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Chembiochem: a European Journal of Chemical Biology

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https://www.readbyqxmd.com/read/27914120/effect-of-glycosylation-on-the-biocatalytic-properties-of-hydroxynitrile-lyase-from-the-passion-fruit-passiflora-edulis-a-comparison-of-natural-and-recombinant-enzymes
#1
Aem Nuylert, Yuko Ishida, Yasuhisa Asano
A hydroxynitrile lyase from the passion fruit, Passiflora edulis (PeHNL) was isolated from the leaves and showed high stability in biphasic co-organic solvent systems for cyanohydrin synthesis. Cyanohydrins are important building blocks for the production of fine chemicals and pharmaceuticals. Thus, to enhance production yields of PeHNL for industrial applications, we cloned and expressed recombinant PeHNL in E. coli BL21 (DE3) and P. pastoris GS115 cells without a signal peptide sequence. The aim of the present study is to determine the effect of N-glycosylation on enzyme stability and catalytic properties in microbial expression systems...
December 3, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27911981/asymmetric-ketone-reduction-by-imine-reductases
#2
Maike Lenz, Jan Meisner, Leann Quertinmont, Stefan Lutz, Johannes Kästner, Bettina Nestl
The rapidly growing area of asymmetric imine reduction by imine reductases (IREDs) has provided alternative routes to chiral amines. Here we report the expansion of the reaction scope of IREDs by showing the stereoselective reduction of 2,2,2-trifluoroacetophenone (1). Assisted by an in silico analysis of energy barriers, we evaluated asymmetric hydrogenations of carbonyls and imines considering the influence of substrate reactivity on the chemoselectivity of this novel class of reductases. We report on the asymmetric reduction of C=N as well as C=O bonds catalyzed by members of the IRED enzyme family...
December 2, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27906500/phylogenetic-studies-gene-cluster-analysis-and-enzymatic-reaction-support-anthrahydroquinone-reduction-as-the-physiological-function-of-fungal-17%C3%AE-hydroxysteroid-dehydrogenase
#3
Leon Fürtges, David Conradt, Michael A Schätzle, Shailesh Kumar Singh, Nada Kraševec, Tea Lanišnik Rižner, Michael Müller, Syed Masood Husain
17β-Hydroxysteroid dehydrogenase (17β-HSDcl) from the filamentous fungus Curvularia lunata (teleomorph Cochliobolus lunatus) catalyzes NADP(H)-dependent oxidoreductions of androgens and estrogens. Despite detailed biochemical and structural characterization of 17β-HSDcl, its physiological function remains unknown. On the basis of amino acid sequence alignment, phylogenetic studies, and the recent identification of the physiological substrates of the homologous MdpC from Aspergillus nidulans and AflM from Aspergillus parasiticus, we propose an anthrahydroquinone as the physiological substrate of 17β-HSDcl...
December 1, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27907247/ship2-structure-function-and-inhibition
#4
Mark P Thomas, Christophe Erneux, Barry V L Potter
SHIP2 is a phosphatase that acts at the 5-position of phosphatidylinositol 3,4,5-trisphosphate. It is one of several enzymes that catalyse dephosphorylation at the 5-position of phosphoinositides or inositol phosphates. SHIP2 has a confirmed role in opsismodysplasia, a disease of bone development, but also interacts with proteins involved in insulin signalling, cytoskeletal function (thus having an impact on endocytosis, adhesion, proliferation and apoptosis) and immune system function. The structure of three domains (constituting about 38% of the protein) is known...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27905174/zirconium-iv-catalyzed-ring-opening-of-on-dna-epoxides-in-water
#5
Lijun Fan, Christopher P Davie
DNA-encoded library technology (ELT) has spurred wide interest in the pharmaceutical industry as a powerful tool for hit and lead generation. In recent years a number of "DNA-compatible" chemical modifications have been published and used to synthesize vastly diverse screening libraries. Herein we report a newly developed, zirconium tetrakis(dodecyl sulfate) [Zr(DS)4] catalyzed ring-opening of on-DNA epoxides in water with amines, including anilines. Subsequent cyclization of the resulting on-DNA β-amino alcohols leads to a variety of biologically interesting, non-aromatic heterocycles...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27905163/fungal-glycolipid-hydrolase-inhibitors-and-their-effect-on-cryptococcus-neoformans
#6
Andres Gonzalez Santana, Christina Tysoe, Guanggan Hu, James Kronstad, Ethan Goddard-Borger, Stephen Withers
Pathogenic fungi kill an estimated 1.3 million people each year. This number is predicted to rise as drug resistance spreads, thus antifungal drugs with novel modes of action are urgently required. Fungal endoglycoceramidase-related proteins 1 and 2 (EGCrP-1 and -2), which hydrolyse glucosylceramide and ergosteryl beta-glucoside, respectively, are important for fungal cell growth and have been identified as potential targets for drug development. A library of iminosugar derivatives was screened against EGCrP-1 and -2, thereby identifying a number of competitive inhibitors with nanomolar affinities...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27905160/improving-the-solubility-of-artificial-ligands-of-streptavidin-to-enable-more-practical-reversible-switching-of-protein-localization-in-cells
#7
Ryo Tachibana, Takuya Terai, Gaelle Boncompain, Shigeru Sugiyama, Nae Saito, Franck Perez, Yasuteru Urano
Chemical inducers that can control target protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the "retention using selective hook" (RUSH) system for reversible localization change of proteins of interest by addition/washout of small molecules called artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS is restricted by limited solubility in water. Here, we overcome this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27900834/transformation-of-free-and-dipeptide-bound-glycated-amino-acids-by-two-strains-of-saccharomyces-cerevisiae
#8
Michael Hellwig, Marie Börner, Falco Beer, Karl-Heinz van Pée, Thomas Henle
The yeast Saccharomyces cerevisiae transforms branched-chain and aromatic amino acids to higher alcohols in the Ehrlich pathway. During microbiological culturing and industrial fermentations, this yeast is confronted with amino acids modified by reducing sugars in the Maillard reaction (glycation). In order to get first insights into the physiological "handling" of glycated amino acids by yeasts, individual Maillard reaction products (MRPs; fructosyllysine, carboxymethyllysine, pyrraline, formyline, maltosine, methylglyoxal-derived hydroimidazolone) were administered to two strains of S...
November 30, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27898188/modern-approaches-to-discovering-new-hydroxynitrile-lyases-for-biocatalysis
#9
REVIEW
Santosh Kumar Padhi
Hydroxynitrile lyases (HNLs) have grown in importance from laboratory to industry due to their potential to catalyze stereoselective C-C bond-formation reactions in the synthesis of several chiral intermediates, such as enantiopure α-cyanohydrins, β-nitro alcohols, and their derivatives with multiple functional groups. With these wide applications, the demand for finding new HNLs has increased, and this has led to exploration not only of new HNLs but also of new ways to discover them. An exclusive review article on HNLs by Asano et al...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27897387/small-molecule-induced-and-cooperative-enzyme-assembly-on-a-14-3-3-scaffold
#10
Anniek den Hamer, Lenne Lemmens, Minke Nijenhuis, Christian Ottmann, Maarten Merkx, Tom de Greef, Luc Brunsveld
Scaffold proteins regulate cell signaling by promoting the proximity of putative interaction partners. While frequently applied in a cellular setting, their fundamental understanding, amongst other in terms of quantitative parameters, has been lagging behind. Here we present a scaffold protein platform based on the native 14-3-3 dimeric protein and under the control of a small-molecule, which allows to be studied in an in vitro setting and mathematically described. Robust small-molecule regulation of caspase-9 activity via induced dimerization on the 14-3-3 scaffold was demonstrated...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27897371/structural-rearrangement-from-oligomer-to-fibril-detected-with-fret-in-a-designed-amphiphilic-peptide
#11
Heng Chi, Timothy A Keiderling
ß-sheet conformation is promoted in peptides with amphiphilic design, and stable ß-turn formation is favored with the unnatural amino acid DPro followed by a flexible residue, such as Gly. A 19-residue peptide (B3) was synthesized with alternating hydrophobic and hydrophilic residues connected by symmetrical DPro-Gly and Gly-DPro turns. B3 forms an oligomeric aggregate, rich in ß-sheet conformation, which reversibly transforms into unordered structure on heating as evidenced by its temperature dependent IR spectra...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27897370/iterative-non-proteinogenic-residue-incorporation-yields-%C3%AE-%C3%AE-peptides-with-a-helix-loop-helix-tertiary-structure-and-high-affinity-for-vegf
#12
James W Checco, Samuel H Gellman
Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues ("α/β-peptides") that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27897367/bifunctionality-of-activ-as-a-cyclase-thioesterase-revealed-by-in-vitro-reconstitution-of-actinorhodin-biosynthesis-in-streptomyces-coelicolor-a3-2
#13
Takaaki Taguchi, Takayoshi Awakawa, Yukitaka Nishihara, Michiho Kawamura, Yasuo Ohnishi, Koji Ichinose
Type II polyketide synthase (PKS) iteratively generates a nascent polyketide thioester of acyl carrier protein (ACP), which is structurally modified to produce an ACP-free intermediate towards its final metabolite. However, the timing of ACP off-loading is not well defined due to the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess a TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27897366/active-site-crowding-of-p450-3a4-as-a-strategy-to-alter-its-selectivity
#14
Paolo Schiavini, Kin J Cheong, Nicolas Moitessier, Karine Auclair
Substrate promiscuous enzymes are a promising starting point for the development of versatile biocatalysts. In this study, human cytochrome P450 3A4, known for its ability to metabolize hundreds of drugs, was engineered to alter its regio- and stereoselectivity. Rational mutagenesis was used to specifically introduce steric hindrance in the large active site of P450 3A4 and favour oxidation at a more sterically accessible position on the substrate. Hydroxylation of a synthetic precursor of (R)-lisofylline, a compound under investigation for its anti-inflammatory properties, was chosen as a first proof-of-principle application of our protein engineering strategy...
November 29, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27885767/novel-amino-acid-based-%C3%AE-phosphorylated-nitroxides-for-probing-acidic-ph-in-biological-systems-by-epr-spectroscopy
#15
Sophie Thétiot-Laurent, Gaëlle Gosset, Jean-Louis Clément, Mathieu Cassien, Anne Mercier, Didier Siri, Anouk Gaudel-Siri, Antal Rockenbauer, Marcel Culcasi, Sylvia Pietri
There is increasing attraction of measuring pH in biological studies using nitroxides having pH-dependent electron paramagnetic resonance (EPR) spectra. Aiming to improve the spectral sensitivity, ΔaX, of these probes (i.e. the difference between the EPR hyperfine splittings (hfs) in their protonated and unprotonated forms), we present here a series of novel linear α-carboxy, α'-diethoxyphosphoryl nitroxides constructed on an amino acid core and featuring a (α or α')-C-H bond. In buffers the three main hfs (aN, aH and aP) of their EPR spectra vary reversibly with pH and, when it is inferred from aP or aH titration curves, a 2-4-fold increase in sensitivity is achieved vs reference imidazoline or imidazolidine nitroxides...
November 25, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27883258/bivalent-display-of-dicysteine-on-pna-for-homogenous-dna-rna-detection-via-in-situ-fluorescence-labelling
#16
Gemin Fang, Oliver Seitz
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached via covalent bonds to an oligonucleotide probe. However, the additional conjugation step increases costs. Herein we introduce a method that avoids the requirement for the preparation of fluorescence labeled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid probes to form a bipartite tetracysteine motif which binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH...
November 24, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27870530/coiled-coil-mediated-activation-of-oligo-arginine-cell-penetrating-peptides
#17
Saskia Bode, Ilmar Kruis, Hans Adams, Wilbert Boelens, Ger Pruijn, Jan Van Hest, Dennis Lowik
A supramolecular approach was undertaken to create functionally activatable cell-penetrating peptides. Two tetra-arginines were assembled into an active cell-penetrating peptide by hetero-dimerizing leucine zippers. Three different leucine zipper pairs were evaluated of which the activation was found to be dependent on the association constant of the coiled-coil peptides. The weaker binding peptides required an additional disulfide linkage to educe cell-penetrating capacity, whereas for the most stable coiled-coil no additional stabilization was needed...
November 21, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27860128/structure-activity-relationships-of-benzenesulfonamide-based-inhibitors-towards-carbonic-anhydrase-isoform-specificity
#18
Avni Bhatt, Brian P Mahon, Vinicius Wilian D Cruzeiro, Benedetta Cornelio, Marie Laronze-Cochard, Mariangela Ceruso, Janos Sapi, Graham A Rance, Andrei N Khlobystov, Antonella Fontana, Adrian Roitberg, Claudiu T Supuran, Robert Mc Kenna
Carbonic anhydrases (CAs) are implicated in a wide range of diseases, including the upregulation of isoforms CA IX and XII in many aggressive cancers. However, effective inhibition of disease-implicated CAs should minimally affect the ubiquitously expressed isoforms including CA I and II to improve directed distribution of the inhibitors to the cancer-associated isoforms and reduce side effects. Four benzenesulfonamide-based inhibitors were synthesized using the "tail approach" and display nM affinities for several CA isoforms...
November 18, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27860220/k-bilds-a-kinase-substrate-discovery-tool
#19
D Maheeka Embogama, Mary Kay H Pflum
Kinases catalyze protein phosphorylation to regulate cell signaling events.However, identifying kinase substrates is challenging due to the often low abundance and dynamic nature of protein phosphorylation. Development of novel techniques to identify kinase substrates is necessary. Here, we report K-BILDS (Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates) as a tool to identify direct substrates of a kinase. As a proof of concept, K-BILDS was applied to PKA (cAMP-dependent protein kinase A) using HeLa cell lysates...
November 17, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27860106/protein-surface-mimetics-understanding-how-ruthenium-tris-bipyridines-interact-with-proteins
#20
Sarah H Hewitt, Maria H Filby, Ed Hayes, Lars T Kuhn, Arnout P Kalverda, Michael E Webb, Andrew John Wilson
Protein surface mimetics achieve high affinity binding by exploiting a scaffold to project binding groups over a large area of solvent exposed protein surface to make multiple co-operative non-covalent interactions. Such recognition is a pre-requisite for competitive/ orthosteric inhibition of protein-protein interactions (PPIs). This paper describes biophysical and structural studies on ruthenium(II) tris(bipyridine) surface mimetics that recognize cytochrome (cyt) c and inhibit the cyt c/ cyt c peroxidase (CCP) PPI...
November 17, 2016: Chembiochem: a European Journal of Chemical Biology
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