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  • Triazolecarbaldehyde Reagents for One‐Step N‐Terminal Protein Modification
    ChemBioChem (IF 2.593) Pub Date : 2020-01-16
    Akira Onoda; Nozomu Inoue; Eigo Sumiyoshi; Takashi Hayashi
    更新日期:2020-01-17
  • Mechanism of diol dehydration by a promiscuous radical‐SAM enzyme homologue of the antiviral enzyme viperin (RSAD2)
    ChemBioChem (IF 2.593) Pub Date : 2020-01-17
    Kourosh Honarmand Ebrahimi; Jack Rowbotham; James McCullagh; William S James

    3´‐deoxy nucleotides are an important class of drugs because they interfere with metabolism of nucleotides and their incorporation into DNA or RNA terminates cell division and viral replication. These compounds have largely been produced via multistep chemical synthesis and an enzyme with the ability to catalyse removal of 3´‐deoxy group from different nucleotides has yet to be described. Here, using a combination of HPLC, high‐resolution mass spectrometry, and NMR spectroscopy we demonstrate that a thermostable fungal radical S‐adenosylmethionine (SAM) enzyme with similarity to the vertebrate antiviral enzyme viperin (RSAD2) can catalyze transformation of CTP, UTP, and 5‐bromo‐UTP to their 3ʹ‐deoxy‐3′,4ʹ‐didehydro analogues. We show that unlike the fungal enzyme human viperin can only catalyse transformation of CTP. Using electron paramagnetic resonance (EPR) spectroscopy and molecular docking and dynamics simulations in combination with mutagenesis studies we provide insight into the origin of the unprecedented substrate promiscuity of the enzyme and the mechanism of dehydration of a nucleotide. Our findings highlight the evolution of substrate specificity in a member of the radical‐SAM enzymes. We predict that our work will help in utilizing a new class of radical‐SAM enzymes for biocatalytic synthesis of 3ʹ‐deoxy nucleotide/nucleoside analogues.

    更新日期:2020-01-17
  • Comparison of the biocatalytic activity of some halotolerant yeasts in freshwater and seawater
    ChemBioChem (IF 2.593) Pub Date : 2020-01-17
    Cecilia Andreu; Marcel·lí del Olmo

    The application of Green Chemistry concepts in catalysis has considerably increased in recent years, and the interest in using sustainable solvents in the chemical industry is growing. One of the recent proposals to fall in line with this is to employ seawater as a solvent in biocatalytic processes. This involves selecting halotolerant strains capable of carrying out chemical conversions in the presence of the salt concentrations found in this solution. Recent studies by our group have revealed the interest in using strains belonging to Debaryomyces and Schwannyomyces for catalytic processes run in this medium. In this work we select several strains based on their halotolerance to widen the scope of this strategy. We consider them for the monoreduction of 1‐phenylpropane‐1,2‐dione, a well‐characterized reaction that produces intermediates of pharmaceutical interest. The results obtained herein indicate that using seawater as a solvent for this reaction is possible, and it even offers advantages for stereoselectivity and biocatalyst reuse with some strains. The data found for S. cerevisiae FY86 and K. marxianus were particularly interesting.

    更新日期:2020-01-17
  • Biosynthesis and Structure Activity Relationship Investigations of the Diazeniumdiolate Antifungal Agent Fragin
    ChemBioChem (IF 2.593) Pub Date : 2020-01-16
    Simon Sieber; Christophe Daeppen; Christian Jenul; Vidya Mannancherril; Leo Eberl; Karl Gademann

    Only a few natural products possessing a diazeniumdiolate have been isolated and usually these compounds display a broad range of biological activities. Only recently the first diazeniumdiolate natural product biosynthetic gene cluster was identified in Burkholderia cenocepacia H111, which produces the fungicide (—)‐fragin and the signal molecule (rac)‐valdiazen. In this study, L‐valine was identified as the initial substrate of (—)‐fragin biosynthesis by feeding experiments using isotopically labeled amino acids. The formation of the diazeniumdiolate was chemically studied by several proposed intermediates. Our results indicate that the functional group is formed during an early stage of the biosynthesis. Furthermore, an oxime compound was identified as a degradation product of (—)‐fragin and was also observed in the crude extract of the wild type strain. Moreover, structure‐activity relationship analysis revealed that each moiety of (—)‐fragin is essential for its biological activity.

    更新日期:2020-01-17
  • Synthetic approaches for accessing pseudaminic acid (Pse) bacterial glycans
    ChemBioChem (IF 2.593) Pub Date : 2020-01-15
    Emily P. K. Flack; Harriet S Chidwick; Matthew Best; Gavin Thomas; Martin Anthony Fascione

    Pseudaminic acid (Pse5Ac7Ac) is a non‐mammalian sugar with structural similarity to the ubiquitous sialic acid sugar Neu5Ac and an important virulence factor for a number of pathogenic bacteria, including emerging multidrug resistant ESKAPE pathogens. Despite their discovery over 30 years ago, relatively little is known about the biological significance of Pse glycans compared to their sialic acid analogues, primarily due to a lack of access to the synthetically challenging Pse architecture. Recently however the Pse backbone has been subjected to increasing synthetic exploration by carbohydrate (bio)chemists, and the total synthesis of complex Pse glycans achieved using inspiration from the biosynthesis and subsequent detailed study of the chemical glycosylation using Pse donors. In this minireview we provide context for these efforts by summarising the recent synthetic approaches pioneered for accessing Pse glycans, which are set to open up this underexplored area of glycoscience to the wider scientific community.

    更新日期:2020-01-15
  • Identification of human IDO1 Enzyme Activity by Genetically Encoded Nitrotyrosine
    ChemBioChem (IF 2.593) Pub Date : 2020-01-15
    Zhaopeng Zheng; Xuzhen Guo; Minling Yu; Xiaoyan Wang; Hongguang Lu; Fahui Li; Jiangyun Wang

    Human indoleamine 2,3‐dioxygenase 1 (IDO1) has become an increasingly valuable target for cancer immunotherapy because it promotes immune escape by tumor cells. To date, the function of posttranslational modifications (PTMs) on IDO1 has not been fully elucidated. Among the many forms of PTMs, it has been identified that three tyrosine sites (Y15, Y345, and Y353) on IDO1 are nitrated and play important roles in c atalytic function. Herein, by genetically encoded 3‐nitro‐L‐tyrosine (NT) into the tyrosine nitration sites of IDO1, we have obtained the homogeneous and native nitrated‐IDO1. We found that nitration of the different tyrosine sites has different effects on IDO1 structure and enzyme activity. Nitration at position Y15 has a negligible effect, but nitration at Y345 or Y353 decreases the enzyme activity, especially Y353. Furthermore, our results demonstrate that the regulation of the catalytic function caused by tyrosine nitration is related to protein structure perturbation and heme‐binding disruption.

    更新日期:2020-01-15
  • Structure validation for G‐rich RNAs in non‐coding regions of the human genome
    ChemBioChem (IF 2.593) Pub Date : 2020-01-14
    Oliver Binas; Irene Bessi; Harald Schwalbe

    We present here the rapid biophysical characterization of six previously reported putative G‐quadruplex forming RNAs from the 5’‐UTR of silvestrol‐sensitive transcripts to investigate their secondary structure. By NMR and CD spectroscopic analysis, we find that only a single sequence, [AGG] 2 [CGG] 2 C, folds into a single well‑defined G‐quadruplex structure. Sequences with longer poly‐G strands form unspecific aggregates, while CGG‐repeat containing sequences exhibit a temperature‐dependent equilibrium between a hairpin and a G‐quadruplex structure. The applied experimental strategy is fast and provide robust readout for G‐quadruplex forming capacities of RNA oligomers.

    更新日期:2020-01-15
  • Versatile 3’ Functionalization of CRISPR Single Guide RNA
    ChemBioChem (IF 2.593) Pub Date : 2020-01-14
    Cody M. Palumbo; Jeton M. Gutierrez-Bujari; Henriette O’Geen; David J. Segal; Peter Beal

    Specific applications of CRISPR/Cas genome editing systems benefit from chemical modifications of the sgRNA. Here we describe a versatile and efficient strategy for functionalization of the 3’ end of a sgRNA. An exemplary collection of six chemically modified sgRNAs was prepared containing crosslinkers, a fluorophore and biotin. Modification of the sgRNA 3’ end was broadly tolerated by S. pyogenes Cas9 in an in vitro DNA cleavage assay. The 3’‐biotinylated sgRNA was used as an affinity reagent to identify IGF2BP1, YB1 and hnRNP K as sgRNA‐binding proteins present in HEK293T cells. Overall, the modification strategy presented here has the potential to expand on current applications of CRISPR/Cas systems.

    更新日期:2020-01-15
  • Chemo‐Enzymatic Preparation of Functional Click Labelled Messenger RNA
    ChemBioChem (IF 2.593) Pub Date : 2020-01-14
    Stefano Croce; Sascha Serdjukow; Thomas Carell; Thomas Frischmuth

    Nowadays synthetic mRNAs are promising candidates for a new class of transformative drugs, which provide genetic information for patients’ cells to develop their own cure. One key advancement to develop so‐called druggable mRNAs was the preparation of chemically modified mRNAs, by replacing standard bases by modified ones, e.g. uridine with pseudouridine capable to ameliorate the immunogenic profile and translation efficiency of the mRNA. Thus the introduction of modified nucleobases was the foundation for clinical usage of such mRNAs. Herein, we describe modular and simple methods to chemo‐enzymatically modify mRNA. Alkyne and or azide‐modified nucleotides are enzymatically incorporated into mRNA and subsequently conjugated to fluorescent dyes using click chemistry. This allows visualization of the labelled mRNA inside of cells. mRNA coding for the enhanced green fluorescent protein (eGFP) was chosen as a model system and the successful expression of eGFP demonstrated that our modified mRNA is accepted by the translation machinery.

    更新日期:2020-01-14
  • pH‐Dependent Protonation of Surface Carboxylates in PsbO Enables Local Buffering and Triggers Structural Changes
    ChemBioChem (IF 2.593) Pub Date : 2020-01-12
    Lisa Maria Gerland; Daniel Friedrich; Linus Hopf; Eavan Donovan; Arndt Wallmann; Natalja Erdmann; Anne Diehl; Martin Bommer; Krzysztof Buzar; Mohamed Ibrahim; Peter Schmieder; Holger Dobbek; Athina Zouni; Ana-Nicoleta Bondar; Holger Dau; Hartmut Oschkinat

    Photosystem II (PSII) catalyzes the splitting of water, releasing protons and dioxygen. Its highly conserved subunit PsbO extends from the oxygen evolving center (OEC) into the thylakoid lumen and stabilizes the catalytic Mn 4 CaO 5 ‐cluster. The high conservation of accessible, negatively charged surface residues in PsbO suggests additional functions, as local pH buffer or by affecting the flow of protons. For this discussion, we provide an experimental basis by determining pK a values of water‐accessible aspartate and glutamate side chain carboxyl groups using NMR. Their distribution is strikingly uneven, with high pK a values around 4.9 clustering on the luminal PsbO side and values below 3.5 on the side facing PSII. pH‐dependent changes of backbone chemical shifts in the area of the lumen‐exposed loops are observed, indicating conformational changes. In conclusion, we present a site‐specific analysis of carboxyl group proton affinites in PsbO, providing a basis to further understand proton transport in photosynthesis.

    更新日期:2020-01-13
  • S‐Adenosyl‐l‐Methionine Salvage Impacts Psilocybin Formation in “Magic” Mushrooms
    ChemBioChem (IF 2.593) Pub Date : 2020-01-10
    Richard Demmler; Janis Fricke; Sebastian Dörner; Markus Gressler; Dirk Hoffmeister
    更新日期:2020-01-10
  • Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein‐Linked Extender Units in Ansamitocin Biosynthesis
    ChemBioChem (IF 2.593) Pub Date : 2020-01-10
    Fa Zhang; Huining Ji; Imtiaz Ali; Zixin Deng; Linquan Bai; Jianting Zheng
    更新日期:2020-01-10
  • A Trifunctional Linker for Palmitoylation and Peptide and Protein Localization in Biological Membranes
    ChemBioChem (IF 2.593) Pub Date : 2020-01-10
    Łukasz Syga; Reinder H. de Vries; Hugo van Oosterhout; Rianne Bartelds; Arnold J. Boersma; Gerard Roelfes; Bert Poolman
    更新日期:2020-01-10
  • Quantitative MS‐based proteomics comparing the MCF‐7 cellular response to hypoxia and a 2‐oxoglutarate analogue
    ChemBioChem (IF 2.593) Pub Date : 2020-01-10
    Jacob T. Bush; Mun Chiang Chan; Shabaz Mohammed; Christopher Schofield

    The hypoxia‐inducible factors (HIFs) are key transcription factors in determining cellular responses involving alterations in protein levels in response to limiting oxygen availability in animal cells. 2‐Oxoglurate dependent oxygenases play key roles in regulating HIF levels and its transcriptional activity. We describe MS‐based proteomics studies employing a lysine demethylation‐based approach in which we compared the results of treating human breast cancer MCF‐7 cells with hypoxia or a cell‐penetrating derivative (dimethyl N‐oxalylglycine) of the stable 2OG analogue N‐oxalylglycine. The proteomic results are consistent with reported transcriptomic analyses and support the proposed key roles of 2OG dependent HIF prolyl‐ and asparaginyl‐hydroxylases in the hypoxic response. Differences between the data sets for hypoxia and DMOG may reflect context‐dependent effects or HIF‐independent effects of DMOG

    更新日期:2020-01-10
  • A modified Arrhenius approach to thermodynamically study regioselectivity in Cytochrome P450 catalyzed substrate conversion
    ChemBioChem (IF 2.593) Pub Date : 2020-01-09
    Rosa A. Luirink; Marlies C.A. Verkade-Vreeker; Jan N.M. Commandeur; Daan Geerke

    The regio‐ (and stereo‐) selectivity and specific activity of Cytochrome P450s are determined by the accessibility of potential sites‐of‐metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction. The accessibility of potential SOMs depends on the relative binding free energy ΔΔ G bind of the catalytically active substrate‐binding poses, and the probability of the substrate to adopt a transition state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction‐rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multi‐step P450‐catalyzed processes which involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multi‐product enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔ G bind values and collision entropies, yielding direct insights into the basis of selectivity in substrate conversion.

    更新日期:2020-01-10
  • Real‐Time BODIPY‐Binding Assay To Screen Inhibitors of the Early Oligomerization Process of Aβ1–42 Peptide
    ChemBioChem (IF 2.593) Pub Date : 2020-01-09
    Nicolo Tonali; Veronica I. Dodero; Julia Kaffy; Loreen Hericks; Sandrine Ongeri; Norbert Sewald
    更新日期:2020-01-09
  • Development of Polyamine‐Substituted Triphenylamine Ligands with High Affinity and Selectivity for G‐Quadruplex DNA
    ChemBioChem (IF 2.593) Pub Date : 2020-01-09
    Isabel Pont; Álvaro Martínez‐Camarena; Cristina Galiana‐Roselló; Roberto Tejero; M. Teresa Albelda; Jorge González‐García; Ramón Vilar; Enrique García‐España
    更新日期:2020-01-09
  • 更新日期:2020-01-09
  • Design and expeditious synthesis of quinoline‐pyrene based ratiometric fluorescent probes for targeting lysosomal pH
    ChemBioChem (IF 2.593) Pub Date : 2020-01-09
    Santosh J. Gharpure; Shobhna Kapoor; Pankaj Hande; Manjari Mishra; Anindya Datta; Fariyad Ali

    Intracellular pH plays a significant role in many pathological and physiological processes. A series of quinoline‐pyrene probes were synthesized in one step by oxonium ion triggered alkyne carboamination sequence involving C‐C, C‐O and C‐N bond formation for intracellular pH sensing. Quinoline‐pyrenes showed significant red shift at low pH. The fluorescence lifetime decay measurements of the probe showed decrease in lifetime at pH 4. The probes showed excellent selectivity in the presence of various interfering agents such as amino acids and cations/anions. Furthermore, the probes were found to be completely reversible in the window of pH 4 and 7. Morpholine based quinoline‐pyrene probe efficiently stained lysosomes with high Pearson’s correlation coefficients (0.86) using lysotracker Deep Red DND‐99 as a reference. Co‐localization study of probe with lysotracker DND‐99 showed selective intracellular targeting and shift in fluorescence emission due to acidic lysosomal pH.

    更新日期:2020-01-09
  • Characterization of a Tryptophan 6‐Halogenase from Streptomyces albus and Its Regioselectivity Determinants
    ChemBioChem (IF 2.593) Pub Date : 2020-01-08
    Jeongchan Lee; Joonwon Kim; Hyun Kim; Eun-Jung Kim; Hee-Jin Jeong; Kwon-Young Choi; Byung-Gee Kim

    Tryptophan halogenases are found in diverse organisms and catalyze regiospecific halogenation. They play an important role in biosynthesis of halogenated indole alkaloids, which are biologically active and are of therapeutic importance. Here, a tryptophan 6‐halogenase (SatH) from Streptomyces albus was characterized using a whole‐cell reaction system in Escherichia coli . SatH showed substrate specificity for chloride and bromide ions, leading to regiospecific halogenation at C6 position of L‐tryptophan. In addition, SatH exhibited higher performance in bromination than previously reported tryptophan halogenases in the whole‐cell reaction system. Through structure‐based protein mutagenesis, we revealed that two consecutive residues, A78/V79 in SatH and G77/I78 in PyrH, are one of the key determinants in regioselectivity difference between tryptophan 6‐ and 5‐halogenases. Substituting the AV with GI residues switched the regioselectivity of SatH by moving the orientation of tryptophan. Our data contribute to the understanding of key residues that determine regioselectivity of tryptophan halogenases.

    更新日期:2020-01-09
  • Homogeneous and universal detection of various targets based on dual‐step transduced toehold switch sensor
    ChemBioChem (IF 2.593) Pub Date : 2020-01-08
    Bingling Li; Yidan Tang; Huan Li

    Toehold switch sensors represent a classic of new advances that allow specific targets triggering in‐situ expression of protein reporter. Even if holding unique advantages of label‐free and high portability, they generally require repeated sequence design, high cost and laborious optimization of toehold switch sequence according to different targets. To further simplify the sensing process and improve the practicability, we innovatively introduce a dual‐step pre‐transduction upon traditional toehold switch sensor. Through two successive toehold‐mediated strand displacement reactions, in respective, initiated by linear and associative trigger, different DNAs, RNAs, or ligands of functional nucleic acids can be generally transduced into the input of one well‐performed toehold switch sensor. This advance largely increases the target range. Furthermore, the whole process is signal‐on, homogeneous, and free of any sophisticated operation such as probe labelling, separation, and reconstruction of toehold switch, being even promising and practical in portable or point‐of‐care assays.

    更新日期:2020-01-08
  • N‐Hydroxysuccinimide‐Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates
    ChemBioChem (IF 2.593) Pub Date : 2020-01-07
    Marc‐André Kasper; Marcus Gerlach; Anselm F. L. Schneider; Christiane Groneberg; Philipp Ochtrop; Stefanie Boldt; Dominik Schumacher; Jonas Helma; Heinrich Leonhardt; Mathias Christmann; Christian P. R. Hackenberger
    更新日期:2020-01-07
  • Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State
    ChemBioChem (IF 2.593) Pub Date : 2020-01-07
    Barbara Eyermann; Maximilian Meixner; Heike Brötz‐Oesterhelt; Iris Antes; Stephan A. Sieber
    更新日期:2020-01-07
  • Using a PCR‐Based Method To Analyze and Model Large, Heterogeneous Populations of DNA
    ChemBioChem (IF 2.593) Pub Date : 2020-01-07
    Helena Andrade; Alvin K. Thomas; Weilin Lin; Francesco V. Reddavide; Yixin Zhang
    更新日期:2020-01-07
  • Asymmetric Reduction of (R)‐Carvone through a Thermostable and Organic‐Solvent‐Tolerant Ene‐Reductase
    ChemBioChem (IF 2.593) Pub Date : 2020-01-07
    Dirk Tischler; Eric Gädke; Daniel Eggerichs; Alvaro Gomez Baraibar; Carolin Mügge; Anika Scholtissek; Caroline E. Paul
    更新日期:2020-01-07
  • Construction and Characterization of a Mirror‐Image l‐DNA i‐Motif
    ChemBioChem (IF 2.593) Pub Date : 2020-01-03
    Yawei Sun; Bo Yang; Yi Hua; Yuanchen Dong; Jianhan Ye; Jiqian Wang; Lijin Xu; Dongsheng Liu
    更新日期:2020-01-04
  • Chemical Methods for N‐ and O‐Sulfation of Small Molecules, Amino Acids and Peptides
    ChemBioChem (IF 2.593) Pub Date : 2020-01-03
    Anna Mary Benedetti; Daniel M. Gill; Chi W. Tsang; Alan M. Jones
    更新日期:2020-01-04
  • Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex
    ChemBioChem (IF 2.593) Pub Date : 2020-01-03
    Wai Ling Cheung‐Lee; Madison E. Parry; Chuhan Zong; Alexis Jaramillo Cartagena; Seth A. Darst; Nancy D. Connell; Riccardo Russo; A. James Link
    更新日期:2020-01-04
  • An expedient synthesis of flexible nucleosides through enzymatic glycosylation of proximal and distal fleximer bases.
    ChemBioChem (IF 2.593) Pub Date : 2020-01-03
    Sophie Vichier-Guerre; Therese Ku; Sylvie Pochet; Katherine L Seley-Radtke

    The structurally unique “fleximer” nucleosides were originally designed to investigate how flexibility in the nucleobase could potentially affect receptor‐ligand recognition and function. Recently they have shown low to sub‐micromolar levels of activity against a number of viruses including coronaviruses, filoviruses and flaviviruses. The synthesis of distal fleximers in particular, has thus far been quite tedious and low yielding. As a potential solution to this issue, a series of proximal fleximer bases (flex‐bases) were successfully coupled to both ribose and 2’‐deoxyribose sugars using the N ‐deoxyribosyltransferase II of Lactobacillus leichmannii ( Ll NDT) and E. coli purine nucleoside phosphorylase (PNP). To explore the range of this facile approach, transglycosylation experiments using a thieno‐expanded tricyclic heterocyclic base, as well as several distal and proximal flex‐bases were performed to determine whether the corresponding fleximer nucleosides could be obtained in this fashion, thus potentially significantly shortening the route to these biologically significant compounds. The results of those studies are reported herein.

    更新日期:2020-01-04
  • BciC‐Catalyzed C132‐Demethoxycarbonylation of Metal Pheophorbide a Alkyl Esters
    ChemBioChem (IF 2.593) Pub Date : 2020-01-03
    Mitsuaki Hirose; Misato Teramura; Jiro Harada; Hitoshi Tamiaki

    Bacteriochlorophyll c molecules self‐aggregate to form large oligomers in the core part of chlorosomes, the main light‐harvesting antenna systems of green photosynthetic bacteria. In the biosynthetic pathway of bacteriochlorophyll c , a BciC enzyme catalyzes the removal of the C13 2 ‐methoxycarbonyl group of chlorophyllide a possessing a free propionate residue at the C17‐position and a magnesium ion as the central metal. The in vitro C13 2 ‐demethoxycarbonylations of chlorophyll a derivatives bearing various alkyl propionate residues and central metals were examined using the BciC enzyme derived from one green sulfur bacteria species, Chlorobaculum tepidum . The BciC enzymatic reactions of zinc pheophorbide a alkyl esters were gradually suppressed with an increase of the alkyl chain length in the C17‐propionate residue (from methyl to pentyl esters) and finally the hexyl ester became inactive for the BciC reaction. Although not only the zinc but also nickel and copper complexes were demethoxycarbonylated by the BciC enzyme, the reactions were largely dependent on the coordination ability of the central metals: Zn > Ni > Cu. The above substrate specificity indicates that the BciC enzyme would not bind directly to the carboxy group of chlorophyllide a , but would bind to its central magnesium to form the stereospecific complex of BciC with chlorophyllide a , giving pyrochlorophyllide a lacking the (13 2 R )‐methoxycarbonyl group.

    更新日期:2020-01-04
  • Strategies to Design and Synthesize Polymer‐Based Stimuli‐Responsive Drug Delivery Nanosystems
    ChemBioChem (IF 2.593) Pub Date : 2019-12-31
    Xing Qin; Yongsheng Li

    The emergence and development of nanomedicine have alleviated the problems existed in traditional chemotherapy drugs, such as short lifetime, concomitant side effects and weak tumor‐targeting capability. Nevertheless, the further applications of drug‐loaded nanocarriers are still limited by their premature leakage, weak targeting capability and insufficient intracellular release. In the past decades, various nanocarriers including gold nanoparticles, porous silica nanoparticles, carbon‐based nanoparticles, micelles, liposomes and polymer‐drug conjugates have been intensively investigated for tumor therapy. Among these, polymer‐based nanocarriers have been paid more attention due to their biocompatibilities and modifiabilities for stimuli‐responsive drug release. In this review, three popular strategies to design and synthesize polymer‐based stimuli‐responsive nanocarriers are discussed. We start our discussion from the stimuli‐responsive polymers with responsive backbones or modified by responsive functional groups for drug encapsulation and release to polymer‐drug conjugates with responsive covalent linkages. Especially, due to the facile synthesis processes and mild reaction conditions of crosslinking structures, the latest progress in responsive crosslinking structures is emphasized. Finally, summary and outlook of these nanomaterials are given, which is expected to provide inspiration for researchers to design more effective and safer tumor‐killing nanomedicines.

    更新日期:2019-12-31
  • Orthogonal Genetic Systems
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    John C. Chaput; Piet Herdewijn; Marcel Hollenstein

    Xenobiology is an area of synthetic biology that aims to create model cellular organisms in which the synthetic biology information is encoded in artificial genetic polymers that can replicate alongside natural genetic polymers. This viewpoint discusses the concept of orthogonal genetic polymers and their relationship to natural genetic polymers.

    更新日期:2019-12-31
  • A Quencher‐Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Keiji Murayama; Hiroyuki Asanuma
    更新日期:2019-12-30
  • Characterisation of the Dynamic Interactions between Complex N‐Glycans and Human CD22
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Cristina Di Carluccio; Enrique Crisman; Yoshiyuki Manabe; Rosa Ester Forgione; Alessandra Lacetera; Jussara Amato; Bruno Pagano; Antonio Randazzo; Angela Zampella; Rosa Lanzetta; Koichi Fukase; Antonio Molinaro; Paul R. Crocker; Sonsoles Martín‐Santamaría; Roberta Marchetti; Alba Silipo
    更新日期:2019-12-30
  • N‐Hydroxysuccinimide‐Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Marc‐André Kasper; Marcus Gerlach; Anselm F. L. Schneider; Christiane Groneberg; Philipp Ochtrop; Stefanie Boldt; Dominik Schumacher; Jonas Helma; Heinrich Leonhardt; Mathias Christmann; Christian P. R. Hackenberger
    更新日期:2019-12-30
  • Ascorbate Oxidase Mimetic Activity of Copper(II) Oxide Nanoparticles
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Shao‐Bin He; Ai‐Ling Hu; Quan‐Quan Zhuang; Hua‐Ping Peng; Hao‐Hua Deng; Wei Chen; Guo‐Lin Hong
    更新日期:2019-12-30
  • Phosphine‐Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Joshua S. Wesalo; Ji Luo; Kunihiko Morihiro; Jihe Liu; Alexander Deiters
    更新日期:2019-12-30
  • 5‐Benzylidene‐4‐Oxazolidinones Are Synergistic with Antibiotics for the Treatment of Staphylococcus aureus Biofilms
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Bram H. Frohock; Jessica M. Gilbertie; Jennifer C. Daiker; Lauren V. Schnabel; Joshua G. Pierce
    更新日期:2019-12-30
  • Preparative and Kinetic Analysis of β‐1,4‐ and β‐1,3‐Glucan Phosphorylases Informs Access to Human Milk Oligosaccharide Fragments and Analogues Thereof
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Ravindra Pal Singh; Giulia Pergolizzi; Sergey A. Nepogodiev; Peterson de Andrade; Sakonwan Kuhaudomlarp; Robert A. Field
    更新日期:2019-12-30
  • Tuning Enzyme Activity for Nonaqueous Solvents: Engineering of an Enantioselective ‘Michaelase’ for Catalysis in High Concentrations of Ethanol
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Chao Guo; Lieuwe Biewenga; Max Lubberink; Ronald van Merkerk; Gerrit J. Poelarends

    Enzymes have evolved to function under aqueous conditions and may not exhibit features essential for biocatalytic application, such as the ability to function in high concentrations of an organic solvent. Consequently, protein engineering is often required to tune an enzyme for catalysis in non‐aqueous solvents. In this study, we have used a collection of nearly all single mutants of 4‐oxalocrotonate tautomerase, which promiscuously catalyzes synthetically useful Michael‐type additions of acetaldehyde to various nitroolefins, to investigate the effect of each mutation on the ability of this enzyme to retain its ‘Michaelase’ activity in elevated concentrations of ethanol. Examination of this mutability landscape allowed the identification of two hotspot positions, Ser‐30 and Ala‐33, at which mutations are beneficial for catalysis in high ethanol concentrations. The ‘hotspot’ position Ala‐33 was then randomized in a highly enantioselective, but ethanol‐sensitive 4‐OT variant (L8F/M45Y/F50A) to generate an improved enzyme variant (L8F/A33I/M45Y/F50A) that showed great ethanol stability and efficiently catalyzes the enantioselective addition of acetaldehyde to nitrostyrene in 40% ethanol (permitting high substrate loading) to give the desired γ‐nitroaldehyde product in excellent isolated yield (89%) and enantiopurity (ee = 98%). The presented work demonstrates the power of mutability‐landscape‐guided enzyme engineering for efficient biocatalysis in non‐aqueous solvents.

    更新日期:2019-12-30
  • Rational‐design engineering to create the flavin reductase variants with thermostable and solvent‐tolerant properties
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Somchart Maenpuen; Vinutsada Pongsupasa; Wiranee Pensook; Piyanuch Anuwan; Napatsorn Kraivisitkul; Chatchadaporn Pinthong; Jittima Phonbuppha; Thikumporn Luanloet; Hein J. Wijma; Marco W. Fraaije; Narin Lawan; Pimchai Chaiyen; Thanyaporn Wongnate; Napatsorn Kraivisitkul

    In this work, we employed computational approaches, FireProt and FRESCO, to predict the thermostable variants of the reductase component (C1) of p‐hydroxyphenylacetate 3‐hydroxylase. Combined with experimental results, two C1 variants; A166L and A58P, were identified as thermotolerant enzymes with their 2.6‐5.6 °C thermostability improvement and increased 2‐3.5‐fold catalytic efficiency. After heat treatment at 45 oC, both of the thermostable C1 variants remain active and generate FMNH‐ for bacterial luciferase and monooxygenase reaction more efficient than wild type (WT). In addition to thermotolerance, A166L and A58P variants exhibited solvent‐tolerant property. The 6‐ns molecular dynamics (MD) simulations at 300‐500 K indicated that mutations of A166 to L and A58 to P resulted in the structural change with increased stabilization of hydrophobic interactions, thus improving thermostability. Our findings demonstrated that the improvement in thermostability of C1 enzyme can lead to the broad‐spectrum uses of C1 as a redox biocatalyst for future industrial applications.

    更新日期:2019-12-30
  • Stepwise Construction of Disulfides in Peptides
    ChemBioChem (IF 2.593) Pub Date : 2019-12-30
    Rongjun He; Pan Jia; John Philip Mayer; Fa Liu

    The disulfide bond plays an important role in biological systems. It defines global conformation, and ultimately the biological activity and stability of the peptide or protein. It is frequently present, singly or multiply, in biologically important peptide hormones and toxins. Numerous disulfide‐containing peptides have been approved by the regulatory agencies as marketed drugs. Chemical synthesis is one of the prerequisite tools needed to gain deep insights into the structure‐function relationships of these biomolecules. Along with the development of solid‐phase peptide synthesis, a number of methods of disulfide construction have been established. This mini‐review will focus on the regiospecific, stepwise construction of multiple disulfides utilized in the chemical synthesis of peptides. We intend for this article to serve a reference for peptide chemists conducting complex peptide syntheses and also hope to stimulate future development of disulfide methodologies.

    更新日期:2019-12-30
  • EPR and MCD spectra of the nitrogenase M cluster precursor suggest sulfur migration upon oxidation: A proposal for substrate and inhibitor binding
    ChemBioChem (IF 2.593) Pub Date : 2019-12-27
    Kresimir Rupnik; Kazuki Tanifuji; Lee Rettberg; Markus Walter Ribbe; Yilin Hu; Brian Hales

    The active site of the nitrogen fixing enzyme, Mo‐nitrogenase, is the M cluster ([MoFe7S9C·R‐homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical‐SAM enzyme, is instrumental in the assembly of the L cluster ([Fe8S9C]), a precursor and an all‐iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe8S8C]), which lacks the final 9th sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled LOx and [L*]Ox, respectively. This study shows that both LOx and [L*]Ox have nearly identical EPR and MCD spectra, suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from LOx following oxidation, rendering the cluster identical to [L*]Ox. It is proposed that a similar migration could occur to the M cluster upon oxidation and that it is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding.

    更新日期:2019-12-29
  • Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms
    ChemBioChem (IF 2.593) Pub Date : 2019-12-27
    Zhenrun J. Zhang; Yen‐Chih Wang; Xinglin Yang; Howard C. Hang
    更新日期:2019-12-27
  • Tackling Achilles’ heel in synthetic biology: pairing intracellular synthesis of non‐canonical amino acids with genetic code expansion to foster biotechnological applications.
    ChemBioChem (IF 2.593) Pub Date : 2019-12-23
    Hernan Daniel Biava

    For the last two decades, synthetic biologists have been able to unlock and expand the genetic code, generating proteins with unique properties through the incorporation of non‐canonical amino acids (ncAAs). These evolved biomaterials have shown great potential for applications in industrial biocatalysis, therapeutics, bioremediation, bioconjugation, and other areas. Our ability to continue developing such technologies depends on having relatively easy access to ncAAs. However, the synthesis of enantiomerically pure ncAAs in practical quantitates for large‐scale processes remains to be a challenge. Biocatalytic ncAA production has emerged as an excellent alternative to traditional organic synthesis in terms of cost, enantioselectivity, and sustainability. Moreover, biocatalytic synthesis offers the opportunity of coupling intracellular generation of ncAAs with genetic code expansion to overcome the limitations of an external supply of amino acid. In this minireview, we examine some of the most relevant achievements of this approach and its implications for improving technological applications derived from synthetic biology.

    更新日期:2019-12-23
  • In vivo Expression of Genetic Information from Phosphoramidate‐DNA
    ChemBioChem (IF 2.593) Pub Date : 2019-12-23
    Hoai Nguyen; Mikhail Abramov; Elena Eremeeva; Piet Herdewijn

    Chemically modified genes and genomes with customized properties will become a valuable tool in numerous fields, including synthetic biology, biotechnology, and medicine. These genetic materials are meant to store and exchange information with DNA and RNA while tuning their functionality. Here we outline the development of an alternative genetic system carrying phosphoramidate linkage that successfully propagates genetic information in bacteria and at the same time is labile to acidic conditions. The P3' ‐> N5' phosphoramidate‐containing DNA (PN‐DNA) was enzymatically synthesized using 5'‐amino‐2',5'‐deoxycytidine 5'‐N‐triphosphates (NH‐dCTPs) as substrates for DNA polymerases and employed to encode antibiotic resistance in Escherichia coli. The resulting PN‐DNA can be efficiently destroyed by mild acidic conditions, whereas an unmodified counterpart remains intact. A cloning strategy was proposed for assembling modified fragments into a genome. This method can be of interest to scientists working in the field of orthogonal nucleic acid genes and genomes.

    更新日期:2019-12-23
  • In Situ Acetaldehyde Synthesis for Carboligation Reactions
    ChemBioChem (IF 2.593) Pub Date : 2019-12-23
    Lieuwe Biewenga; Andreas Kunzendorf; Gerrit J. Poelarends

    The enzyme 4‐oxalocrotonate tautomerase (4‐OT) can promiscuously catalyze various carboligation reactions using acetaldehyde as a nucleophile. However, the highly reactive nature of acetaldehyde requires intricate handling, which can impede its usage in practical synthesis. Therefore, we investigated three enzymatic routes to synthesize acetaldehyde in situ in one‐pot cascade reactions with 4‐OT. Two routes afforded practical acetaldehyde concentrations, using an environmental pollutant, trans‐3‐chloroacrylic acid, or a biorenewable, ethanol, as starting substrate. These routes can be combined with 4‐OT catalyzed Michael‐type additions and aldol condensations in one pot. This modular systems biocatalysis methodology provides a stepping stone towards the development of larger artificial metabolic networks for the practical synthesis of important chemical synthons.

    更新日期:2019-12-23
  • Mechano‐physical Cues in Extracellular Matrix Regulation of Cell Behaviors
    ChemBioChem (IF 2.593) Pub Date : 2019-12-23
    Dong Kee Yi; Tuntun Wang; Sitansu Sekhar Nanda; Georgia C. Papaefthymiou

    The extracellular matrix (ECM) is a macromolecular network, which can provide biochemical and structural support for cell adhesion and formation. It regulates cell behavior by influencing biochemical and physical cues. It is a dynamic structure whose components are modified, degraded or deposited during connective tissue development, giving tissues strength and structural integrity. The physical properties of the natural ECM environment control the design of naturally or synthetically derived biomaterials to guide cell function in tissue engineering. Tissue engineering is an important field that explores physical cues of ECM to produce new viable tissue for medical applications, such as in organ transplant and organ recovery. Understanding how the ECM exerts physical effects on cell behavior, when cells are seeded in synthetic ECM scaffolds, is of utmost importance. Herein, we review recent findings in this area that report on cell behaviors in a variety of ECMs with different physical properties i.e ., topology, geometry, dimensionality, stiffness and tension.

    更新日期:2019-12-23
  • Identification of Novel Tricyclic P(III) Chiral Auxiliary for Solid Supported Synthesis of Stereopure Phosphorothioate Containing Oligonucleotides
    ChemBioChem (IF 2.593) Pub Date : 2019-12-21
    Sukumar Sakamuri; Dingguo Liu; Laxman Eltepu; Bin Liu; Lisa Jo Reboton; Ryan Preston; Curt W Bradshaw

    Ever since the recognition of oligonucleotides as a therapeutic modality, significant work has been devoted to improving therapeutic properties including nuclease stability. Phosphorothioate (PS) modifications of phosphodiesters is one of the most explored chemical modification that is integral to currently approved oligonucleotide therapeutics including ASOs and siRNAs. Insertion of sulfur into the phosphate bridge leads to 2n isomeric mixtures of phosphorothioates with different nuclease stability and protein binding properties. Efforts to create stereopure phosphorothioate containing oligos spurred interest in identifying new synthetic methods. Here, we report our work on a novel and practical tricyclic P(III) chiral auxiliary and its application in solid supported synthesis of stereopure phosphorothioate containing oligonucleotides.

    更新日期:2019-12-22
  • Role of Posttranslational Modifications in Alzheimer’s Disease
    ChemBioChem (IF 2.593) Pub Date : 2019-12-21
    Thimmaiah Govindaraju; Madhu Ramesh; Pushparathinam Gopinath

    The global burden of Alzheimer’s disease (AD) is growing, as the valiant efforts to develop clinical candidates for the treatment have been continuously met with appalling failures. The currently available palliative treatments are temporary and there is a constant urge to scout for reliable disease pathways, biomarkers and drug‐targets for developing diagnosis and therapy to address the unmet medical needs of AD. The challenges in the drug discovery efforts raise further questions about the strategies of currently practiced conventional diagnosis, drug design, understanding the disease pathways, biomarkers and targets. In this context, posttranslational modifications (PTMs) regulate protein trafficking, function and degradation and their in‐depth study play a significant role in the identification of novel biomarkers and drug‐targets. Aberrant PTMs of the disease relevant proteins could trigger pathological pathways, leading to disease progression. Advancements in the proteomics enabled us to generate patterns or signatures of such modifications thus providing a versatile platform to develop biomarkers based on PTMs. In addition, understanding and targeting the aberrant PTMs of various proteins provide viable avenues for addressing AD drug discovery challenges. This review highlights numerous PTMs of proteins relevant to AD and provides an overview of their adverse effects on the protein structure, function and aggregation propensity that contribute to the disease pathology. The critical discussion offers ways to develop PTMs signature and interfere with the aberrant PTMs to develop viable diagnostics and therapeutic interventions in AD.

    更新日期:2019-12-22
  • Impact of Phosphorothioate Chirality on Double‐stranded siRNAs: A Systematic Evaluation of Stereopure siRNA Designs
    ChemBioChem (IF 2.593) Pub Date : 2019-12-21
    Sukumar Sakamuri; Laxman Eltepu; Dingguo Liu; Son Lam; Bryan R Meade; Bin Liu; Giuseppe Dello Iacono; Ayman Kabakibi; Lena Luukkonen; Tom Leedom; Mark Foster; Curt W Bradshaw

    Oligonucleotides are important therapeutic approaches as evidenced by recent clinical successes with anti‐sense oligonucleotides (ASOs) and double‐stranded siRNAs. Decades of research leading to stabilized oligonucleotides using sugar, nucleobase and phosphate backbone modifications are one of the contributing factors for their success. Phosphorothioate (PS) modifications are a standard feature in the current generation of oligo therapeutics but are typically isomeric mixtures leading to 2 n isomers. All currently marketed therapeutic oligonucleotides (ASOs and siRNAs) are complex isomeric mixtures. Recent chemical methodologies for stereopure PS insertions have resulted in preliminary rules for ASOs with multiple stereopure ASOs moving into clinical development. Although siRNAs have comparatively fewer PS, the field has yet to embrace the idea of stereopure siRNAs. We investigated whether the individual isomers contribute equally to in vivo potency of a representative siRNA. Here, we report the results of a systematic evaluation of stereopure PS incorporation into siRNA demonstrating that individual PS isomers dramatically affect in vivo activity.

    更新日期:2019-12-22
  • Azido‐desferrioxamine siderophores as functional click chemistry probes generated in culture upon adding a diazo‐transfer reagent
    ChemBioChem (IF 2.593) Pub Date : 2019-12-20
    Michael P Gotsbacher; Rachel Codd

    This work aimed to undertake the in situ conversion of the terminal amine group of bacterial DFO siderophores, including desferrioxamine B (DFOB), to an azide group to enable downstream click chemistry. Initial studies trialled a precursor‐directed biosynthesis (PDB) approach. Supplementing Streptomyces pilosus culture with blunt‐end azido‐amine non‐native substrates designed to replace 1,5‐diaminopentane (DP) as the native diamine substrate in the terminal amine position of DFOB did not produce azido‐DFOB. Adding the diazo‐transfer reagent imidazole‐1‐sulfonyl azide hydrogen sulfate to spent S. pilosus medium that was cultured in the presence of 1,4‐diaminobutane (DB), as a viable native substrate to expand the suite of native DFO‐type siderophores, successfully generated the cognate suite of azido‐DFO analogues. Cu(I)‐mediated or strain‐promoted Cu(I)‐free click chemistry reactions between this minimally processed mixture and the appropriate alkyne‐biotin reagents produced the cognate suite of 1,4‐disubstituted triazole‐linked DFO‐biotin compounds as potential molecular probes, detected as Fe(III)‐loaded species. The amine‐to‐azide transformation of amine‐bearing natural products in a complex mixture by the direct addition of a diazo‐transfer reagent to deliver functional click chemistry reagents adds to the toolbox for chemical proteomics, chemical biology and drug discovery.

    更新日期:2019-12-21
  • A structural rationale for N‐methylbicuculline acting as a promiscuous competitive antagonist of inhibitory pentameric ligand gated ion channels.
    ChemBioChem (IF 2.593) Pub Date : 2019-12-20
    William Nigel Hunter; Mathew J. Jones; Alice Dawson; Tim G. Hales

    Bicuculline, a valued chemical tool in neurosciences research, is a competitive antagonist of specific GABA A receptors and affects other pentameric ligand gated ion channels including the glycine, nicotinic acetylcholine and 5‐hydroxytryptamine type 3 receptors. We used a fluorescence quenching assay and isothermal titration calorimetry to record low micromolar dissociation constants for N‐methylbicuculline interacting with acetylcholine binding protein and an engineered version called glycine‐binding protein (GBP), which provides a surrogate for the heteromeric interface of the extracellular domain of the glycine receptor (GlyR). The 2.4 Å resolution crystal structure of the GBP:N‐methylbicuculline complex, sequence and structural alignments reveal similarities and differences between GlyR and the GABA A receptor bicuculline interactions. N‐methylbicuculline displays a similar conformation in different structures but adopts distinct orientations enforced by interactions and steric blocks with key residues and plasticity in the binding sites. These features explain the promiscuous activity of bicuculline against the principal inhibitory pentameric ligand gated ion channels in the CNS.

    更新日期:2019-12-20
  • Analysis of the Destabilization of Bacterial Membranes by Quaternary Ammonium Compounds: A Combined Experimental and Computational Study
    ChemBioChem (IF 2.593) Pub Date : 2019-12-20
    Saleh Alkhalifa; Megan Jennings; Daniele Granata; Michael Klein; William M. Wuest; Kevin Minbiole; Vincenzo Carnevale

    The mechanism of action of quaternary ammonium compound (QAC) antiseptics has long been assumed to be straightforward membrane disruption, although the process of approaching and entering the membrane has little modelling precedent. Furthermore, questions have more recently arisen regarding bacterial resistance mechanisms, and why select classes of QACs (specifically, multicationic QACs) are less prone to resistance. In order to better understand such subtleties, a series of molecular dynamics simulations were utilized to help identify these molecular determinants, directly comparing mono‐, bis‐, and triscationic QACs in simulated membrane intercalation models. Three distinct membranes were simulated, mimicking the surfaces of E. coli and S. aureus, as well as a neutral phospholipid control. By analyzing the resulting trajectories in the form of a timeseries analysis, insight was gleaned regarding the significant steps and interactions involved in the destabilization of phospholipid bilayers within the bacterial membranes. Finally, to more specifically probe the effect of the hydrophobic section of the amphiphile that presumably penetrates the membrane, a series of alkyl‐ and ester‐based biscationic quaternary ammonium compounds were prepared, tested for antimicrobial activity against both Gram‐positive and Gram‐negative bacteria, and modelled.

    更新日期:2019-12-20
  • Metals in Biotechnology: Cr‐Driven Stereoselective Reduction of Conjugated C=C Double Bonds
    ChemBioChem (IF 2.593) Pub Date : 2019-12-19
    Marine C. R. Rauch; Yann Gallou; Léna Delorme; Caroline E. Paul; Isabel W. C. E. Arends; Frank Hollmann
    更新日期:2019-12-19
  • Differential Inhibition of APOBEC3 DNA‐Mutator Isozymes by Fluoro‐ and Non‐Fluoro‐Substituted 2′‐Deoxyzebularine Embedded in Single‐Stranded DNA
    ChemBioChem (IF 2.593) Pub Date : 2019-12-19
    Maksim V. Kvach; Fareeda M. Barzak; Stefan Harjes; Henry A. M. Schares; Harikrishnan M. Kurup; Katherine F. Jones; Lorraine Sutton; John Donahue; Richard T. D'Aquila; Geoffrey B. Jameson; Daniel A. Harki; Kurt L. Krause; Elena Harjes; Vyacheslav V. Filichev
    更新日期:2019-12-19
  • Oxidative DNA Cleavage with Clip‐Phenanthroline Triplex‐Forming Oligonucleotide Hybrids
    ChemBioChem (IF 2.593) Pub Date : 2019-12-19
    Alessandro Panattoni; Afaf H. El‐Sagheer; Tom Brown; Andrew Kellett; Michal Hocek
    更新日期:2019-12-19
  • The l‐Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis
    ChemBioChem (IF 2.593) Pub Date : 2019-12-19
    Tai L. Ng; Monica E. McCallum; Christine R. Zheng; Jennifer X. Wang; Kelvin J. Y. Wu; Emily P. Balskus
    更新日期:2019-12-19
  • Proton‐detected solid‐state NMR of the cell‐free synthesized α‐helical transmembrane protein NS4B from hepatitis C virus
    ChemBioChem (IF 2.593) Pub Date : 2019-12-18
    Vlastimil Jirasko; Nils-Alexander Lakomek; Susanne Penzel; Marie-Laure Fogeron; Ralf Bartenschlager; Beat H Meier; Anja Böckmann

    Proton‐detected 100 kHz magic‐angle‐spinning (MAS) solid‐state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell‐free synthesized Hepatitis C virus (HCV) non‐structural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid‐environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D 1H‐detected 1H‐15N and 3D 1H‐13C‐15N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino‐acid‐selectively labelled NS4B can be readily obtained using cell‐free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.

    更新日期:2019-12-19
  • Analyzing the substrate specificity of a novel class of, longhorned beetle‐derived, xylanases using synthetic arabinoxylan oligo‐ and polysaccharides
    ChemBioChem (IF 2.593) Pub Date : 2019-12-18
    Yannick Pauchet; Colin Ruprecht; Fabian Pfrengle

    Xylophagous longhorned beetles thrive in challenging environments. To access nutrients, they secrete plant‐cell‐wall‐degrading enzymes in their gut fluid, among them, cellulases of the subfamily 2 of glycoside hydrolase family 5 (GH5_2). Recently, we discovered that several beetle‐derived GH5_2s use xylan as a substrate instead of cellulose, which is unusual for this family of enzymes. Here, we analyze the substrate specificity of a GH5_2 xylanase from the beetle Apriona japonica (AJAGH5_2‐1) using commercially available substrates and synthetic arabinoxylan oligo‐ and polysaccharides. We demonstrate that AJAGH5_2‐1 deals with arabinoxylan polysaccharides in a way that is distinct from classical xylanase families like GH10 and GH11. AJAGH5_2‐1 is active on long oligosaccharides and cleaves at the non‐reducing end of a substituted xylose residue (position +1) only if (i) three xylose residues are present upstream and downstream of the cleavage site and (ii) xylose residues at positions ‐1, ‐2, +2 and +3 are not substituted.

    更新日期:2019-12-19
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