholm, Jørgen Kjems, Kira Astakhova
For decades the detection of nucleic acids and their interactions at low abundances has been a challenging task that has thus far been solved by enzymatic target amplification. In this work we aimed at developing efficient tools for amplification-free nucleic acid detection, which resulted in the synthesis of new fluorescent nanoparticles. Here, the fluorescent nanoparticles were made by simple and inexpensive radical emulsion polymerization of butyl acrylate in the presence of fluorescent dyes and additional functionalization reagents...
July 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28678390/natural-product-withanolide-inspired-small-molecules-as-potent-inhibitors-of-wnt-signaling
#13
Herbert Waldmann, Michael Sheremet, Shobhna Kapoor, Peter Schröder, Kamal Kumar, Slava Ziegler
Wnt signaling is a fundamental pathway that drives embryonic development and is essential for stem cell maintenance and tissue homeostasis. Dysregulation of Wnt signaling is linked to various diseases and a constitutively active Wnt pathway drives tumorigenesis. Thus, disruption of the Wnt response is deemed a promising strategy for cancer drug discovery. However, only few clinical drug candidates that target Wnt signaling are available so far and new small molecules modulators of Wnt-related processes are in high demand...
July 5, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28660650/rational-design-of-domain-swapping-based-c-type-cytochrome-heterodimers-using-chimeric-proteins
#14
Mohan Zhang, Tsukasa Nakanishi, Masaru Yamanaka, Satoshi Nagao, Sachiko Yanagisawa, Yasuhito Shomura, Naoki Shibata, Takashi Ogura, Yoshiki Higuchi, Shun Hirota
Design of protein oligomers with multi active sites has been gaining interest, owing to their potential use for biomaterials, which has encouraged researchers to develop a new design method. 3D domain swapping is the unique phenomenon that protein molecules exchange the same structural region between them. Herein, to construct oligomeric heme proteins with different active sites utilizing domain swapping, we constructed two c-type cytochrome-based chimeric proteins and domain swapped them. According to X-ray crystallographic analysis, the two chimeric proteins formed a domain-swapped dimer with two His/Met coordinate hemes...
June 28, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28658518/two-completely-different-mechanisms-for-highly-specific-na-recognition-by-dnazymes
#15
Wenhu Zhou, Runjhun Saran, Jinsong Ding, Juewen Liu
Our view on the interaction between Na+ and nucleic acids is changed by a few recently discovered Na+-specific RNA-cleaving DNAzymes. Herein, two such DNAzymes, EtNa and Ce13d, are compared to elucidate the mechanisms of Na+ binding. Mutation studies indicate they have different sequence requirements. Phosphorothioate substitution at the scissile phosphate drops the activity of the EtNa by 140-fold, and it cannot be rescued by thiophilic Cd2+ or Mn2+, while the Ce13d can be rescued. Na+-dependent activity assays indicate two Na+ ions bind cooperatively in the EtNa, likely both each interacting with a non-bridging oxygen atoms in the scissile phosphate, while the Ce13d binds only one Na+ in a well-defined Na+ aptamer...
June 28, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28650563/unusual-lipid-a-from-a-cold-adapted-bacterium-detailed-structural-characterization
#16
Maria Michela Corsaro, Angela Casillo, Marcello Ziaco, Buko Lindner, Ermenegilda Parrilli, Dominik Schwudke, Aurora Holgado, Lynn Verstrepen, Filomena Sannino, Rudi Beyaert, Rosa Lanzetta, Maria Luisa Tutino
Colwellia psychrerythraea 34H is a Gram-negative cold-adapted microorganism that adopts many strategies to cope with the limitations due to the low temperatures of its habitat. In this study, we reported the complete characterization of the lipid A moiety from the lipopolysaccharide of Colwellia, to find out if structural features could be linked to the cold-adaptation strategy. The lipid A and its partially deacylated derivative were completely characterized by means of high resolution mass spectrometry, NMR spectroscopy, and chemical analysis...
June 26, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28650092/photoactivatable-mussel-based-underwater-adhesive-proteins-by-an-expanded-genetic-code
#17
Mathias Hauf, Florian Richter, Tobias Schneider, Thomas Faidt, Berta M Martins, Tobias Baumann, Patrick Durkin, Holger Dobbek, Karin Jacobs, Andreas Möglich, Nediljko Budisa
Marine mussels exhibit potent underwater adhesion abilities under hostile conditions employing 3,4-dihydroxy-phenylalanine (Dopa)-rich mussel-adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Here, we have developed a novel strategy based on genetic code expansion by engineering efficient aminoacyl-tRNA synthetases (aaRSs) for the photocaged non-canonical amino acid (ncAA) ortho-nitrobenzyl Dopa (ONB-Dopa). The engineered ONB-DopaRS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-Dopa yielding spatiotemporally controlled underwater adhesives...
June 26, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28643453/small-molecule-inhibitors-of-the-tumor-suppressor-fhit
#18
Andreas Marx, Sandra Lange, Stephan Hacker, Philipp Schmid, Martin Scheffner
The tumor suppressor Fhit and its substrate diadenosine triphosphate (Ap3A) are important factors in cancer development and progression. Fhit has Ap3A hydrolase activity and cleaves Ap3A into adenosine monophosphate (AMP) and adenosine diphosphate (ADP) which is believed to terminate Fhit-mediated signaling. How the catalytic activity of Fhit is regulated and how the Fhit-Ap3A complex exerts its growth-suppressive function remain to be discovered. Small molecule inhibitors of the enzymatic activity of Fhit would provide valuable tools for the elucidation of its tumor-suppressive functions...
June 23, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28640486/dendrimer-based-signal-amplification-of-click-labelled-dna-in-situ
#19
Nada Raddaoui, Samuele Stazzoni, Leonhard Möckl, Bastien Viverge, Florian Geiger, Hanna Engelke, Christoph Bräuchle, Thomas Carell
The in vivo incorporation of alkyne modified bases into the genome of cells is today the basis for efficient detection of cell proliferation. Cells are grown in the presence of ethinyl-dU (EdU), fixed and permeabilized. The incorporated alkynes are then efficiently detected using azide-containing fluorophores and the Cu(I) catalyzed alkyne-azide click reaction. In a world where constant improvement of the sensitivity of a given method is driving diagnostic advancement, we developed azide and alkyne modified dendrimers that allow to establish sandwich-type detection assays that show significantly improved signal intensities and signal to noise ratios far beyond of what is currently possible...
June 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28639727/switching-futile-para-quinone-to-efficient-ros-generator-ubiquitin-specific-protease-2-inhibition-electrocatalysis-and-quantification
#20
Ashraf Brik, Pushparathinam Gopinath, Atif Mahammed, Tal Eilon-Shaffer, Mickal Nawatha, Shimrit Ohayon, Doron Shabat, Zeev Gross
Understanding the correlation between structural features of small molecule drugs to its mode of action is a fascinating topic and crucial for the drug discovery process. However, in many cases the exact parameters that dictate the mode of action is still lacking. Following a large screening for USP2 inhibition identified effective para-quinone based inhibitor with unclear mode of action. For gaining a deep knowledge on its mechanism of inhibition, a set of para-quinones was prepared and studied for USP2 inhibition, electrocatalysis and ROS quantification...
June 22, 2017: Chembiochem: a European Journal of Chemical Biology
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