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Chembiochem: a European Journal of Chemical Biology

Ting Jiang, Pratik Kumar, Wei Huang, Wei-Siang Kao, Adrian O Thompson, Frank M Camarda, Scott Laughlin
We describe a modular activation strategy for the cyclopropene-tetrazine ligation. The activation strategy uses chemically diverse enzyme or photolabile protecting groups as cyclopropene reactivity cages. Linkages between caging groups and the cyclopropene are via carbamates, permitting application of diverse cages to activate bioorthogonal reactivity by administering enzymes or light.
April 16, 2019: Chembiochem: a European Journal of Chemical Biology
Michelle Ac Reed, Jennie Roberts, Peter Gierth, Ēriks Kupče, Ulrich L Günther
Tracer-based metabolism is becoming increasingly important to study metabolic mechanisms in cells. NMR offers several approaches to measure label incorporation in metabolites, including 13C and 1H-detected spectra. The latter are generally more sensitive but quantification depends on the proton carbon 1JCH coupling constant which varies significantly between different metabolites. It is therefore not possible to have one experiment optimised for all metabolites and quantification of 1H-edited spectra such as HSQCs requires precise knowledge of coupling constants...
April 16, 2019: Chembiochem: a European Journal of Chemical Biology
Yanping He, Yangyang Chang, Da Chen, Juewen Liu
Fluorescent metal sensors based on DNA often rely on changes in end-to-end distance or local environmental near fluorophore labels. Since metal ions can also non-specifically interact with DNA via various mechanisms such as charge screening, base binding, and increase or decrease duplex stability, robust and specific sensing of metal ions has been quite challenging. In this work, we performed a side-by-side comparison of two signaling strategies on a Na+-specific DNAzyme that contained a Na+ binding aptamer...
April 15, 2019: Chembiochem: a European Journal of Chemical Biology
Angela Berg, Bianca Sperl, Thorsten Berg
Although naturally-occurring low-molecular weight compounds have many known roles within the cell, these do not usually involve the direct inhibition of protein-protein interactions. Based on the results of high-throughput screening of a library of bioactive compounds and neurotransmitters, we report that the four nucleoside triphosphates ATP, GTP, CTP and UTP inhibit the SH2 domain of the tumor-related transcription factor STAT5b. ATP and GTP are the most active nucleoside triphosphates and show specificity for STAT5b over STAT5a, STAT3, STAT6 and the p53-binding protein HDM2...
April 15, 2019: Chembiochem: a European Journal of Chemical Biology
Mohit Chawla, Yury Minenkov, Khanh B Vu, Romina Oliva, Luigi Cavallo
We theoretically characterized the impact that the 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications have on the geometry and stability of the G:C Watson-Crick (cWW) base pair and of the G:iC and iG:C reverse Watson-Crick (tWW) base pairs. In addition, we investigated the effect on the same base pairs of seven C7-substituted DAG and DAiG, some of which have been previously experimentally characterized. Our calculations indicate that all these modifications have a negligible impact on the geometry of the above base pairs, and that the modification of the heterocycle skeleton has small impact on the base pair interaction energies...
April 14, 2019: Chembiochem: a European Journal of Chemical Biology
Michael R Mortensen, Mikkel B Skovsgaard, Kurt Vesterager Gothelf
The plethora of methods developed for the creation of protein conjugates often differs significantly with regard to the heterogeneity of the resulting products, in the degree of genetic manipulation of the protein required, and in the technical skills required to perform the conjugation procedure. Affinity guided protein conjugation is a protein labeling methodology based on non-covalent binding interactions between a labeling probe and the protein of interest. These interactions increase the local concentration of a reactive group in the probe on the protein surface thus facilitating the conjugation in proximity of the complexation site...
April 14, 2019: Chembiochem: a European Journal of Chemical Biology
Shuaiqi Meng, Jia Guo, Kaili Nie, Tianwei Tan, Haijun Xu, Luo Liu
Fatty acids are versatile precursors for fuels, chemicals, polymers, perfumes, etc. The properties and applications of fatty acid derivatives depend on chain-length and functional groups, and their positions. To tailor fatty acids for desired properties, an engineered P450 monooxygenase was here employed for enhanced selective hydroxylation of fatty acids. After oxidation of the hydroxyl group into the corresponding ketone, a Baeyer-Villiger oxidation could be applied to introduce an oxygen atom into the hydrocarbon chain to form esters, which were finally hydrolyzed into a hydroxylated fatty acid or dicarboxylic fatty acid...
April 14, 2019: Chembiochem: a European Journal of Chemical Biology
Carina Patrizia Glindemann, Anita Backenköhler, Matthias Strieker, Ute Wittstock, Philipp Klahn
The synthesis of the first example of a fluorescent glucosinolate-BODIPY conjugate (GSL-BODIPY) based on an azide containing artificial GSL precursor (GSL-N3) is reported. The biochemical evaluation of the novel artificial GSLs revealed that the compounds are converted to the corresponding isothiocyanates in the presence of myrosinase. Furthermore, myrosinase-catalyzed hydrolysis in the presence of plant specifier proteins yielded the expected alternative products, namely nitriles. The easy assembly of the fluorescent GSL-BODIPY conjugate via click chemistry from GSL-N3 holds potential for the application as fluorescence labeling tool for the investigation of GSL-associated processes...
April 12, 2019: Chembiochem: a European Journal of Chemical Biology
Zhaoxia Wang, Linna Wei, Yue Sheng, Genlin Zhang
The design of improved synthetic parts is an important research field of synthetic biology. The terminator responsible for terminating gene transcription is a necessary part for yeast gene expression. The efficiency element, positioning element and poly(A) site are identified as the necessary elements for yeast terminator to perform function. However, the function on the linker 1 and the linker 2 in the terminator are still controversial. Here, we thus designed and synthesized a yeast synthetic terminator library with a random 10 bp linker 1...
April 11, 2019: Chembiochem: a European Journal of Chemical Biology
Kei Yamada, Yuji Ito
Antibody-drug conjugates (ADCs), which consist of three components- antibody, linker, and payload, can function as "magic bullets". These conjugates offer the ability to target drug delivery to specific cells, based on cell-specific recognition and the binding of an antigen by a monoclonal antibody (mAb). In particular, by delivering a cytotoxic payload to cancer cells, ADCs are expected to provide a breakthrough in oncology treatments by providing a way to increase efficacy and decrease toxicity in comparison with traditional chemotherapeutic treatments...
April 11, 2019: Chembiochem: a European Journal of Chemical Biology
Katharina Streichert, Carina Seitz, Eugenia Hoffmann, Irene Boos, Wolfgang Jelkmann, Thomas Brunner, Carlo Unverzagt, Marina Rubini
The biological activity of glycoprotein hormone erythropoietin (EPO) is dependent mainly on the structure of its N-linked glycans. We aimed at readily attaching N-glycans to EPO via defined alkyne groups. EPO variants with an alkyne bearing amino acid (Plk) at the N-glycosylation sites 24, 38 and 83 were obtained by amber suppression followed by refolding. Click-conjugation of the alkinyl EPOs with biantennary N-glycan azides provided biologically active site-specifically modified EPO glycoconjugates.
April 11, 2019: Chembiochem: a European Journal of Chemical Biology
Océane Flores, Denis Velic, Nesrine Mabrouk, Ali Bettaieb, Christophe Tomasoni, Jean-Michel Robert, Catherine Paul, Christine Goze, Christos Roussakis, Ewen Bodio
A family of bimetallic and of tetrametallic phosphine-gold(I)-dithiocarbamate complexes were synthesized starting from cyclam and dimethylcyclam polyazamacrocycles respectively, along with their monometallic chlorido-phosphine gold(I) precursors. Their antiproliferative properties were evaluated on two cancer cell lines (A549 and NSCLC-N6-L16). Most of the mono and bimetallic complexes displayed strong activities, and especially one bimetallic derivatives showed anti-proliferative properties in the low micromolar range...
April 10, 2019: Chembiochem: a European Journal of Chemical Biology
Chao Wang, Daniel Abegg, Brendan Dwyer, Alexander Adibekian
Serine hydrolases play crucial biological roles and are important therapeutic targets in many clinical applications. Activity-based protein profiling of serine hydrolases using fluorophosphonate probes, pioneered by Cravatt and coworkers, has been a powerful tool for interrogating serine hydrolases in various biological systems. In this report, we present novel phenoxy phosphonate probes with an azide handle for "click" chemistry that offer remarkable improvements over the classical fluorophosphonate serine hydrolase activity-based probes including ease of preparation, excellent cell permeability, and distinct reactivity profiles as controlled by the phenolate leaving group...
April 9, 2019: Chembiochem: a European Journal of Chemical Biology
Yuanchen Dong, Youdong Mao
Since first reported in 2006, the DNA origami approach has attracted increasingly more attention due to their programmable shapes, structural stability, bio-compatibility and fantastic addressability. Here in this review, we will focus on the recent development of DNA origami as scaffolds for templating self-assembly of distinct bio-components, basically proteins and lipids, into a diverse spectrum of integrative supramolecular architectures. First, the historical development of DNA origami concept will be briefly reviewed...
April 9, 2019: Chembiochem: a European Journal of Chemical Biology
Hannes M Beyer, Hideo Iwai
Protein splicing domains are frequently used engineering tools finding application for the in vivo and in vitro ligation of protein domains. Directed evolution is among the most promising technologies used to advance this technology. However, available screening systems for protein splicing activity are associated with bottlenecks such as the selection of pseudo-positive clones arising from off-pathway reaction products or fragment complementation. Here, we report a stringent screening method for protein splicing activity in cis and trans, exclusively selecting productively splicing domains...
April 8, 2019: Chembiochem: a European Journal of Chemical Biology
Xun-Cheng Su, Bin-Bin Pan, Yin Yang
Accumulation of filamentous aggregates of α-synuclein (AS) in Lewy bodies and neurites characterizes neurodegenerative diseases such as Parkinson's disease. Inhibition of AS fibrillation is helpful for understanding of AS aggregate structure and for developing chemical therapies. Herein we report that the Pt(II)-containing antitumor drug cisplatin suppresses filamentous aggregation of AS in solution. Pt(II) contrasts strongly with reported transition-metal ions such as Mn(II), Fe(III), and Cu(II), which accelerate AS aggregation...
April 8, 2019: Chembiochem: a European Journal of Chemical Biology
Di Wu, Yonghao Chen, Shuai Hou, Wenjun Fang, Hongwei Duan
Surface-enhanced Raman scattering (SERS) with greatly amplified fingerprint spectra holds great promise in biochemical and biomedical research. In particular, the possibility of exciting a library of SERS probes and differentially detecting them simultaneously stimulates widespread interest in multiplexed biodetection. In this review, we summarize the recent progress in developing SERS-active plasmonic nanostructures for cellular and intracellular detection. We highlight the development of the nanosensors with tailored plasmonic and multifunctional properties for profiling molecular and pathological processes...
April 8, 2019: Chembiochem: a European Journal of Chemical Biology
Masahiro Abe, Ryo Nishihara, Yuma Ikeda, Takahiro Nakajima, Moritoshi Sato, Naoko Iwasawa, Shigeru Nishiyama, Ramasamy Paulmurugan, Daniel Citterio, Sung Bae Kim, Koji Suzuki
A coelenterazine (CTZ) analogue emitting near infrared (NIR) bioluminescence was synthesized for through-bond energy transfer (TBET)-based imaging modalities. The analogue was made by conjugating cyanine-5 (Cy5) dye to CTZ via an acetylene linker and named as Cy5-CTZ. This novel derivative is intrinsically fluorescent and emits NIR shifted luminescence when reacting with an appropriate luciferase, the Renilla luciferase (RLuc). This Cy5-CTZ substrate is optically stable in physiological samples and rapidly permeabilize through plasma membrane into the cytosolic compartment in live cells...
April 7, 2019: Chembiochem: a European Journal of Chemical Biology
Huaimin Wang, Zhaoqianqi Feng, Bing Xu
Biological systems have evolved to create a structural and dynamic continuum of biomacromolecular assemblies for the purpose of optimizing their functions. The formation of these dynamic higher-order assemblies are precisely controlled by biological cues. However, controlling self-assembly of synthetic molecules spatiotemporally in or on live cell is still a big challenge, especially for performing functions. This concept article introduces the use of in-situ reactions as a spatiotemporal control to form the assemblies of small molecules that induce cell morphogenesis or apoptosis...
April 7, 2019: Chembiochem: a European Journal of Chemical Biology
Narayanaswamy Jayaraman, Avisek Mahapa, Gopal Ch Samanta, Krishnagopal Maiti, Dipankar Chatterji
Lipomannan and lipoarabinomannan are integral components of mycobacterial cell wall. Our earlier studies demonstrated that synthetic arabinan and arabinomannan glycolipids act as inhibitors of mycobacterial growth, in addition to exhibiting inhibitory activities of mycobacterial biofilm. In the present study, we demonstrate that synthetic mannan glycolipids are better inhibitors of the mycobacterial growth, whereas, lipoarabinomannan has higher inhibition efficiencies to biofilm. Syntheses of mannan glycolipids with graded number of mannan moieties and an arabinomannan glycolipid are conducted by chemical methods and subsequent mycobacterial growth and biofilm inhibition studies are conducted on M...
April 5, 2019: Chembiochem: a European Journal of Chemical Biology
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