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Chembiochem: a European Journal of Chemical Biology

Nigel Scrutton, Uzma Choudry, Derren Heyes, Samantha Hardman, Michiyo Sakuma, Igor Sazanovich, Joyce Woodhouse, Eugenio De La Mora, Martin Pederson, Michael Wulff, Martin Weik, Giorgio Schiro
Phytochromes are bilin-containing photoreceptors that are typically sensitive to the red / far-red region of the visible spectrum. Recently phytochromes from certain eukaryotic algae have become attractive targets for optogenetic applications because of their unique ability to respond to multiple wavelengths of light. Here, we have used a combination of time-resolved spectroscopy and structural approaches across picosecond to second timescales to map photochemical mechanisms and structural change in this atypical group of phytochromes...
March 15, 2018: Chembiochem: a European Journal of Chemical Biology
Dagmara Jankowska, Tobias Heck, Mark Schubert, Alpaslan Yerlikaya, Christophe Weymuth, Daniel Rentsch, Irene Schober, Michael Richter
Lignin is the most abundant aromatic biopolymer functioning as an integral compound of woody materials. In its unmodified form it shows limited water solubility and is relatively unreactive. Thus, biotechnological lignin valorisation for high performance applications is highly underexploited. To expand its application, a new synthesis route towards novel concrete dispersing agents was developed. The route relies on a lignin functionalization by enzymatic transformation. Screening of lignin modifying systems resulted in functionalized lignin polymers with improved solubility in aqueous systems...
March 15, 2018: Chembiochem: a European Journal of Chemical Biology
Jian Liu, Fuzhong Ouyang, Zhihao Zhao, Ruifang Gao, Rui Shi, Enhui Wu, Rui Lv, Guoqiang Xu
A dual maleimides (DuMal) tagging method has been developed for both relative and absolute quantitation of cysteine-containing peptides (CCPs) in combination with MALDI-TOF mass spectrometry. We choose a pair of maleimides with the minimal difference in their chemical structures, including N-Methylmaleimide (NMM) and N-Ethylmaleimide (NEM), which allow for tagging CCPs in the Michael Addition reaction with a high efficiency rapidly (~minutes). We have validated that the DuMal Tagging technique is sensitive and reliable in quantitative analysis of CCPs...
March 15, 2018: Chembiochem: a European Journal of Chemical Biology
Dhiraj P Murale, Seong Cheol Hong, Md Mamunul Haque, Jun-Seok Lee
Glutathione (GSH) is one of major anti-oxidant inside cells that regulates oxido-reduction homeostasis. Recently, there have been extensive efforts to visualize GSH in live cells, but most of the probes available today are simple detection sensor without detail cellular localization. Here, we have developed a new fluorescent probe (pcBD2-Cl), which are cell permeable and selectively react with GSH in-situ. The in-situ GSH labeled probe (pcBD2-GSH) exhibited quenched fluorescence, but subsequent binding to cellular abundant Glutathione S-transferase (GST) recovers the fluorescence intensity that makes possible to imaging GSH-GST complex in live cells...
March 14, 2018: Chembiochem: a European Journal of Chemical Biology
Tianmeng Yu, Wenhu Zhou, Juewen Liu
The EtNa DNAzyme was isolated during the isopropanol precipitation step of an in vitro selection effort. Although inactive with the intended cofactor, its RNA cleavage activity was observed under a few conditions. With Na+, EtNa is highly active in around 50% ethanol, while in water it is highly active with Ca2+. In this work, we show that the EtNa DNAzyme is accelerated by freezing in water in the presence of Na+. The apparent Kd reached 6.2 mM Na+ under the frozen condition, over 20-fold tighter than that in water at room temperature...
March 14, 2018: Chembiochem: a European Journal of Chemical Biology
Anthony Watts
Saturation transfer difference (STD) NMR constitutes one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. This is due to its robustness and the fact that it is focused on the signals of the ligand, without any need for NMR information of the macromolecular target. This technique is most commonly applied to systems involving different types of ligands (e.g. small organic molecules, carbohydrates, or lipids) and a protein as the target, where the latter is selectively saturated...
March 14, 2018: Chembiochem: a European Journal of Chemical Biology
Zhijun Chen, Xiaoliang Wang, Yang Liu, Jiao Liu
Protein-polymer microcapsules attracted much attention due to their special feature and potential in biological use. How to make the most of this type of bio-abiotic hybrid material is an intriguing question. Nevertheless, several unsatisfactory technical issues significantly limited the application of these materials. For instance, introducing various biomolecules and cross-linking for the capsules remain challenging and problematic. In this report, recombinant mCherry protein was covalently linked with PNIPAAm to form amphiphilic protein-polymer conjugates, assembled into microcapsules...
March 14, 2018: Chembiochem: a European Journal of Chemical Biology
Bérénice Jahn, Arjan Pol, Henning Lumpe, Thomas Barends, Andreas Dietl, Carmen Hogendoorn, Huub Op den Camp, Lena Daumann
Since the discovery of the biological relevance of rare earth elements (REE) for numerous different bacteria, the questions of the advantage of REE in the active site of methanol dehydrogenase (MDH) over calcium(II) and why bacteria prefer light REE have been a subject of debate. Here we report the cultivation and purification of the strictly REE-dependent methanotrophic bacterium Methyl-acidiphilum fumariolicum SolV with europium(III) as well as structural and kinetic analyses of the first Eu-substituted methanol dehydrogenase...
March 10, 2018: Chembiochem: a European Journal of Chemical Biology
Xiguang Zhao, Noemi Kedei, Aleksandra M Michalowski, Nancy E Lewin, Gary E Keck, Peter M Blumberg
Important strides are being made in understanding the structural features of bryostatin 1, a candidate therapeutic agent for cancer and dementia, conferring its potency for protein kinase C and the unique spectrum of biological responses which it induces. A critical pharmacophoric element in bryostatin 1 is a secondary hydroxyl, whereas a primary hydroxyl group plays the analogous role in binding of the phorbol esters to protein kinase C. Here, we describe the synthesis of a bryostatin homolog where the hydroxyl group is primary, as in the phorbol esters, and show that its biological activity is almost indistinguishable from that of the corresponding compound with the secondary hydroxyl group...
March 8, 2018: Chembiochem: a European Journal of Chemical Biology
Franziska Hemmerling, Karen Lebe, Johannes Wunderlich, Frank Hahn
The divinylcyclopropane (DVC) fragment of the ambruticins is proposed to be formed via a unique polyene cyclization mechanism in which the unusual didomain AmbG plays a key role. It is proposed to activate the branched thioester carboxylic acid resulting from the polyene cyclisation and to transfer it to its associated ACP. After oxidative decarboxylation, the intermediate is channeled back into polyketide synthase (PKS) processing. AmbG was previously annotated as an adenylation-thiolation didomain with a very unusual substrate selectivity code, but has not yet been biochemically studied...
March 8, 2018: Chembiochem: a European Journal of Chemical Biology
Piyush K Jain, Simon H Friedman
There is a need for methods to chemically incorporate photocleavable labels into synthetic and biologically sourced nucleic acids in a chemically defined and reversible manner. We have previously demonstrated that the light cleaved diazo-DMNPE group (diazo di-methoxy nitro phenyl ethyl) has a remarkable regiospecificity for modifying terminally phosphorylated siRNA. Building on this observation, we have identified conditions by which a new diazo-DMNPE reagent (diazo-DMNPE-azide or DDA) is able to singly modify any nucleic acid (RNA, DNA, single stranded, double stranded, 3' or 5' phosphate)...
March 7, 2018: Chembiochem: a European Journal of Chemical Biology
Philip A Cistrone, Anthony P Silvestri, Jordi C J Hintzen, Philip E Dawson
Peptide macrocycles are widely utilized in the development of high affinity ligands including stapled α-helices. The linear rigidity of a 1,3-diynyl linkage provides an optimal distance (7 Å) between β- carbons of the i, i+4 amino acid side chains, suggesting its utility in stabilizing α-helical structures. Here we report the development of an on-resin strategy for an intramolecular Glaser reaction between two alkyne-terminated side chains using copper chloride, an essential bpy-diol ligand, and diisopropylethylamine, at room temperature...
March 7, 2018: Chembiochem: a European Journal of Chemical Biology
Charlène Gadais, Emmanuelle Devillers, Vincent Gasparik, Evelyne Chelain, Julien Pytkowicz, Thierry Brigaud
In order to accurately probe the local hydrophobicity increase of peptide sequences by trifluoromethylated amino acids (TfmAAs) incorporation, the chromatographic hydrophobicity indexes (φ0) of three series of tripeptides containing three unnatural trifluoromethylated amino acids have been measured and compared to the indexes of their non-fluorinated analogs. The hydrophobic contribution of each fluorinated amino acids was quantified by varying the position and the protection of (R) and (S)-α-trifluoromethyl alanine (TfmAla), (S)-trifluoromethyl cysteine (TfmCys) and (L)-trifluoromethionine (TFM) in a short peptide sequence...
March 7, 2018: Chembiochem: a European Journal of Chemical Biology
Bikash Dangi, Ki-Hwa Kim, Sang-Ho Kang, Tae-Jin Oh
CYP154C8 from Streptomyces sp. was identified as a novel cytochrome P450 with substrate flexibility to different sets of steroids. The in vitro reaction of these steroids with CYP154C8 revealed interesting product formation patterns with the same group of steroids. Nuclear magnetic resonance study revealed the major product of corticosterone hydroxylated at the C21 position; while progesterone, androstenedione, testosterone, and 11-ketoprogesterone were exclusively hydroxylated at 16α position. However, the 16α-hydroxylated product of progesterone was further hydroxylated to yield dihydroxylated products...
March 7, 2018: Chembiochem: a European Journal of Chemical Biology
Margaret McAuley, Noel Mesa-Torres, Aisling McFall, Sarah Morris, Meilan Huang, Angel Pey, David J Timson
Galactokinase catalyses the site- and stereospecific phosphorylation of α-D-galactose. As such it has attracted interest as a biocatalyst for the introduction of phosphate groups into monosaccharides. However, attempts to broaden the substrate range of human galactokinase have generally resulted in substantially reduced activity. The enzyme also has biotechnological potential in enzyme replacement therapy (ERT) for type II galactosemia. The return-to-consensus approach can be used to identify residues which can be altered to increase protein stability and enzyme activity...
March 5, 2018: Chembiochem: a European Journal of Chemical Biology
Jianfeng Wang, Zhongmei Liu, Zhemin Zhou
Anoxybacillus sp. WB42 pullulanase (PulWB42) is a novel thermophilic amylopullulanase which is assigned to the glycoside hydrolase family 13 subfamily 14 (GH13_14) type I pullulanases in the carbohydrate-active enzymes database. Its N-terminal domain (Met1-Phe101) was identified as the carbohydrate-binding module 68 (CBM68) via homology modeling. The N-domain-deleted PulWB42 exhibited an equivalent Km for pullulan and significant decreases in pullulytic activity, amylose selectivity, and thermostability as compared to PulWB42 having high alpha-amylase-to-pullulanase activity ratio...
March 1, 2018: Chembiochem: a European Journal of Chemical Biology
Liangliang Zhang, Changmai Chen, Xinli Fan, Xinjing Tang
Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker...
February 28, 2018: Chembiochem: a European Journal of Chemical Biology
David Straßburger, Natascha Stergiou, Moritz Urschbach, Hajime Yurugi, Daniel Spitzer, Dieter Schollmeyer, Edgar Schmitt, Pol Besenius
We describe a modular route to prepare functional self-assembling dendritic peptide amphiphiles decorated with mannosides (Man) to effectively target antigen-presenting cells such as macrophages. The monomeric building blocks were equipped with tetraethylene glycols (TEG) or labelled with a Cy3 fluorescent probe. Experiments on the uptake of the multifunctional supramolecular particles into murine macrophages (Mϕs) were monitored by confocal microscopy and fluorescence-activated cell sorting (FACS). Mannose-decorated supramolecular polymers trigger a significantly higher cellular uptake and distribution, compared to TEG carrying bare polymers...
February 27, 2018: Chembiochem: a European Journal of Chemical Biology
K Muniyappa, Mangesh Hanumant Kaulage, Santanu Bhattacharya
The G/C-rich sequences within the promoters (PI and PII) of human acetyl-CoA carboxylase 1 (ACC1) gene play a vital role in determining hormone- or diet-inducible expression of ACC1. The PI and PII promoters contain consecutive runs of 3 and 3-5 G/C base pairs respectively. Typically, stretches of C-rich sequences that coexist with stretches of guanines have the capacity to form another four-stranded secondary structure known as an i-motif. However, studies on i-motif structure are limited and its functional significance is unclear...
February 27, 2018: Chembiochem: a European Journal of Chemical Biology
Linlin Yang, Hyun-Bum Kim, Jai-Yoon Sul, Sean B Yeldell, James H Eberwine, Ivan J Dmochowski
Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at sub-micron spatial resolution, through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures based on their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yield through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC)...
February 25, 2018: Chembiochem: a European Journal of Chemical Biology
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