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    Spatial Control of Inducible Cre-Mediated Recombination Using Cyanine Photocages.
    Chembiochem 2018 Feb 22. Epub 2018 Feb 22.
    National Cancer Institute, Chemical Biology Laboratory, 376 Boyles Street, 21702, Frederick, UNITED STATES.
    Optical control over protein expression could provide a means to interrogate a range of biological processes. One approach has employed caged ligands of the estrogen receptor (ER) in combination with broadly used ligand-dependent Cre recombinase proteins. Existing approaches used UV or blue wavelengths, which hinders their application in tissue settings. Read More

    Tracking the oxygen status in the cell nucleus by using a Hoechst-tagged phosphorescent ruthenium complex.
    Chembiochem 2018 Feb 21. Epub 2018 Feb 21.
    Kyoto University, Energy and Hydrocarbon Chemistry, Kyoto Univ. Katsura, Nishikyo-ku, 615-8510, Kyoto, JAPAN.
    Molecular oxygen in living cells is distributed and consumed inhomogeneously, depending on the activity of each organelle. Therefore, tractable methods that can be used to monitor the oxygen status in each organelle are needed to understand cellular function. Here, we report the design of a novel oxygen-sensing probe for use in the cell nucleus. Read More

    Targeted delivery of activatable fluorescent probe for detection of furin activity in living cells.
    Chembiochem 2018 Feb 21. Epub 2018 Feb 21.
    Furin, a protein convertase, play a crucial role in the progression of tumor. In this work, a new fluorescent probe 1 consisting of a peptide Arg-val-Arg-Arg (RVRR) and aminoluciferin fluorophore was designed and prepared for responsive and activatable detecting furin activity in vitro and in living cells. We demonstrated that probe 1 could be response toward furin with an "off-on" florescence signal to generate ~3. Read More

    MSN-on-a-Chip: Cell-Based Screenings Made Possible on a Small Molecule Microarray of Native Natural Products.
    Chembiochem 2018 Feb 21. Epub 2018 Feb 21.
    Standard small molecule microarray (SMM) is not well-suited for cell-based screening assays. Of the few attempts made thus far to render SMM cell-compatible, all were met with major limitations. We report herein the first mesoporous silica nanoparticle (MSN)-on-a-chip platform capable of conducting high-throughput cell-based screening on SMM. Read More

    Near-infrared light-controlled gene expression and protein targeting in neurons and non-neuronal cells.
    Chembiochem 2018 Feb 21. Epub 2018 Feb 21.
    Near-infrared (NIR) light-inducible binding of bacterial phytochrome BphP1 to its engineered partner QPAS1 is used for optical protein regulation in mammalian cells. However, there are no data on the application of the BphP1-QPAS1 pair in cells derived from various mammalian tissues. Here, we tested functionality of two BphP1-QPAS1-based optogenetic tools, such as an NIR and blue light-sensing system for control of protein localization (iRIS) and an NIR light-sensing system for transcription activation (TA), in several cell types including cortical neurons. Read More

    Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway.
    Chembiochem 2018 Feb 20. Epub 2018 Feb 20.
    Ernst-Moritz-Arndt-Universität, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY.
    A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analog, a novel quadruplex fold with an inversion of a single G-tract and the conversion of a propeller into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and interresidual F***H8-C8 pseudohydrogen bonds within the modified quadruplexes. Read More

    Amide Neighbouring Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer.
    Chembiochem 2018 Feb 19. Epub 2018 Feb 19.
    Nature uses proteins as medium for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides. Read More

    Substrate binding drives active site closing of human blood group B galactosyltransferase as revealed by hot-spot labeling and NMR experiments.
    Chembiochem 2018 Feb 19. Epub 2018 Feb 19.
    University of Lübeck, GERMANY.
    Crystallography has shown that human blood group A (GTA) and B (GTB) glycosyltransferases undergo transitions between "open", "semi-closed", and "closed" conformations upon substrate binding. However, the time scales of corresponding conformational reorientations are unknown. Crystal structures show that Trp and Met residues are located at "conformational hot spots" of the enzymes. Read More

    Clickable polyamine derivatives as chemical probes for the polyamine transport system.
    Chembiochem 2018 Feb 16. Epub 2018 Feb 16.
    University of Leuven, Cellular and Molecular Medicine, Herestr. 49, box 802, 3000, Leuven, BELGIUM.
    Polyamines are essential for cell growth and differentiation, but their trafficking by the polyamine transport system is not fully understood. In this paper, we describe the synthesis of several azido-derivatized polyamines for easy conjugation by click chemistry. Attachment of a BODIPY-dye gave fluorescent polyamine probes, which were tested in cell culture. Read More

    Light-dependent cytoplasmic recruitment enhances the dynamic range of a nuclear import photoswitch.
    Chembiochem 2018 Feb 14. Epub 2018 Feb 14.
    University of North Carolina, Biochemistry and Biophysics, 120 Mason Farm Rd, 27599, Chapel Hill, UNITED STATES.
    Cellular signal transduction is often regulated at multiple steps in order to achieve more complex logic or precise control of a pathway. For instance, some signaling mechanisms couple allosteric activation with localization to achieve high signal to noise. Here, we create a system for light activated nuclear import that incorporates two levels of control. Read More

    Lysine-241 has a role in coupling 2OG turnover with substrate oxidation during KDM4-catalysed histone demethylation.
    Chembiochem 2018 Feb 14. Epub 2018 Feb 14.
    University of leicester, Chemistry, Henry Wellcome Building, Lancaster Road, LE1 7RH, Leicester, UNITED KINGDOM.
    The JmjC histone demethylases (KDMs) play important roles in modulating histone methylation states and have the potential to be regulated by oxygen availability. Lys-241 of the KDM4 subfamily is proposed to be important in oxygen binding by KDM4A. We report evidence that, although K241 is unlikely to be directly involved in oxygen binding, it has an important role in coupling 2-oxoglutarate cosubstrate oxidation with lysine demethylase activity. Read More

    Optogenetic Control by Pulsed Illumination.
    Chembiochem 2018 Feb 14. Epub 2018 Feb 14.
    Universitat Bayreuth, Biochemistry, Universitaetsstrasse 30, 95447, Bayreuth, GERMANY.
    Sensory photoreceptors evoke numerous adaptive responses in Nature and serve as light-gated actuators in optogenetics to enable the spatiotemporally precise, reversible and noninvasive control of cellular events. The output of optogenetic circuits can often be dialed in by varying illumination quality, quantity and duration. Here, we devise a programmable matrix of light-emitting diodes to efficiently probe the response of optogenetic systems to intermittently applied light of varying intensity and pulse frequency. Read More

    Dual Labeling of the CBP/p300 KIX domain for 19F NMR leads to identification of a new small molecule binding site.
    Chembiochem 2018 Feb 11. Epub 2018 Feb 11.
    University of Minnesota, Chemistry, 207 Pleasant St. SE, 312 Smith Hall, 55455, United States, 55455, Minneapolis, UNITED STATES.
    Protein-Observed Fluorine NMR Spectroscopy (PrOF NMR) is an emerging technique for screening and characterizing small molecule-protein interactions. The choice of which amino acid to label for PrOF NMR can be critical for analysis. Here we report the first use of a protein containing two different fluoroaromatic amino acids for NMR studies. Read More

    Alanine and lysine scans of the LL-37 derived peptide fragment KR-12 reveal key residues for antimicrobial activity.
    Chembiochem 2018 Feb 11. Epub 2018 Feb 11.
    Uppsala University, Department Medicinal Chemistry, Division Pharmacognosy, BMC Box 574, 75123, Uppsala, SWEDEN.
    The human host defence peptide LL-37 is a broad-spectrum antibiotic with immunomodulatory functions. Residues 18-29 in LL-37 have previously been identified as a minimal peptide (KR-12) that retains antibacterial activity with decreased cytotoxicity. In this study, we generated analogues of KR-12 by Ala and Lys scans to identify key elements for activity. Read More

    Discovery of a short chain dehydrogenase from Catharanthus roseus that produces a novel monoterpene indole alkaloid.
    Chembiochem 2018 Feb 9. Epub 2018 Feb 9.
    John Innes Centre, Biological Chemistry, Norwich Research Park, NR4 7UH, Norwich, UNITED KINGDOM.
    Monoterpene indole alkaloids, a large class of plant natural products, derive from the biosynthetic intermediate strictosidine aglycone. Strictosidine aglycone, which can exist as a variety of isomers, can be reduced to form numerous different structures. We have discovered a short chain alcohol dehydrogenase (SDR) from monoterpene indole alkaloid producing plants (Catharanthus roseus and Rauvolfia serpentina) that reduce strictosidine aglycone and produce an alkaloid that does not correspond to any previously reported compound. Read More

    Synthesis and Biological Evaluation of Fluorescent Bryostatin Analogues.
    Chembiochem 2018 Feb 9. Epub 2018 Feb 9.
    To investigate the cellular distribution of tumor-promoting vs nontumor-promoting bryostatin analogues, we synthesized fluorescently labeled variants of two bryostatin derivatives that have previously shown either phorbol ester-like or bryostatin-like biological activity on U937 cells. These new fluorescent analogues both displayed high affinity for PKC binding and retained the basic properties of the parent, unlabeled compounds in U937 assays. The fluorescent compounds showed similar patterns of intracellular distribution in cells, however, arguing against an existing hypothesis that varying patterns of intracellular distribution contributed to the difference in biological activity. Read More

    A miniaturized E. coli green light sensor with high dynamic range.
    Chembiochem 2018 Feb 8. Epub 2018 Feb 8.
    Rice University, Department of Bioengineering, 6100 Main St, MS-142, 77005, Houston, UNITED STATES.
    Genetically-engineered photoreceptors enable unrivaled control over gene expression. Previously, we ported the Synechocystis PCC 6803 CcaSR two-component system, which is activated by green light and de-activated by red, into E. coli, resulting in a sensor with 6-fold dynamic range. Read More

    Npom-protected NONOate enables light-triggered NO/cGMP signalling in primary vascular smooth muscle cells.
    Chembiochem 2018 Feb 8. Epub 2018 Feb 8.
    Universität Tübingen, Interfakultäres Institut für Biochemie, Auf der Morgenstelle 15, Verfügungsgebäude IFIZ, 72076, Tübingen, GERMANY.
    Diazeniumdiolates (NONOates) are a class of nitric oxide (NO)-releasing substances widely used in studies of NO/cGMP signalling. Since spatiotemporal control is highly desirable for such purposes, we synthesised a novel Npom-caged pyrrolidine NONOate. A kinetic analysis together with a Griess Assay show the photo-dependent release of NO with high quantum yield (UV light). Read More

    Design of a short thermally stable α-helix embedded in a macrocycle.
    Chembiochem 2018 Feb 7. Epub 2018 Feb 7.
    UCSF, Pharm Chem, 16th St., 94158, San Francisco, UNITED STATES.
    Although helices play key roles in peptide-protein and protein-protein interactions, the helical conformation is generally unstable for short peptides (10 - 15 residues) in aqueous solution in the absence of their binding partners. Thus, stabilizing the helical conformation of peptides can lead to increases in binding potency, specificity, and stability towards proteolytic degradation. Helices have been successfully stabilized by introducing sidechain-to-sidechain cross-links within the central portion of the helix. Read More

    Screening for selective protein inhibitors using IANUS peptide array.
    Chembiochem 2018 Feb 7. Epub 2018 Feb 7.
    Martin-Luther-University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Weinbergweg 22, 6120, Halle Saale, GERMANY.
    The IANUS (Induced orgANization of strUcture by matrix-assisted togethernesS) peptide array was build up on a hypothesis that two peptides from two interacting protein epitopes are also able to interact when immobilized on a solid support. This peptide-peptide interactions can be visualized by FRET effects caused by close proximity of fluorescent labeled peptide chains. The biggest advantage of this low-resolution method is that no soluble protein probe or selective antibodies are needed. Read More

    Structural Diversity and Anticancer Activity of Marine-Derived Elastase Inhibitors: Key Features and Mechanisms Mediating the Antimetastatic Effects in Invasive Breast Cancer.
    Chembiochem 2018 Feb 5. Epub 2018 Feb 5.
    University of Florida, Medicinal Chemistry, 1345 Center Drive, 32610, Gainesville, UNITED STATES.
    Three new 3-amino-6-hydroxy-2-piperidone (Ahp)-containing cyclic depsipeptides named loggerpeptins A-C (1-3) along with molassamide (4) were discovered from a marine cyanobacterium, extending the structural diversity of this prevalent scaffold of cyanobacterial serine protease inhibitors. Molassamide (4), containing the 2-amino-butenoic (Abu) unit in the cyclic core, was the most potent and selective analogue against human neutrophil elastase (HNE). Given the growing evidence supporting the role of HNE in breast cancer progression and metastasis, we assessed the cellular effects of compounds 3 and 4 in the context of targeting invasive breast cancer. Read More

    Construction of T-motif-based DNA nanostructures using enzymatic reactions.
    Chembiochem 2018 Feb 4. Epub 2018 Feb 4.
    Tohoku UNiversity, Graduate School of Engineering, Deptartment of Robotics, 6-6-01, Aobayama, 980-8579, Sendai, JAPAN.
    The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced using enzymatic reactions, they could be applied in various environments, including in vivo. Here, we report an enzymatic method that we developed to construct a DNA nanostructure from a simple motif called a T-motif. Read More

    Loganic Acid Methyltransferase: Insights into the specificity of methylation on an iridoid glycoside.
    Chembiochem 2018 Feb 5. Epub 2018 Feb 5.
    University of Illinois-Urbana Champaign, Biochemistry, 600 S. Mathews Ave, 61802, Urbana, UNITED STATES.
    : Loganin is an iridoid glycoside of interest as both an intermediate in the biosynthesis of indole alkaloids in plants and as a bioactive compound itself. The loganic acid methyltransferase catalyzes the methylation of a monoterpenoid glycoside precursor to produce loganin, and demonstrates stereospecificity for the (6S,7R) substrate. Here, we biochemically characterize this biocatalyst and elucidate the basis for its strict substrate specificity. Read More

    The unfold story of general anesthesia.
    Chembiochem 2018 Feb 4. Epub 2018 Feb 4.
    MTA TTK, Biomolecular Self-Assembly Group, Magyar tudósok körútja 2., H-1117, Budapest, HUNGARY.
    Inhalational anesthetics are routinely employed in the clinical practice to accomplish general anesthesia. Concerns have recently been emerged regarding deleterious impact of these volatile agents on cognitive performance, immune functions, tumor recurrence and metastasis. These agents have shown to modify the gene expression pattern as well as cell signaling in tumor cells but the underlying molecular mechanisms remain a matter of conjecture. Read More

    Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs.
    Chembiochem 2018 Feb 3. Epub 2018 Feb 3.
    Indian Institute of Science Education Research Pune, Chemistry, Dr. Homi Bhabha Road, Pashan, 411008, Pune, INDIA.
    Fluorescence-based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in the cells. However, certain limitations like target accessibility and hybridization efficiency in cellular environment hamper their broad application as RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of (i) a new microenvironment-sensitive fluorescent nucleobase analog, derived by attaching the Lucifer chromophore (1,8-naphthalimide) at the 5-position of uracil, and (ii) peptide nucleic acid (PNA), which is capable of forming stable hybrids with RNA. Read More

    Site-specific labelling of native mammalian proteins for single-molecule FRET measurements.
    Chembiochem 2018 Feb 2. Epub 2018 Feb 2.
    Universität Regensburg, Department of Biochemistry, Genetics and Microbiology, Institute of Mikrobiologie, Universitätsstraße 31, 93053, Regensburg, GERMANY.
    Human cells are complex entities in which molecular recognition and selection are critical for cellular processes often driven by structural changes and dynamic interactions. Biomolecules appear in different chemical states and modifications like phosphorylation affect their function. Hence, using proteins in their chemically native state in biochemical and biophysical assays is essential. Read More

    Single-molecule kinetics of an enzyme in the presence of multiple substrates.
    Chembiochem 2018 Feb 2. Epub 2018 Feb 2.
    Indian Institute of Science Education Research Pune, chemistry, Dr. Homi Bhabha Road, 411008, Pune, INDIA.
    In this work, we study the catalytic activity of a single enzyme in the presence of multiple substrates. We broadly discuss three different mechanisms of bisubstrate binding, namely ordered sequential, random sequential and ping-pong non-sequential pathway. Using the chemical master equation approach we obtain exact expressions for the waiting time distributions the mean turnover time and the randomness parameter as a function of the substrate concentration, such that both concentrations are fixed but one of them is changed quasistatically. Read More

    Mechanism-based Inhibitor of DNA Cytosine-5 Methyltransferase (DNMT) via a SNAr Reaction with an Oligodeoxyribonucleotide Containing 2-Amino-4-Halopyridine-C-Nucleoside (dXP).
    Chembiochem 2018 Feb 2. Epub 2018 Feb 2.
    In chromatin, 5-methylcytosine (mC), which represents the 5th nucleobase in genomic DNA, plays a role as an inducer of epigenetic changes. Tumor cells exhibit aberrant DNA methylation patterns, and inhibition of human DNA cytosine-5 methyltransferase (DNMT), which is responsible for generating mC in CpG sequences, is an effective strategy to treat various cancers. Here, we describe the design, synthesis, and evaluation of the properties of 2-amino-4-halopyridine-C-nucleosides (dXP) and oligodeoxyribonucleotides (ODNs) containing dXP as a novel mechanism-based inhibitor of DNMTs. Read More

    Tuning a Protein Labeling Reaction to Achieve Highly Site-Selective Lysine Conjugation.
    Chembiochem 2018 Jan 31. Epub 2018 Jan 31.
    Genomics Institute of the Novartis Research Foundation (GNF), Biotherapeutics & Biotechnology, 10675 John Jay Hopkins Dr., 92121, San Diego, UNITED STATES.
    Activated esters are widely used to label proteins at lysine sidechains and N-termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site-selective modification. In a unique case, fluoro-phenyl esters are shown to preferentially label human kappa antibodies at a single lysine (K188) within the light chain constant domain. Read More

    Design and Synthesis of a BODIPY-Tetrazole Based "Off-On" In-Cell Fluorescent Reporter of Hydrogen Peroxide.
    Chembiochem 2018 Jan 31. Epub 2018 Jan 31.
    The BODIPY-linked bithiophene-tetrazoles were designed and synthesized for bioorthogonal photoclick reactions in vitro and in vivo. The reactivity of these tetrazoles toward dimethyl fumarate was found to depend on BODIPY attachment site, with the meta-linked BODIPY-tetrazole being the most reactive. The resulting BODIPY-pyrazolines showed drastically reduced BODIPY fluorescence. Read More

    Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls.
    Chembiochem 2018 Jan 31. Epub 2018 Jan 31.
    Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.
    The plant cell wall is a cellular exoskeleton consisting predominantly of a complex polysaccharide network that defines the shape of cells. During growth, this network can be loosened through the action of xyloglucan endotransglycosylases (XETs), glycoside hydrolases that "cut and paste" xyloglucan polysaccharides through a transglycosylation process. We have analyzed cohorts of XETs in different plant species to evaluate the substrate specificities of xyloglucan acceptors by using a set of synthetic oligosaccharides obtained by automated glycan assembly. Read More

    Pyridone Luciferins and Mutant Luciferases for Bioluminescence Imaging.
    Chembiochem 2018 Jan 31. Epub 2018 Jan 31.
    Department of Chemistry, University of California, 1120 Natural Sciences II, Irvine, CA, 92697, USA.
    New applications for bioluminescence imaging require an expanded set of luciferase enzymes and luciferin substrates. Here, we report two novel luciferins for use in vitro and in cells. These molecules comprise regioisomeric pyridone cores that can be accessed from a common synthetic route. Read More

    Chimeric Styrene Monooxygenase with Increased Efficiency in Asymmetric Biocatalytic Epoxidation.
    Chembiochem 2018 Jan 29. Epub 2018 Jan 29.
    University of Amsterdam, van't Hoff Institute for Molecular Sciences, Science Park 904, 1098 XH, Amsterdam, NETHERLANDS.
    The styrene monooxygenase (SMO) system from Pseudomonas sp. is constituted by two enzymes (StyA and StyB). StyB catalyses the reduction of FAD at the expense of NADH. Read More

    Improvement in the Photobiological Hydrogen Production of Aggregated Chlorella by Dimethyl Sulfoxide.
    Chembiochem 2018 Jan 27. Epub 2018 Jan 27.
    Department of Chemistry, Center for Biomaterials and Biopathways, Zhejiang University, Hangzhou, 310027, China.
    Photobiological hydrogen production plays a vital role in generating clean renewable energy owing to its low energy consumption and environmental friendliness. Although materials-induced Chlorella aggregates have been developed to achieve sustained photobiological hydrogen production under normal aerobic conditions, the yield is relatively low and equals only 0.42 % of the light-to-Henergy-conversion efficiency. Read More

    Site-Selective Functionalization of Flagellin by Steric Self-Protection: A Strategy to Facilitate Flagellin as a Self-Adjuvanting Carrier in Conjugate Vaccine.
    Chembiochem 2018 Jan 29. Epub 2018 Jan 29.
    National Taiwan University, Department of Chemistry, Department of Chemistry, Roosevelt Road, 106, Taipei, TAIWAN.
    Flagellin (FliC) can act as a carrier protein in preparation of conjugate vaccine to elicit the T-cell dependent immune response, and as an intrinsic adjuvant to activate the toll-like receptor (TLR5) for enhancement of the vaccine potency. To enable the use of FliC as a self-adjuvanting carrier, an effective method for site-selective modification (SSM) of pertinent amino acid residues in the D2 and D3 domains of FliC is explored without excessive modification of the D0 and D1 domains that are responsible for activation and binding with TLR5. In a high concentration of Na2SO4 solution, FliC monomers form flagellar filaments, in which the D0 and D1 domains are situated inside the tubular structure. Read More

    Indoloazepinone-Constrained Oligomers as Cell-Penetrating and Blood-Brain Barrier Permeable Compounds.
    Chembiochem 2018 Jan 29. Epub 2018 Jan 29.
    Vrije Universiteit Brussel, Chemistry and Bioengineering Sciences, Pleinlaan 2, 1050, Brussels, BELGIUM.
    Non-cationic and amphipathic indoloazepinone-constrained (Aia) oligomers have been synthesized as new vectors for intracellular delivery. The conformational preferences of the [L-Aia-Xxx]n oligomers were investigated using circular dichroism and NMR spectroscopy. While Boc-[L-Aia-Gly]2,4-OBn 12-13 and Boc-[L-Aia-β3-h-L-Ala]2,4-OBn 16-17 oligomers were totally or partially disordered, Boc-[L-Aia-L-Ala]2-OBn 14 induced a typical turn stabilized by C5- and C7-membered H-bond pseudo-cycles and aromatic interactions. Read More

    Pentachloropseudilin inhibits transforming growth factor-β (TGF-β) activity by accelerating cell-surface type II TGF-β receptor turnover in target cells.
    Chembiochem 2018 Jan 25. Epub 2018 Jan 25.
    National Sun Yat-sen University College of Science, Biological Sciences, 70 Lienhai Rd, Dept. of Biological Sciences, 80424, 80424, Kaohsiung, TAIWAN.
    Pentachloropseudilin (PClP) is a chlorinated phenylpyrrole compound that was isolated first from Actinoplanes and found to have a marine origin. Its structure has been confirmed by chemical synthesis. PClP shows a broad range of antimicrobial activity against gram-negative and gram-positive bacteria, protozoa, fungi, and yeast. Read More

    Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin.
    Chembiochem 2018 Jan 25. Epub 2018 Jan 25.
    Robert Koch-Institut Berlin, ZBS6 Proteomics and Spectroscopy, Seestrasse 10, 13353, Berlin, Germany.
    Paenibacillus polymyxa strains are qualified for agro-biotechnological uses such as plant growth promotion and for biocontrol strategies against deleterious phytopathogenic competitors in the soil depending on their attractive arsenal of bioactive compounds. Moreover, they are potent producers of antibiotics for medical applications. To identify new products of such organisms, genome mining strategies in combination with mass spectrometry are the methods of choice. Read More

    Hedgehog antagonist pyrimidine-indole hybrid molecule inhibits ciliogenesis through microtubule destabilization.
    Chembiochem 2018 Jan 24. Epub 2018 Jan 24.
    Bose Institute, 700032, Kolkata, INDIA.
    One of the crucial regulators of embryonic patterning and tissue development is the Hedgehog-Glioma (Hh-Gli) signaling pathway; however its uncontrolled activation has been implicated in different types of cancer in adult tissues. Primary cilium is one of the important factors required for the activation of Hh signaling, for it brings the critical components together for key protein-protein interactions required for Hh pathway regulation. Most of the synthetic and natural small molecule modulators of the pathway primarily antagonize Smoothened (Smo) or other effectors like Hh ligand or Gli. Read More

    Fine Tuning of Antibiotic Activity by a Tailoring Hydroxylase in a Trans-AT Polyketide Synthase Pathway.
    Chembiochem 2018 Jan 24. Epub 2018 Jan 24.
    University of Birmingham, Biosciences, Edgbaston, B15 2TT, Birmingham, UNITED KINGDOM.
    Hydroxylation modulates the activity of many pharmacological biomolecules. It can be integral to the basic biosynthetic factory or result from tailoring steps. For anti-MRSA antibiotic mupirocin, removal of C8-hydroxyl late in biosynthesis gives the active pseudomonic acid A. Read More

    A Comparative Analysis of the CO-Reducing Activities of MoFe Proteins Containing Mo- and V-Nitrogenase Cofactors.
    Chembiochem 2018 Jan 24. Epub 2018 Jan 24.
    Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA.
    The Mo and V nitrogenases are structurally homologous yet catalytically distinct in their abilities to reduce CO to hydrocarbons. Here we report a comparative analysis of the CO-reducing activities of the Mo- and V-nitrogenase cofactors (i.e. Read More

    Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis.
    Chembiochem 2018 Jan 22. Epub 2018 Jan 22.
    Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands.
    Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced crosslinks, fixed tissue proteins are difficult to extract, which hampers mass spectrometry (MS) proteomic analyses. Recent years have seen the use of different combinations of high temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixed paraffin-embedded tissue proteomes. Read More

    A Modular Nanoswitch for Mix-and-Detect Protein Assay Based on Binding-Induced Cascade Dissociation of Kissing Complex.
    Chembiochem 2018 Jan 22. Epub 2018 Jan 22.
    Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China.
    A new modular nanoswitch was described for versatile, rapid (within 1 h), homogeneous, and sensitive protein detection. The system employs two hairpins (HP1 and HP2) that can be reciprocally recognized through the apical loop-loop interaction. HP2 possesses a conformation-switching stem-loop structure, with appended single-stranded tails on each end, which can hybridize with the recognition-element-conjugated DNA strands to construct a protein-responsive HP2 scaffold. Read More

    Synthesis and Characterization of Photoactivatable Doxycycline Analogues Bearing Two-Photon-Sensitive Photoremovable Groups Suitable for Light-Induced Gene Expression.
    Chembiochem 2018 Jan 17. Epub 2018 Jan 17.
    Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67400, Illkirch, France.
    We report the synthesis and photolytic properties of caged 9-aminodoxycycline derivatives modified with 2-{4'-bis-[2-(2methoxyethoxy)ethyl]-4-nitrobiphenyl-3-yl}prop-1-oxy (EANBP) and PEG7-ylated (7-diethylamino-2-oxo-2H-chromen-4-yl)methyl (PEG7-DEACM) groups. 9-Aminodoxycycline is a tetracycline analogue capable of activating transcription through the inducible TetOn transgene expression system and can be regioselectively coupled to two-photon-sensitive photo-removable protecting groups by carbamoylation. The EANBP-based caged 9-aminodoxycycline showed complex photochemical reactions but did release 10 % of 9-aminodoxycycline. Read More

    Control of protein activity and gene expression by cyclofen-OH uncaging.
    Chembiochem 2018 Jan 16. Epub 2018 Jan 16.
    Ecole Normale Superieure, Physique, 24 rue Lhomond, 75005, Paris, FRANCE.
    The use of light to control the expression of genes and the activity of proteins is a rapidly expanding field. While many of these approaches use a fusion between a light activable protein and the protein of interest to control the activity of the later, it is also possible to control the activity of a protein by uncaging a specific ligand. In that context, controlling the activation of a protein fused to the modified estrogen receptor (ERT) by uncaging its ligand cyclofen-OH has emerged as a generic and versatile method to control the activation of proteins quantitatively, quickly and locally in a live organism. Read More

    The Fourth Wave of Biocatalysis Emerges- The 13 th International Symposium on Biocatalysis and Biotransformations.
    Chembiochem 2018 Feb 16;19(4):284-287. Epub 2018 Jan 16.
    Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary.
    Ride the wave! Biocatalysis uses nature's catalysts, enzymes and whole cell systems, for synthetic purposes. In a biotransformation, the biocatalyst transforms a well-defined substrate to the desired product, in contrast to the fermentation process, which produces the desired product from a complex mixture of nutrients. Biocatalysis has reached an industrially established level through several waves of technological evolution; participants of the BioTrans 2017 conference in Budapest could witness the newest wave of this technology. Read More

    Efficient Catalytic Oxidation of 5-Hydroxymethylfurfural to 2,5-Furandicarboxylic Acid by Magnetic Laccase Catalyst.
    Chembiochem 2018 Jan 15. Epub 2018 Jan 15.
    Institute of Biochemical Engineering, Collaborative Innovation Center for Marine Biomass Fibers, Materials and Textiles of Shandong Province, School of Materials Science and Engineering, Qingdao University, Qingdao, 266071, China.
    2,5-Furandicarboxylic acid (FDCA) is a bio-based platform chemical for the production of polyethylene furanoate (PEF) and other valuable furanic chemicals. A magnetic laccase catalyst with (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) as the mediator has the remarkable capability of oxidizing 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA). Under optimal reaction conditions, a quantitative yield (90. Read More

    Investigating Nucleosome Accessibility for MNase, Fe Peplomycin, and Duocarmycin Bby Using Capillary Electrophoresis.
    Chembiochem 2018 Jan 15. Epub 2018 Jan 15.
    Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
    Capillary electrophoresis, coupled with DNA 5' Texas Red labeling, was used to investigate the ability of MNase, Fepeplomycin, and duocarmycin Bto access the nucleosome. Distinct accessibility patterns of these species to the nucleosome were observed. MNase was completely prevented from approaching the nucleosome core and exhibited a higher site specificity for targeting DNA sites located close to the core region. Read More

    Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases.
    Chembiochem 2018 Jan 14. Epub 2018 Jan 14.
    Universität Bielefeld, Fakultät für Chemie Organische Chemie I, Universitätsstr. 25, 33615, Bielefeld, GERMANY.
    Nitriles belong to the product classes, which are mostly needed and produced by the chemical industry, playing a major role in various industry segments ranging from high-volume low-price sectors such as polymers to low-volume high-price sectors such as the chiral pharma drugs. A common industrial technology for nitrile production is ammonoxidation as a gas phase reaction at high temperature. A further popular approach are substitution or addition reactions with hydrogen cyanide or derivatives thereof. Read More

    MicroRNA Detection by DNA-Mediated Liposome Fusion.
    Chembiochem 2017 Dec 7. Epub 2017 Dec 7.
    Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
    Membrane fusion is a process of fundamental importance in biological systems that involves highly selective recognition mechanisms for the trafficking of molecular and ionic cargos. Mimicking natural membrane fusion mechanisms for the purpose of biosensor development holds great potential for amplified detection because relatively few highly discriminating targets lead to fusion and an accompanied engagement of a large payload of signal-generating molecules. In this work, sequence-specific DNA-mediated liposome fusion is used for the highly selective detection of microRNA. Read More

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