5,597 results match your criteria ChemBioChem [Journal]


Biochemical and structural characterization of XoxG and XoxJ and their roles in activity of the lanthanide-dependent methanol dehydrogenase, XoxF.

Chembiochem 2019 Apr 24. Epub 2019 Apr 24.

Pennsylvania State University, Chemistry, 220 Chemistry Building, Penn State University, 16802, University Park, UNITED STATES.

Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have been recently shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems comprise two other proteins, XoxG (a c-type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. Here, we biochemically and structurally characterize these proteins from the methyltroph, Methylobacterium extorquens AM1. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900184DOI Listing
April 2019
1 Read

Heavy enzymes and the rational redesign of protein catalysts.

Chembiochem 2019 Apr 24. Epub 2019 Apr 24.

SPAIN.

An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled "heavy" dihydrofolate reductases and their natural abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimized for hydride transfer. In alcohol dehydrogenase, non-natural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. Read More

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http://dx.doi.org/10.1002/cbic.201900134DOI Listing

Automatically Full Glycan Structural Determination with Logically Derived Sequence Tandem Mass Spectrometry.

Chembiochem 2019 Apr 23. Epub 2019 Apr 23.

Academia Sinica, Institute of Atomic and Molecular Sciences, No.1, Sec. 4, Roosevelt, Rd., 10617, Taipei, TAIWAN.

Glycans have diverse functions and play vital roles in many biological systems such as influenza, vaccines, and cancer biomarkers. However, fully structural identification of glycans remains challenging. Glycan structure was conventionally determined by chemical methods or nuclear magnetic resonance spectroscopy which require a large amount of sample and are not readily applicable for glycans extracted from biological samples. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019002
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http://dx.doi.org/10.1002/cbic.201900228DOI Listing
April 2019
1 Read

Biocatalytic Reversal of Advanced Glycation End Product Modification.

Chembiochem 2019 Apr 23. Epub 2019 Apr 23.

Yale, Chemistry and Microbial Pathogenesis, P.O. Box 27392, 06516-7392, West Haven, UNITED STATES.

Advanced glycation end products (AGEs) are a heterogeneous group of molecules that emerge from the condensation of sugars and proteins via the Maillard reaction. Despite a significant number of studies showing strong associations between AGEs and the pathologies of aging-related illnesses, it has been a challenge to establish AGEs as causal agents primarily due to the lack of tools in reversing AGE modifications at the molecular level. Here, we show that MnmC, an enzyme involved in a bacterial tRNA-modification pathway, is capable of reversing the AGEs carboxyethyl-lysine (CEL) and carboxymethyl-lysine (CML) back to their native lysine structure. Read More

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http://dx.doi.org/10.1002/cbic.201900158DOI Listing

Construct Cyan Fluorescence by De Novo Tripeptides: An In Vitro Mutation Study on the Role of Single Amino Acid Residues and Their Sequence.

Chembiochem 2019 Apr 23. Epub 2019 Apr 23.

Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital, Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 511436, P. R. China., Yuexiu Road, CHINA.

Amino acids are a natural choice as building blocks for developing bio-functional entities owing to their superior diversity and versatile physicochemical properties compared to nucleotide bases. A simple permutation of amino acids creates a broad palette of proteins that are successfully engineered as useful bio-functional agents. For example, the intrinsic ultraviolet fluorescence of phenylalanine (F) and tryptophan (W) have been engineered to emit in the visible spectrum [1, 2], that has broad applications as imaging/sensing probes, photothermal therapy agents, optogenetic switches, etc. Read More

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http://dx.doi.org/10.1002/cbic.201900166DOI Listing

Physicochemical Characterization of Polymer-stabilized Coacervate Protocells.

Chembiochem 2019 Apr 22. Epub 2019 Apr 22.

Eindhoven University of Technology, Department of Bio-medical engineering and Chemical engineering & Chemistry, building 14, Helix (STO 3.39) Het Kranenveld, 5600 MB, Eindhoven, NETHERLANDS.

The bottom-up construction of cell mimics has produced a range of membrane-bound protocells that have been endowed with functionality and biochemical processes reminiscent of living systems. The contents of these compartments, however, experience semi-dilute conditions, whereas macromolecules in the cytosol are in a protein-rich crowded environment that affects their physicochemical properties such as diffusion and catalytic activity. Recently, complex coacervates have emerged as attractive protocellular models because their condensed interior is expected to better mimic this crowding. Read More

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http://dx.doi.org/10.1002/cbic.201900195DOI Listing

C34 Dimeric Derivatives Utilizing Disulfide Bridges as Novel HIV-1 Fusion Inhibitors.

Chembiochem 2019 Apr 22. Epub 2019 Apr 22.

Tokyo Medical and Dental University, Institute of Biomaterials and Bioengineering, Kandasurugadai 2-3-10, Chiyoda-ku, 101-0062, Tokyo, JAPAN.

A 34-mer fragment peptide (C34) is contained in the HIV-1 envelope protein gp41. A dimeric derivative of C34 linked by a disulfide bridge in its C-terminus was synthesized and found to have potent anti-HIV activity, comparable to that of a previously reported pegylated dimer of C34REG. The downsizing of the linker moiety for dimerization was thus successful, and this result might shed some light on the mechanism of the suppression of 6-helical bundle formation by these C34 dimeric derivatives. Read More

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http://dx.doi.org/10.1002/cbic.201900187DOI Listing

Solubilizing Trityl-type Tag to Synthesize Asx/Glx-containing Peptides.

Chembiochem 2019 Apr 18. Epub 2019 Apr 18.

Peptide Institute, Inc., SAITO Research Center, 7-2-9 Saito-Asagi, 5670085, Ibaraki-shi, JAPAN.

A novel solubilizing tag system for Asp/Asn/Glu/Gln-containing peptides is described. In this method, an Asp/Glu[Dbz-Cys-NH2]-containing peptide (Dbz: 3,4-diaminobenzoic acid) is first synthesized by Fmoc solid-phase peptide synthesis. The solubilizing moiety containing an oligo-Lys group is then attached to the peptide in hexafluoroisopropanol solution via a trityl anchor to afford a hydrophilic tagged peptide. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900193DOI Listing
April 2019
3 Reads

Probing the substrate promiscuity of isopentenyl phosphate kinase as a platform for hemiterpene analogue production.

Chembiochem 2019 Apr 18. Epub 2019 Apr 18.

North Carolina State University, Department of Chemistry, Campus Box 8204, 27695-8204, Raleigh, UNITED STATES.

Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. Read More

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http://dx.doi.org/10.1002/cbic.201900135DOI Listing

RNA dynamics by NMR.

Chembiochem 2019 Apr 17. Epub 2019 Apr 17.

Karolinska Institute, Medical Biochemistry and Biophysics, Scheeles Väg 2, 17177, Stockholm, SWEDEN.

An ever-increasing number of functional RNAs require mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new Nuclear Magnetic Resonance (NMR) methods have been developed to elucidate these dynamics in RNA with atomic resolution. Read More

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http://dx.doi.org/10.1002/cbic.201900072DOI Listing

Cell-Penetrating Peptide Foldamers: Drug Delivery Tools.

Authors:
Makoto Oba

Chembiochem 2019 Apr 18. Epub 2019 Apr 18.

Nagasaki University, Graduate School of Biomedical Scienc, 1-14 Bunkyo-machi, 852-8521, Nagasaki, JAPAN.

Highly efficient drug delivery tools for membrane-impermeable compounds, proteins, and nucleic acids in living cells are useful in the field of chemical biology and drug discovery, and such tools have been widely studied. One strategy in the development of novel drug delivery tools is utilizing cell-penetrating peptide (CPP) foldamers. CPP foldamers are folded oligopeptides that possess cell membrane permeability. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019002
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http://dx.doi.org/10.1002/cbic.201900204DOI Listing
April 2019
1 Read

Modular Enzyme- and Light-Based Activation of the Cyclopropene-Tetrazine Ligation.

Chembiochem 2019 Apr 16. Epub 2019 Apr 16.

Stony Brook University, Chemistry, 529 Chemistry, 11794-3400, Stony Brook, UNITED STATES.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900137DOI Listing

NMR Methods for Quantitative Isotopomer Rates in Real-Time Metabolism of Cells.

Chembiochem 2019 Apr 16. Epub 2019 Apr 16.

University of Birmingham, HWB-NMR, CR UK Institute of Cancer Studies, Vincent Drive, Edgbaston, B15 2TT, Birmingham, UNITED KINGDOM.

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. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019000
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http://dx.doi.org/10.1002/cbic.201900084DOI Listing
April 2019
2 Reads

Probing Local Folding Allows for Robust Metal Sensing based on a Na+-specific DNAzyme.

Chembiochem 2019 Apr 15. Epub 2019 Apr 15.

University of Waterloo, Department of Chemistry, 200 University Avenue West, N2L 3G1, Waterloo, CANADA.

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. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900143DOI Listing
April 2019
1 Read

ATP inhibits the transcription factor STAT5b.

Chembiochem 2019 Apr 15. Epub 2019 Apr 15.

University of Leipzig, Institute for Organic Chemistry, Johannisallee 29, 4103, Leipzig, GERMANY.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900173DOI Listing

Structural and Energetic Impact of Non-natural 7-Deaza-8-Azaguanine, 7-Deaza-8-Azaisoguanine and their 7-Substituted Derivatives on H-bonding Pairing with Cytosine and Isocytosine.

Chembiochem 2019 Apr 14. Epub 2019 Apr 14.

University of Salerno, MoLNaC: Modeling Lab for Nanostructures and Catalysis, Via Giovanni Paolo II, 132, 84084, Fisciano - Salerno, ITALY.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900245DOI Listing
April 2019
1 Read

Considerations on probe design for affinity guided protein conjugation.

Chembiochem 2019 Apr 14. Epub 2019 Apr 14.

Aarhus University, Centre for DNA Nanotechnology at the Dept. of Chemsitry and iNANO, Gustav Wieds Vej 14, 8000, Aarhus, DENMARK.

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. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900157DOI Listing
April 2019
1 Read

Chemoenzymatic Synthesis of Musk Flavors from Stearic Acid.

Chembiochem 2019 Apr 14. Epub 2019 Apr 14.

Beijing University of Chemical Technology, Beijing Bioprocess Key Laboratory, College of Life Science and Technology, BeiSanHuan East Road 15, 100029, Beijing, CHINA.

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. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019002
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http://dx.doi.org/10.1002/cbic.201900210DOI Listing
April 2019
1 Read

Synthesis and Biochemical Evaluation of an Artificial, Fluorescent Glucosinolate (GSL).

Chembiochem 2019 Apr 12. Epub 2019 Apr 12.

Institute of Organic Chemistry, Technische Universität Carolo Wilhelmina zu Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.

The synthesis of the first example of a fluorescent glucosinolate (GSL)-BODIPY conjugate based on an azide-containing artificial GSL precursor (GSL-N ) is reported. Biochemical evaluation of the 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. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900148DOI Listing
April 2019
3 Reads

Fine Regulation of Linker Sequences on the Yeast Synthetic Terminator Strength.

Chembiochem 2019 Apr 11. Epub 2019 Apr 11.

Shihezi University, School of Chemistry and Chemical Engineering, North 4 Rord, 832000, Shihezi, CHINA.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900163DOI Listing
April 2019
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Recent Chemical Approaches for Site-specific Conjugation of Native Antibodies: Technologies toward Next Generation Antibody-Drug Conjugates.

Authors:
Kei Yamada Yuji Ito

Chembiochem 2019 Apr 11. Epub 2019 Apr 11.

Kagoshima Daigaku, JAPAN.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900178DOI Listing
April 2019
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Synthesis of erythropoietins site-specifically conjugated with complex-type N-glycans.

Chembiochem 2019 Apr 11. Epub 2019 Apr 11.

University College Dublin, Department of Organic Chemistry/Cellular Chemistry, --, --, Dublin, IRELAND.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900023DOI Listing

Rapid synthesis and anti-proliferative properties of polyazamacrocycle-based bi- and tetra-gold(I) phosphine dithiocarbamate complexes.

Chembiochem 2019 Apr 10. Epub 2019 Apr 10.

Burgundy University, Institut de Chimie Moleculaire de l'Universite de Bourgogne - UMR CNRS 6302, 9 avenue Alain Savary, BP 47870, 21078, Dijon, FRANCE.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900227DOI Listing

Discovery and Evaluation of Novel Activity-Based Probes for Serine Hydrolases.

Chembiochem 2019 Apr 9. Epub 2019 Apr 9.

Scripps Florida, Department of Chemistry, 130 Scripps Way, Jupiter, FL 33458, USA, 33458, Jupiter, UNITED STATES.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900126DOI Listing
April 2019
1 Read

Off-pathway-sensitive protein splicing screening based on a toxin/antitoxin system.

Chembiochem 2019 Apr 8. Epub 2019 Apr 8.

University of Helsinki, Institute of Biotechnology, Viikinaari 1 POBOX 65, 00014, Helsinki, FINLAND.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900139DOI Listing

DNA origami as scaffolds for self-assembly of lipids and proteins.

Chembiochem 2019 Apr 9. Epub 2019 Apr 9.

Dana-Farber Cancer Institute, Harvard Medical School, Cancer Immunology and Virology, 450 Brookline Ave, CLS 1010, 02215, Boston, UNITED STATES.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900073DOI Listing
April 2019
3.088 Impact Factor

Coordination of platinum to α-synuclein inhibits filamentous aggregation in solution.

Chembiochem 2019 Apr 8. Epub 2019 Apr 8.

ISRAEL.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900224DOI Listing
April 2019
1 Read

Intracellular and Cellular Detection by SERS-Active Plasmonic Nanostructures.

Chembiochem 2019 Apr 8. Epub 2019 Apr 8.

Nanyang Technological University, School of Chemical and Biomedical Engineering, 70 Nanyang Drive, 637457, Singapore, SINGAPORE.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900191DOI Listing
April 2019
3.088 Impact Factor

Near Infrared bioluminescence imaging with Through-Bond Energy Transfer Cassette.

Chembiochem 2019 Apr 7. Epub 2019 Apr 7.

JAPAN.

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). Read More

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http://dx.doi.org/10.1002/cbic.201900149DOI Listing
April 2019
1 Read

Dynamic Continuum of Molecular Assemblies for Controlling Cell Fates.

Chembiochem 2019 Apr 7. Epub 2019 Apr 7.

Brandeis University, Department of Chemistry, 415 South St, 02454, 2454, Waltham, UNITED STATES.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900168DOI Listing

Mannopyranoside Glycolipids Inhibit Mycobacterial Growth, Biofilm and Potentiate Isoniazid Inhibition Activities in M. smegmatis.

Chembiochem 2019 Apr 5. Epub 2019 Apr 5.

Indian Institute of Science, Molecular Biophysics Unit, Indian Institute of Science, 560012, Bangalore, INDIA.

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. Read More

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http://dx.doi.org/10.1002/cbic.201900040DOI Listing
April 2019
1 Read

Fluorescent Probes for Studying Thioamide Positional Effects on Proteolysis Reveal Insight into Resistance to Cysteine Proteases.

Chembiochem 2019 Apr 5. Epub 2019 Apr 5.

University of Pennsylvania, Chemistry, 231 South 34th Street, 19104-6323, Philadelphia, UNITED STATES.

Thioamide substitutions of the peptide backbone have been shown to reduce proteolytic degradation, and this property can be used to generate competitive protease inhibitors and to stabilize peptides toward degradation in vivo. Here, we present a straightforward sensor design that allows a systematic study of the positional effects of thioamide substitution using real-time fluorescence. Thioamide scanning in peptide substrates of five papain family cysteine proteases demonstrates that a thioamide at or near the scissile bond can slow proteolysis in all cases, but that the magnitude of the effects varies with position and protease in spite of high sequence homology. Read More

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http://dx.doi.org/10.1002/cbic.201900115DOI Listing
April 2019
1 Read

Exploring of minimal RNA substrate of flexizymes.

Chembiochem 2019 Apr 5. Epub 2019 Apr 5.

Nagoya University, Department of Biomolecular Engineering, Furo-cho, Chikusa-ku, 464-8603, Nagoya, JAPAN.

Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogs. However, their minimal RNA substrate has not been investigated. Read More

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http://dx.doi.org/10.1002/cbic.201900150DOI Listing

Crenolanib-derived Probes Suitable for Cell- and Tissue-based Protein Profiling and Single Cell Imaging.

Chembiochem 2019 Apr 3. Epub 2019 Apr 3.

CHINA.

Crenolanib (CP-868,596), a potent inhibitor of FLT3 and PDGFRα/β, is currently under phase III clinical investigation for treatment of acute myeloid leukemia (AML). However, the protein targets of Crenolanib in cancer cells remain obscure, resulting in difficulties in understanding the mechanism of actions and side effects. To alleviate this issue, in this study, a photoaffinity probe and two fluorescent probes were created based on Crenolanib, followed by competitive protein profiling and bioimaging studies, aiming to characterize the cellular targets. Read More

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http://dx.doi.org/10.1002/cbic.201900067DOI Listing
April 2019
2 Reads

Additive-free, enzymatic phosphorylation and ligation of artificial oligonucleotides composed of C-nucleosides at the reaction points.

Chembiochem 2019 Apr 2. Epub 2019 Apr 2.

University or Toyama, Graduate School of Pharmaceutical Sciences, Sugitani 2630, 930-0194, Toyama, JAPAN.

We report enzymatic phosphorylation and additive-free ligation of DNAs containing non-natural, artificial C-nucleotide residues by T4 polynucleotide kinase and T4 DNA ligase. The artificial units are composed of an alkynyl deoxyribose and non-natural nucleobases D*, T*, G*, and C*, corresponding to natural A, T, G, and C, respectively, from a viewpoint of hydrogen-bonding pattern. Phosphorylation progressed quantitatively at the 5'-end of all of the artificial units in the chimera DNAs. Read More

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http://dx.doi.org/10.1002/cbic.201900217DOI Listing

Biocatalytic protein-based materials for integration into energy devices.

Chembiochem 2019 Apr 2. Epub 2019 Apr 2.

Centro de Investigacion Cooperativa en Biomateriales, Paseo de Miramón 182, 20014, San Sebastian, SPAIN.

There is a current need to fabricate new biobased functional materials. Bottom-up approaches to assemble simple molecular units have shown promise for biomaterial fabrication due to their tunability and versatility to incorporate functionalities. Here, we demonstrate the fabrication of catalytic protein thin films by the entrapment of catalase into protein films composed of a scaffolding protein. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019000
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http://dx.doi.org/10.1002/cbic.201900047DOI Listing
April 2019
9 Reads

Branched DNA Architectures via PCR-based Assembly as Gene Compartment for Cell-free Gene Expression Reactions.

Chembiochem 2019 Apr 2. Epub 2019 Apr 2.

Tianjin University, room 328, building 54, 300350, Tianjin, CHINA.

The physical distance between genes plays important roles in controlling gene expression reactions in vivo. In this work, we report the design and synthesis of branched gene which integrates three transcription units in one architecture via polymerase chain reaction (PCR)-based assembly, and exploit these constructs as gene compartment for cell-free gene expression reactions, probing the impact of this physical environment on gene transcription and translation. We find that branched gene enhances gene expression yields, in particular at low concentrations of DNA and RNA polymerase (RNAP); furthermore, in crowded microenvironment that mimics the intracellular microenvironment, gene expression from branched genes maintains a relatively high level. Read More

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http://dx.doi.org/10.1002/cbic.201900094DOI Listing
April 2019
3.088 Impact Factor

Potentides: Novel Cysteine-Rich Peptides with Unusual Disulfide Connectivity from Potentilla anserina.

Chembiochem 2019 Mar 30. Epub 2019 Mar 30.

School of Biological Sciences, Nanyang Technological University, Singapore, Singapore, SINGAPORE.

Cysteine-rich peptides (CRPs), disulfide-constrained peptides with three to five disulfide bonds and molecular weights of 2 to 6 kDa, are generally hyperstable and resistant to thermal, chemical and enzymatic degradation. Here, the discovery and characterization of a novel suite of CRPs, collectively named potentides pA1- pA16 from the root of the medicinal herb Potentilla anserina L, are described. Using a combination of proteomic and transcriptomic methods, we showed that 35-residue potentide pA3, the most abundant member of potentides, exhibits high stability against heat, acidic and proteolytic degradation. Read More

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http://dx.doi.org/10.1002/cbic.201900127DOI Listing

Identification of the Hypertension Drug Guanfacine as an Anti-virulence Agent in Pseudomonas aeruginosa.

Chembiochem 2019 Mar 30. Epub 2019 Mar 30.

Princeton University, Chemistry, Washington University, Frick Chemistry Lab, Room 333, 08544, Princeton, UNITED STATES.

An alternative solution to the cyclical development of new antibiotics is the concept of disarming pathogens without affecting growth, thereby eliminating selective pressures that lead to resistant phenotypes. Herein, we employ our previously developed HiTES methodology to identify one such compound against the ESKAPE pathogen Pseudomonas aeruginosa. Rather than induce silent biosynthetic gene clusters, we used HiTES to suppress actively-expressed virulence genes. Read More

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http://dx.doi.org/10.1002/cbic.201900129DOI Listing

Design of an ultra-fast G protein switch based on a mouse melanopsin variant.

Chembiochem 2019 Mar 28. Epub 2019 Mar 28.

Ruhr-Universität Bochum, Biophysik, Universitätsstr. 150, 44801, Bochum, GERMANY.

The primary goal of optogenetics is the light-controlled non-invasive and specific manipulation of various cellular processes. Here, we present a hybrid strategy for targeted protein engineering combining computational techniques with electrophysiological and UV/VIS spectroscopic experiments. We validated our concept for channelrhodopsin 2 and applied it to modify the less-well studied vertebrate opsin melanopsin. Read More

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http://dx.doi.org/10.1002/cbic.201900110DOI Listing
March 2019
1 Read

Structural and Dynamic Characterization of Artificially Linked Ubiquitin Dimers by NMR spectroscopy.

Chembiochem 2019 Mar 28. Epub 2019 Mar 28.

Universitat Konstanz, Chemie, Universitaetsstraße 10, 78457, Konstanz, GERMANY.

As one of the most prevalent post-translational modifications in eukaryotic cells, ubiquitylation plays vital roles in many cellular processes such as protein degradation, DNA metabolism, and cell differentiation. Substrate proteins can be tagged by distinct types of polymeric ubiquitin (Ub) chains, which determine the eventual fate of the modified protein. We recently established a facile, click chemistry-based approach for the efficient generation of linkage-defined Ub chains including Ub dimers. Read More

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http://dx.doi.org/10.1002/cbic.201900146DOI Listing

Evaluating the impact on the local hydrophobicity of the incorporation of monofluoroalkene in the backbone of short peptides.

Chembiochem 2019 Mar 28. Epub 2019 Mar 28.

Universite Laval, Chemistry, 1045 avenue de la Médecine, Pavillon Alexandre-Vachon, G1V 0A6, Québec, CANADA.

The local hydrophobicity of an amino acid in a peptide sequence can be determined by measuring the hydrophobicity index (φ0) by reverse-phase high-performance liquid chromatography (RP-HPLC). Herein, the impact of the replacement of an amide by a monofluoroalkene unit in short peptides on the local hydrophobicity was studied. Monofluoroalkene-containing dipeptides and tripeptides were synthesized, as well as their natural analogues, and the hydrophobicity indexes of these short peptides were determined. Read More

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http://dx.doi.org/10.1002/cbic.201900082DOI Listing

The human macrophage galactose-type lectin, MGL, recognizes the outer core of E. coli lipooligosaccharide.

Chembiochem 2019 Mar 28. Epub 2019 Mar 28.

ITALY.

Carbohydrate-lectin interactions intervene in and mediate most biological processes, including a crucial modulation of immune responses to pathogens. Despite the growing interest in investigating the association between host receptor lectins and exogenous glycan ligands, the molecular mechanisms underlying bacterial recognition by human lectins are still not fully understood. Here we describe a novel molecular interaction between the human macrophage galactose-type lectin (MGL) and the lipooligosaccharide (LOS) of E. Read More

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http://dx.doi.org/10.1002/cbic.201900087DOI Listing

A Bis-Zn²+-Pyridyl-Salen-Type Complex Conjugated to the ATP-Aptamer: An ATPase Mimicking Nucleoapzyme.

Chembiochem 2019 Mar 25. Epub 2019 Mar 25.

The Hebrew University of Jerusalem, Institute of Chemistry, Givat Ram, 91904, Jerusalem, ISRAEL.

Catalytic nucleic acids composed of a bis-Zn2+-salen complex conjugated to the ATP aptamer act as ATPase mimicking catalysts (nucleoapzymes). By the direct linkage of the Zn2+-complex to the 3'-end or 5'-end of the aptamer (nucleoapzymes I and II) or its conjugation to the 3'- or 5'-ends of the aptamer through bis-thymidine spacers (nucleoapzymes III and IV) a set of nucleoapzymes exhibiting variable catalytic activities is achieved. While the separated bis-Zn2+-salen catalyst and the ATP aptamer do not show any noticeable catalytic activity, the 3'-catalyst modified nucleoapzyme, (I) and specifically the nucleoapzyme consisting of the catalyst linked to the 3'-position through the spacer, (III), reveals enhanced catalytic features as compared to the analog nucleoapzymes substituted at the 5'-position. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2019001
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http://dx.doi.org/10.1002/cbic.201900182DOI Listing
March 2019
4 Reads
3.088 Impact Factor

Fatty acid biosynthesis: Chain length regulation and control.

Chembiochem 2019 Mar 25. Epub 2019 Mar 25.

GERMANY.

De novo biosynthesis of fatty acids undergoes an iterative process with strict regulation of the length of the produced fatty acids. In this review, we focus on the factors determining the chain length in fatty acid biosynthesis. In a nutshell, the process of chain length regulation can be understood as a competition between the output of a chain elongating C-C bond forming reaction and a terminating fatty acid release function. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.2018008
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http://dx.doi.org/10.1002/cbic.201800809DOI Listing
March 2019
3 Reads

Genetically encoded biotin analogs: Incorporation and application in bacterial and mammalian cells.

Chembiochem 2019 Mar 21. Epub 2019 Mar 21.

GERMANY.

The biotin-streptavidin interaction is among the strongest known in nature. Here, we report the site-directed incorporation of biotin and 2-iminobiotin bearing non-canonical amino acids (ncAA) into proteins. 2-Iminobiotin lysine was employed for protein purification based on the pH-dependent dissociation constant to streptavidin. Read More

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http://dx.doi.org/10.1002/cbic.201900015DOI Listing
March 2019
3.088 Impact Factor

Microneedle array-based platforms for future theranostic applications.

Chembiochem 2019 Mar 21. Epub 2019 Mar 21.

Institut des Biomolécules Max Mousseron - UMR5247, Université de Montpellier, Faculté de Pharmacie, 34093 Montpellier, (France), FRANCE.

Theranostics involves finding the biomarkers of a disease, fighting them through site specific drug delivery and following them for prognosis of the disease. Microneedle array technology has been used for drug delivery and extended for continuous monitoring of analytes present in the skin compartment. We envisage the use of microneedle arrays for future theranostic applications. Read More

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http://dx.doi.org/10.1002/cbic.201900112DOI Listing
March 2019
3.088 Impact Factor

Distinct Dynamical and Conformational Features of Human STING in Response to 2'3'-cGAMP and c-di-GMP.

Chembiochem 2019 Mar 20. Epub 2019 Mar 20.

CHINA.

Human stimulator of interferon genes protein (hSTING) can bind cyclic dinucleotides (CDNs) to activate the production of type I interferons and inflammatory cytokines. These CDNs can be both bacterial second messengers, 3'3'-CDNs and endogenous 2'3'-cGAMP. The cGAMP with a unique 2'-5' bond is the most potent activator of hSTING among all CDNs. Read More

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http://dx.doi.org/10.1002/cbic.201900051DOI Listing
March 2019
2 Reads

Polymer-based module for NAD+ regeneration with visible light.

Chembiochem 2019 Mar 18. Epub 2019 Mar 18.

Max Planck Institute for Polymer Research, Dept. Physical Chemistry of Polymer Research, Ackermannweg 10, 55128, Mainz, GERMANY.

Regeneration of enzymatic cofactors by cell-free synthetic modules is a key step towards producing a purely synthetic cell. Here, we demonstrate the regeneration of the enzyme cofactor NAD+ by photo-oxidation of NADH under visible-light irradiation, using metal-free conjugated polymer nanoparticles. Encapsulation of the light-active nanoparticles in the lumen of polymeric vesicles produced a fully organic module able to regenerate NAD+ in an enzyme-free system. Read More

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http://dx.doi.org/10.1002/cbic.201900093DOI Listing

Strategies for stabilizing DNA nanostructures to biological conditions.

Chembiochem 2019 Mar 15. Epub 2019 Mar 15.

Arizona State University, School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, PO Box 877301, 85287, Tempe, UNITED STATES.

DNA is one of the most promising building blocks for creating functional nanostructures for applications in biology and medicine. However, these highly programmable nanomaterials (e.g. Read More

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http://dx.doi.org/10.1002/cbic.201900075DOI Listing
March 2019
1 Read