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Chembiochem: a European Journal of Chemical Biology

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https://www.readbyqxmd.com/read/29144009/immobilization-of-superoxide-dismutase-on-polyelectrolyte-functionalized-titania-nanosheets
#1
Paul Rouster, Marko Pavlovic, Istvan Szilagyi
Superoxide dismutase (SOD) enzyme was successfully immobilized on titania nanosheets (TNS) functionalized with poly(diallyldimethylammonium chloride) (PDADMAC) polyelectrolyte. The TNS-PDADMAC solid support was prepared by hydrothermal synthesis followed by self-assembled polyelectrolyte layer formation. It was found that the SOD strongly adsorbed on the oppositely charged TNS-PDADMAC through electrostatic and hydrophobic interactions. The TNS-PDADMAC-SOD material was characterized by light scattering and microscopy techniques...
November 16, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29139594/a-multi-perspective-approach-to-solvent-regulation-of-enzymatic-activity-hmg-coa-reductase
#2
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/29131473/production-of-hydroxynitrile-lyase-from-d-tyermanii-dthnl-in-komagataella-phaffii-and-its-immobilization-as-clea-to-generate-a-robust-biocatalyst
#3
Elisa Lanfranchi, Birgit Grill, Zainab Raghoebar, Sander van Pelt, Roger Sheldon, Kerstin Steiner, Anton Glieder, Margit Winkler
Hydroxynitrile lyase from the white rabbit's foot fern Davallia tyermanii (DtHNL) catalyzes the enantioselective synthesis of α-cyanohydrins, key building blocks for pharmaceutical and agrochemical industries. An efficient and competitive process necessitates the availability and robustness of the biocatalyst. Herein, the recombinant production of DtHNL1 in Komagataella phaffii is described, yielding approximately 900,000 U/L. DtHNL1 constitutes approximately 80% of the total protein content. The crude enzyme was immobilized...
November 13, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29125207/specificity-of-donor-structures-for-endo-%C3%A3-n-acetylglucosaminidase-catalyzed-transglycosylation-reactions
#4
Nozomi Ishii, Ken Ogiwara, Kanae Sano, Jyunichi Kumada, Kenji Yamamoto, Yuji Matsuzaki, Ichiro Matsuo
To demonstrate the structural specificity of the glycosyl donor for the transglycosylation reaction using endo-b-N-acetylglucosaminidase from Mucor hiemalis (endo-M), a series of tetrasaccharide oxazoline derivatives was synthesized. These derivatives correspond to the core structure of an asparagine-linked glycoprotein glycan with a b-mannose units of non-natural-type monosaccharides, including b-glucose, b-galactose, and b-talose in place of the b-mannose moiety. Using these tetrasaccharide donors with p-nitrophenyl N-acetylglucosaminide (GlcNAc-pNp), the transglycosylation activity of wild-type (WT) endo-M and two mutants, N175Q and N175A, was examined...
November 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29124839/expanding-the-scope-of-sortase-mediated-ligations-using-sortase-homologs
#5
Keyvan D Nikghalb, Nicholas M Horvath, Jesse L Prelesnik, Orion G B Banks, Pavel A Filipov, R David Row, Travis J Roark, John M Antos
Sortase-catalyzed transacylation reactions are widely used for the construction of non-natural protein derivatives. However, the most commonly used enzyme for these strategies (sortase A from Staphylococcus aureus) is limited by its narrow substrate scope. To expand the range of substrates compatible with sortase-mediated reactions, we have characterized the in vitro substrate preferences of eight sortase A homologs. From these studies, we identified sortase A enzymes that recognize multiple substrates which are unreactive toward sortase A from S...
November 9, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29120530/improvement-of-the-thermostability-of-a-%C3%AE-amino-acid-converting-%C3%AF-transaminase-using-foldx
#6
Oliver Buß, Delphine Muller, Sven Jager, Jens Rudat, Kersten S Rabe
ω-Transaminases (ω-TAs) are important biocatalysts for the synthesis of active, chiral pharmaceutical ingredients containing amino groups, such as β-amino acids which are important in peptidomimetics and as building blocks for drugs. However, the application of ω-TAs is limited by the availability and stability of enzymes with high conversion rates. One strategy for the synthesis and optical resolution of β-phenylalanine and other important aromatic β-amino acids, is the biotransformation utilizing an ω-transaminase from Variovorax paradoxus...
November 9, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29120508/synthesis-and-immunological-evaluation-of-a-multicomponent-cancer-vaccine-candidate-containing-a-long-muc1-glycopeptide
#7
Geert-Jan Boons, Nitin T Supekar, Vani Lakshminarayanan, Chantelle J Capicciotti, Anju Sirohiwal, Cathy S Madsen, Margreet A Wolfert, Peter A Cohen, Sandra J Gendler
A fully synthetic MUC1-based cancer vaccine has been designed and chemically synthesized that contains an endogenous helper T-epitope (MHC class II epitope). The vaccine elicited robust IgG titers that could neutralize cancer cells by antibody-dependent cell-mediated cytotoxicity (ADCC). It also activated cytotoxic T-lymphocytes and collectively the immunological data demonstrate engagement of helper T-cells in immune activation. A synthetic methodology was developed for a penta-glycosylated MUC1 glycopeptide and anti-sera of mice immunized by the new vaccine recognized such a structure...
November 9, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29120074/a-fret-sensor-to-monitor-bivalent-sumo-sim-interactions-in-sumo-chain-binding
#8
Lisa J Kost, Henning D Mootz
The small ubiquitin-like modifier (SUMO) can be assembled into polymeric chains as part of its diverse biochemical signal pattern when conjugated to substrate proteins. SUMO chain recognition is facilitated by receptor proteins containing at least two SUMO-interacting motifs (SIMs). Only little is known about the structure of SUMO chains, both in unliganded form and when complexed with multi-SIM protein partners. We have developed a FRET sensor based on a linear dimer of human SUMO-2 as a minimal SUMO chain analog...
November 9, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29119720/phage-display-on-anti-infective-target-dxs-led-to-an-acceptor-substrate-competitive-peptidic-inhibitor
#9
Alessio Marcozzi, Tiziana Masini, Di Zhu, Diego Pesce, Boris Illarionov, Markus Fischer, Andreas Herrmann, Anna Katharina Herta Hirsch
Enzymes of the 2-C-methyl-d-erythritol-4-phosphate pathway for the biosynthesis of isoprenoid precursors are validated drug targets. By performing phage display on 1-deoxy-d-xylulose 5-phosphate synthase (DXS), which catalyzes the first step of this pathway, we discovered several peptide hits and recognized false positive hits. The enriched peptide binder P12 emerged as substrate (d-glyceraldehyde 3-phosphate) competitive against Deinococcus radiodurans DXS. The result indicates possible overlapping of cofactor- and acceptor-substrate-binding pockets, and provides inspiration for the design of inhibitors of DXS with a unique and novel mechanism...
November 8, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29119717/enzymes-as-enhancers-for-biodegradation-of-synthetic-polymers-in-wastewater
#10
Karolina Härnvall, Sabine Zitzenbacher, Antonino Biundo, Motonori Yamamoto, Michael Bernhard Schick, Doris Ribitsch, Georg M Guebitz
Synthetic polyesters are today the second largest class of ingredient in household products and are entering WWTP after product utilization. One approach to improve polymer biodegradation in wastewater would be to complement current processes with polyester hydrolyzing enzymes and their microbial producers. In this study, hydrolysis of polyoxyethylene terephthalate polymer by hydrolases from wastewater microorganisms was investigated in in-vitro and under realistic WWTP conditions. An esterase and a cutinase from Pseudomonas pseudoalcaligenes and a lipase from Pseudomonas pelagia were heterologous expressed in E...
November 8, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29116682/flavin-n5-covalent-intermediate-in-the-non-redox-dehalogenation-reaction-catalyzed-by-an-atypical-flavoenzyme
#11
Yumin Dai, Karina Kizjakina, Ashley C Campbell, David A Korasick, John J Tanner, Pablo Sobrado
The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme from has been expressed in Escherichia coli, purified, and characterized. 2-HAH is monomeric in solution and contains a non-covalent, yet tightly bound, FAD. Although the reaction catalyzed is redox neutral, 2-HAH is active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry...
November 8, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29115742/nucleophilic-water-capture-or-proton-loss-single-amino-acid-switch-converts-delta-cadinene-synthase-to-germacradien-4-ol-synthase
#12
Rudolf K Allemann, Marianna Loizzi, Veronica Gonzalez, David Miller
Delta-Cadinene synthase is a sesquiterpene cyclase that utilizes the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene -cadinene and ~2% germacradien-4-ol, which is also generated from FDP by the cyclase germacradien-4-ol synthase. Here, the mechanism, by which sesquiterpene synthases discriminate between deprotonation and reaction with a nucleophilic water molecule was investigated by site directed mutagenesis of -cadinene synthase. When W279 in -cadinene synthase was replaced with various smaller amino acids the ratio of alcohol versus hydrocarbon product was directly proportional to the van der Waals volume of the amino acid side chain...
November 8, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29115013/a-t7-rna-polymerase-mutant-enhances-the-yield-of-5-thienoguanosine-initiated-rnas
#13
Seth Lyon, Venkat Gopalan
Spectroscopic methods, which are used to establish RNA structure-function relationships, require strategies for post-synthetic, site-specific incorporation of chemical probes into target RNAs. For RNAs >50 nt, the enzymatic incorporation of a nucleoside or nucleotide monophosphate guanosine analog (G-analog) at their 5'-end is routinely achieved by in vitro transcription (IVT) using T7 RNA polymerase (T7RNAP) and a DNA template with a GTP-initiating class III Φ6.5 promoter. However, when high G-analog:GTP ratios are used to bias G-analog incorporation at the 5'-end, RNA yield is compromised...
November 8, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29112789/kinetic-analysis-of-prmt1-reveals-multifactorial-processivity-and-a-sequential-ordered-mechanism
#14
Jennifer I Brown, Timo Koopmans, Jolinde van Strien, Nathaniel I Martin, Adam Frankel
Arginine methylation is a prevalent post-translational modification in eukaryotic cells. Two significant debates exist within the field: do these enzymes dimethylate their substrates in a processive or distributive manner, and do these enzymes operate using a random or sequential method of bisubstrate binding? We reveal human protein arginine N-methyltransferase 1 (PRMT1) enzyme kinetics are dependent on substrate sequence. Further, peptides containing a Nη-hydroxyarginine generally demonstrate substrate inhibition and have improved KM values, which evokes a possible role in inhibitor design...
November 7, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29111574/laccase-mediated-grafting-on-biopolymers-and-synthetic-polymers-a-critical-review
#15
Sjoerd Slagman, Han Zuilhof, Maurice Charles René Franssen
Laccase-mediated grafting on lignocelluloses has gained considerable attention as an environmentally benign method to covalently modify wood, paper and cork. Over the past decades this technique has been employed to also modify fibres with a polysaccharide backbone such as cellulose or chitosan to infer colouration, anti-microbial activity or anti-oxidant activity to the material. The scope of this approach has been further widened by researchers who apply mediators or high redox potential laccases and those that modify synthetic polymers and proteins...
November 7, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29110405/nested-puf-proteins-extending-target-rna-elements-for-gene-regulation
#16
Kouki Shinoda, Shogo Tsuji, Shiroh Futaki, Miki Imanishi
RNA-binding proteins recognizing unique sequences within large transcriptomes serve as a powerful tool to control RNA metabolism. Pumilio and fem-3 mRNA-binding factor (PUF) proteins are considered as a good candidate for such tools because they are typically composed of eight highly homologous repeat segments and can be designed to recognize arbitrary 8-nucleotide (nt) RNA sequences. However, a specific 8-nt RNA sequence is found at multiple sites in various RNAs in the transcriptome, making it difficult to specifically target a single RNA...
November 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29105934/toward-a-novel-drug-to-target-the-egf-egfr-interaction-design-of-metabolically-stable-bicyclic-peptides
#17
Salvador Guardiola, Jesús Seco, Monica Varese, Mireia Díaz-Lobo, Jesus Garcia, Meritxell Teixido, Laura Nevola, Ernest Giralt
In cancer, proliferation of malignant cells is driven by overactivation of growth signaling mechanisms, such as the EGF-EGFR pathway. Despite its therapeutic relevance, this extracellular protein-protein interaction (PPI) has remained elusive to inhibition by synthetic molecules, mostly due to its large size and lack of binding pockets and cavities. Designed peptides, featuring cyclic motifs and other structural constraints, have the potential to modulate such challenging PPIs. Here we present the structure-based design of a series of bicyclic constrained peptides that mimic an interface domain of EGFR and inhibit the EGF-EGFR interaction by targeting the smaller partner (EGF)...
November 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29105927/resveratrol-interferes-with-an-early-step-in-the-fibrillation-pathway-of-human-lysozyme-and-modulates-it-towards-less-toxic-off-pathway-aggregates
#18
Fatima Kamal Zaidi, Rajiv Bhat
Effect of the red wine polyphenol, resveratrol, was investigated on the amyloid fibril formation of human lysozyme (HuL), towards elucidating the mechanism of resveratrol action and probing its role as a possible modulator of lysozyme aggregation and toxicity. Using a number of biophysical tools, resveratrol was observed to alter the fibrillation kinetics of HuL and inhibit its fibrillation by binding with weak to moderate affinity to the conformations populated at the early stages of the pathway with concomitant stabilization of these initial conformations...
November 4, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29105250/improved-enantioselectivity-of-subtilisin-carlsberg-towards-secondary-alcohols-by-protein-engineering
#19
Robin Dorau, Tamás Görbe, Maria Svedendahl Humble
Generally, the catalytic activity of subtilisin Carlsberg (SC) for transacylation reactions using secondary alcohols in organic solvent is low. Enzyme immobilization and protein engineering was performed to improve the enantioselectivity of SC towards secondary alcohols. Possible amino acid residues for mutagenesis were found by combining available literature data with molecular modeling. SC variants were created by site-directed mutagenesis and evaluated for a model transacylation reaction containing 1-phenylethanol in THF...
November 4, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29105291/enhanced-permeability-and-binding-activity-of-isobutylene-grafted-peptides
#20
Shuang Sun, Ismael Compañón, Nuria Martínez-Sáez, João D Seixas, Omar Boutureira, Francisco Corzana, Gonçalo J L Bernardes
We present a new peptide macrocyclization strategy with an isobutylene graft. The reaction is mild and proceeds rapidly and efficiently both on linear and cyclic peptides. The resulting isobutylene-grafted peptides possess improved passive membrane permeability due to the shielding of the polar backbone of the amides, as demonstrated by NMR and molecular dynamics (MD) simulations. The isobutylene-stapled structures are fully stable in human plasma and in the presence of glutathione. This strategy can be applied to bioactive cyclic peptides such as somatostatin...
November 3, 2017: Chembiochem: a European Journal of Chemical Biology
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