General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations.
Abstract The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycos...
Source: Chembiochem - December 10, 2019 Category: Biochemistry Authors: Kaspar F, Giessmann RT, Hellendahl K, Neubauer P, Wagner A, Gimpel M Tags: Chembiochem Source Type: research
Calcium Regulates S100A12 Zinc Sequestration by Limiting Structural Variations.
Abstract Antimicrobial proteins such as S100A12 and S100A8/A9 are highly expressed and secreted by neutrophils during infection and participate in human immune response by sequestering transition metals. At neutral pH, S100A12 sequesters Zn 2+ with nanomolar affinity, which is further enhanced upon calcium binding. We investigated the pH-dependence of human S100A12 zinc sequestration by using Co 2+ as a surrogate. Apo-S100A12 exhibits strong Co 2+ binding between pH 7.0 - 10.0 that progressively diminishes as the pH is reduced to 5.3. Ca 2+ -S100A12 can retain nanomolar Co 2+ binding up to pH 5.7. NMR measurements...
Source: Chembiochem - December 10, 2019 Category: Biochemistry Authors: Wang Q, Aleshintsev A, Jose A, Aramini J, Gupta R Tags: Chembiochem Source Type: research
A trifunctional linker for palmitoylation and peptide and protein localization in biological membranes.
Abstract Attachment of lipophilic groups is an important post-translational modification of proteins, which involves the coupling of one or more anchors such as fatty acids, isoprenoids, phospholipids or glycosylphosphatidyl inositols. To study its impact on the membrane partitioning of hydrophobic peptides or proteins, we designed a tyrosine-based trifunctional linker. The linker allows in a single step facile incorporation of two different functionalities at a cysteine. We determined the effect of the lipid modification on the membrane partitioning of the synthetic α-helical model peptide WALP&nb...
Source: Chembiochem - December 9, 2019 Category: Biochemistry Authors: Syga L, De Vries RH, van Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B Tags: Chembiochem Source Type: research
Phototemtide A, a Cyclic Lipopeptide Heterologously Expressed from Photorhabdus temperata Meg1, Shows Selective Antiprotozoal Activity.
Abstract A new cyclic lipopeptide, phototemtide A (1), was isolated from Escherichia coli expressing the biosynthetic gene cluster pttABC from Photorhabdus temperata Meg1. The structure of 1 was elucidated by HR-ESI-MS and NMR experiments. The absolute configurations of amino acids and 3-hydroxyoctanoic acid in 1 were determined by using the advanced Marfey's method and comparison after total synthesis of 1, respectively. Additionally, three new minor derivatives, phototemtides B-D (2-4), were identified by detailed HPLC-MS analysis. Phototemtide A (1) showed ...
Source: Chembiochem - December 9, 2019 Category: Biochemistry Authors: Zhao L, Vo TD, Kaiser M, Bode HB Tags: Chembiochem Source Type: research
Supramolecular Chemistry in the Biomembrane.
Abstract The combination of supramolecular functional systems with biomolecular chemistry has been a fruitful exercise for decades leading to a greater understanding of biomolecules as well as to a great variety of applications, e.g. in drug delivery and sensing. Within these developments, the phospholipid bilayer membrane surrounding live cells with all its functions has also intrigued supramolecular chemists. Herein, we review recent efforts from the supramolecular chemistry community to mimic natural functions of lipid membranes such as sensing, molecular recognition, membrane fusion, signal transduction, and g...
Source: Chembiochem - December 5, 2019 Category: Biochemistry Authors: Barba-Bon A, Nilam M, Hennig A Tags: Chembiochem Source Type: research
Computational investigations of the chemical mechanism of the enzyme nitrogenase.
Abstract The chemical mechanism of nitrogenase, catalyzing N2 + 8e- + 8H+ ® 2NH3 + H2, occurs at a large multi-metal cluster (FeMo-co) with composition CFe7MoS9(homocitrate). This requires more than 20 steps. Experimental elucidation of this mechanism is thwarted, for various reasons, and computational approaches have a valuable role. This review critically surveys recent density functional calculations of the coordination chemistry and relevant reactions of FeMo-co, within the protein surrounds. Topics covered include the accurac...
Source: Chembiochem - December 5, 2019 Category: Biochemistry Authors: Dance IG Tags: Chembiochem Source Type: research
S-Adenosyl-l-methionine Salvage Impacts Psilocybin Formation in 'Magic' Mushrooms.
r D Abstract Psychotropic Psilocybe mushrooms biosynthesize their principal natural product psilocybin in five steps, among them a phosphotransfer- and two methyltransfer reactions, which consume one equivalent of 5´-adenosyl-triphosphate (ATP) and two equivalents of S-adenosyl-l-methionine (SAM). This short but cosubstrate-intensive pathway requires nucleoside-cofactor salvage to maintain high psilocybin production rates. We characterized the adenosine kinase (AdoK) and S-adenosyl-l-homocysteine (SAH) hydrolase (SahH) of P. cubensis. Both enzymes are directly or indirectly involved in regenerating SAM. qRT-...
Source: Chembiochem - December 4, 2019 Category: Biochemistry Authors: Demmler R, Fricke J, Dörner S, Gressler M, Hoffmeister D Tags: Chembiochem Source Type: research
Proteome-wide survey of cysteine oxidation using a norbornene probe.
JM Abstract Rapid detection of cysteine oxidation in living cells is critical in advancing our understanding of responses to reactive oxygen species (ROS) and oxidative stress. Accordingly, there is a need to develop chemical probes that facilitate proteome-wide detection of cysteine's many oxidation states. Herein, we report the first whole-cell proteomics analysis using a norbornene probe to detect the initial product of cysteine oxidation: cysteine sulfenic acid. The oxidized proteins identified in the HeLa cell model represent the first targets of the reactive oxygen species hydrogen peroxide. The panel of pr...
Source: Chembiochem - December 4, 2019 Category: Biochemistry Authors: Alcock LJ, Langini M, Stühler K, Remke M, Perkins MV, Bernardes GJL, Chalker JM Tags: Chembiochem Source Type: research
Triazolecarbaldehyde Reagents for One-step N-Terminal Protein Modification*.
Abstract Site-specific modification of peptides and proteins is a key aspect of protein engineering. We developed a method for modification of the N-terminus of proteins using 1 H -1,2,3-triazole-4-carbaldehyde (TA4C) derivatives, which can be prepared in one step. The N-terminal specific labeling of bioactive peptides and proteins with the TA4C derivatives proceeds under mild reaction conditions in excellent conversion (angiotensin I: 92%, ribonuclease A: 90%). This method enables site-specific conjugation of various functional molecules such as fluorophores, biotin, and polyethylene glycol attached to the triazo...
Source: Chembiochem - December 3, 2019 Category: Biochemistry Authors: Onoda A, Inoue N, Sumiyoshi E, Hayashi T Tags: Chembiochem Source Type: research
Photo-crosslinking: An emerging chemical tool for investigating molecular networks in live cells.
Abstract Studying protein-protein interactions (PPIs) is useful for understanding cellular functions and mechanisms. Evaluating these PPIs under conditions as similar as possible to native conditions can be achieved using photo-crosslinking methods because of their on-demand ability to generate reactive species in situ by irradiation with UV light. Various fusion tag, metabolic incorporation, and amber codon suppression approaches using various crosslinkers containing aryl-azide, benzophenone, and diazirines have been applied in live cells. Mass spectroscopy and immunological techniques are used to identify crossl...
Source: Chembiochem - December 3, 2019 Category: Biochemistry Authors: Mishra PK, Yoo CM, Hong E, Rhee HW Tags: Chembiochem Source Type: research
Corrigendum: A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Q β Replicase.
Corrigendum: A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Qβ Replicase. Chembiochem. 2019 Dec 02;20(23):2968 Authors: Ueda K, Mizuuchi R, Matsuda F, Ichihashi N PMID: 31789448 [PubMed - in process] (Source: Chembiochem)
Source: Chembiochem - December 2, 2019 Category: Biochemistry Authors: Ueda K, Mizuuchi R, Matsuda F, Ichihashi N Tags: Chembiochem Source Type: research
Structural and Biochemical insights to the Recruitment of Acyl Carrier Protein-linked Extender Units in Ansamitocin Biosynthesis.
Abstract A few acyltransferase (AT) domains of modular polyketide synthases (PKSs) recruit acyl carrier protein (ACP)-linked extender units with unusual C2 substituents to confer functionalities that are not available in coenzyme A (CoA)-linked ones. Here, an AT specific for methoxymalonyl (MOM)-ACP in the third module of the ansamitocin PKS was structurally and biochemically characterized. The AT uses a conserved tryptophan at the entrance of the substrate binding tunnel to discriminate between different carriers. A W275R mutation switches its carrier specificity from the ACP protein to the CoA molecule. The acyl...
Source: Chembiochem - November 27, 2019 Category: Biochemistry Authors: Zhang F, Ji H, Ali I, Deng Z, Bai L, Zheng J Tags: Chembiochem Source Type: research
Scytodecamide from the Cultured Scytonema sp. UIC 10036 Expands the Chemical and Genetic Diversity of Cyanobactins.
Scytodecamide from the Cultured Scytonema sp. UIC 10036 Expands the Chemical and Genetic Diversity of Cyanobactins. Chembiochem. 2019 Nov 26;: Authors: Crnkovic CM, Braesel J, Krunic A, Eustáquio AS, Orjala J Abstract Cyanobactins are a large family of cyanobacterial ribosomally synthesized and post-translationally modified peptides (RiPPs) often associated with biological activities, such as cytotoxicity, antiviral, and antimalarial activities. They are traditionally described as cyclic molecules containing heterocyclized amino acids. However, this definition has been recently challenged by ...
Source: Chembiochem - November 26, 2019 Category: Biochemistry Authors: Crnkovic CM, Braesel J, Krunic A, Eustáquio AS, Orjala J Tags: Chembiochem Source Type: research
JM Abstract Looking back, looking forward: In 2000, ChemBioChem debuted. The chemistry of carbohydrates, nucleic acids, peptides, proteins, natural products and other small molecules had reached a level that allowed biological questions to be probed. Today, there is no end in sight to studying biological matter with chemical tools or making use of biological methods to produce chemicals. PMID: 31769931 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 26, 2019 Category: Biochemistry Authors: Fersht AR, Gölitz P, Lehn JM Tags: Chembiochem Source Type: research
Halogen Bonding in Biomimetic Deiodination of Thyroid Hormones, their Metabolites and Halogenated Nucleosides.
Abstract Thyroid hormones (THs) are key players of the endocrine system, and play pivotal roles in carbohydrate and fat metabolism, protein synthesis, overall growth and brain development. Thyroid gland predominantly produces thyroxine or 3,5,3',5'-tetraiodothyronine (T4) as a prohormone and three isoforms of mammalian selenoenzyme, iodothyronine deiodinase (DIO1, DIO2 and DIO3) catalyze the regioselective deiodination of T4 to produce the biologically active and inactive metabolites. While DIO1 catalyzes both 5- and 5'-deiodination of T4, DIO2 and DIO3 selectively mediates 5- and 5'-deiodinations, respectively. I...
Source: Chembiochem - November 26, 2019 Category: Biochemistry Authors: Mondal S, Manna D, Raja K, Mugesh G Tags: Chembiochem Source Type: research
Discovery of ubonodin, an antimicrobial lasso peptide active against members of the Burkholderia cepacia complex.
We report the heterologous expression, structure, and antimicrobial activity of a lasso peptide, ubonodin, encoded in the genome of Burkholderia ubonensis . The topology of ubonodin is unprecedented amongst lasso peptides with 18 of its 28 amino acids found in the mechanically-bonded loop segment. Ubonodin inhibits RNA polymerase in vitro and has potent antimicrobial activity against several pathogenic members of the Burkholderia genus, most notably B. cepacia and B. multivorans , causative agents of lung infections in cystic fibrosis patients. PMID: 31765515 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 25, 2019 Category: Biochemistry Authors: Cheung-Lee WL, Parry M, Zong C, Jaramillo Cartagena A, Darst S, Connell N, Russo R, Link AJ Tags: Chembiochem Source Type: research
The Two Classic Pb2+-selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity.
This study links these two classic and widely used DNAzymes, and offers new insights into the sequence/activity relationship related to metal selectivity. PMID: 31755629 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 22, 2019 Category: Biochemistry Authors: Ren W, Huang PJ, He M, Lyu M, Wang S, Wang C, Liu J Tags: Chembiochem Source Type: research
The multifaceted inhibitory effects of an alkyl quinolone on the diatom Phaeodactylum tricornutum.
Lepetit B Abstract The mechanisms underlying interactions between diatoms and bacteria are crucial to understand diatom behaviour and proliferation, and can result in far-reaching ecological consequences. Recently, 2-alkyl-4-quinolones have been isolated from marine bacteria, both of which (the bacterium and isolated chemical) inhibited growth of microalgae, suggesting these compounds could mediate diatom - bacteria interactions. We investigated the effects of several quinolones on three diatom species. The growth of all three was inhibited, with half-maximal inhibitory concentrations reaching the sub-micromolar r...
Source: Chembiochem - November 20, 2019 Category: Biochemistry Authors: Dow L, Stock F, Peltekis A, Szamosvári D, Prothiwa M, Lapointe A, Böttcher T, Bailleul B, Vyverman W, Kroth PG, Lepetit B Tags: Chembiochem Source Type: research
A V-nitrogenase variant containing a citrate-substituted cofactor.
Abstract Nitrogenase catalyzes the ambient reduction of N2 and CO at its cofactor site. Here, we present a biochemical and spectroscopic characterization of an Azotobacter vinelandii V-nitrogenase variant expressing a citrate-substituted cofactor. Designated VnfDGKCit, the catalytic component of this V-nitrogenase variant has an αβ2(δ) subunit composition and carries an 8Fe P*-cluster and a citrate-substituted V-cluster analog in the αβ-dimer, as well as a 4Fe cluster in the 'orphaned' β-subunit. Interestingly, when normalized based on the amount of the cofactor, VnfDGKCit shows a ...
Source: Chembiochem - November 20, 2019 Category: Biochemistry Authors: Newcomb M, Lee CC, Tanifuji K, Jasniewski A, Liedtke J, Ribbe MW, Hu Y Tags: Chembiochem Source Type: research
Validation of L-tellurienylalanine as a phenylalanine isostere.
Abstract Mass cytometry (MC) and imaging mass cytometry (IMC TM ) have emerged as important tools for the study of biological heterogeneity. We recently demonstrated the use of L-2-Tellurienylalanine (TePhe), a mimic of phenylalanine (Phe), as an MC and IMC TM compatible protein synthesis reporter. In this work, the biochemical similarity of TePhe and its cognate analogue, Phe, are examined in the context of the RNase S complex. Isothermal titration calorimetry studies show that incorporation of TePhe preserves the interaction of S-peptide with S-protein and the dissociation constants for the interaction of the Ph...
Source: Chembiochem - November 19, 2019 Category: Biochemistry Authors: Vurgun N, Nitz M Tags: Chembiochem Source Type: research
Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems.
Abstract Dynamic nuclear polarization (DNP) has shown great promise as a tool to enhance the nuclear magnetic resonance (NMR) signals of proteins in the cellular environment. As the sensitivity increases, the ability to select and efficiently polarize a specific macromolecule over the cellular background has become desirable. Here, we address this need and present a tetrazine-based DNP polarization agent that can be targeted selectively to proteins containing the unnatural amino acid (UAA) norbornene-lysine. The UAA can be introduced efficiently by genetic means in the cellular milieu. Our approach is bio-orthogon...
Source: Chembiochem - November 19, 2019 Category: Biochemistry Authors: Lim BJ, Ackermann BE, Debelouchina GT Tags: Chembiochem Source Type: research
New PtII triazol thiosemicarbazone' complexes. Analysis of their reactivity and potential antitumoral action.
We report the synthesis and characterization of three new platinum complexes using 3,5-diacetyl-1,2,4-triazol bis(4N-isopropylthiosemicarbazone) as a ligand. We describe the specific conditions in which solvent coordination takes place and we resolve the X-ray structure of the complex with one solvent molecule of dmso (dimethyl sulfoxide). The analysis of these platinum compounds' reactivity helped us find the best solution profile for the biological investigations. Then, we study the complexes' interaction with biological models such as CT DNA using UV spectroscopy and tracking the changes in the electrophoretic mobility ...
Source: Chembiochem - November 19, 2019 Category: Biochemistry Authors: Matesanz AI, Herrero J, Faraco EJ, Cubo L, Gomez Quiroga A Tags: Chembiochem Source Type: research
Chemical reporters for exploring microbiology and microbiota mechanisms.
Abstract The advances in bioorthogonal chemical reporters have afforded new tools to explore the targets and functions of specific metabolites in diverse microbes. Here we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease. PMID: 31730246 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 15, 2019 Category: Biochemistry Authors: Zhang Z, Wang YC, Yang X, Hang HC Tags: Chembiochem Source Type: research
Metals in biotechnology: Cr-driven-stereoselective reduction of conjugated C=C-double bonds.
Abstract Elementary metals are shown to be suitable sacrificial electron donors to drive stereoselective reduction of conjugated C=C-double bonds using old yellow enzymes as catalysts. Both, direct electron transfer from the metal to the enzyme as well as mediated electron transfer is feasible, though the latter excels by higher reaction rates. The general applicability of this new chemoenzymatic reduction method is demonstrated as well as current limitations are outlined. PMID: 31713969 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 12, 2019 Category: Biochemistry Authors: Rauch M, Gallou Y, Delorme L, Paul C, Arends I, Hollmann F Tags: Chembiochem Source Type: research
New vocabulary for bacterial communication.
Abstract Quorum sensing (QS) is widely accepted as a procedure that bacteria use to converse. However, prevailing thinking places acyl-homoserine lactones (AHLs) at the forefront of this communication pathway in Gram-negative bacteria. With the advent of high throughput genomics and the subsequent influx of bacterial genomes, bioinformatics analysis has determined that the genes encoding AHL biosynthesis, originally discovered to be indispensable for QS (LuxI-like proteins and homologs), are often absent in QS capable bacteria. Instead, the sensing protein (LuxR-like proteins) is present with an apparent inability...
Source: Chembiochem - November 11, 2019 Category: Biochemistry Authors: Tobias NJ, Brehm J, Kresovic D, Brameyer S, Bode HB, Heermann R Tags: Chembiochem Source Type: research
Synthesis and evaluation of cyclic sulfite diesters as sulfur dioxide (SO2) donors.
We report 1,2-cyclic sulfite diesters as a new class of reliable SO2 donors that dissociate in buffer through a nucleophilic displacement to produce SO2 with tuneable release profiles. We provide data in support of the suitability of these SO2 donors to enhance intracellular levels of SO2 at an efficiency superior to sodium bisulfite, the most commonly used SO2 donor for cellular studies. PMID: 31709695 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - November 10, 2019 Category: Biochemistry Authors: Malwal S, Pardeshi KA, Chakrapani H Tags: Chembiochem Source Type: research
Deploying Fluorescent Nucleoside Analogues for High Throughput Inhibitor Screening.
Abstract High-throughput small molecule screening in drug discovery processes commonly rely on fluorescence-based methods including fluorescent polarization and fluorescence/Förster resonance energy transfer. These techniques use highly accessible instrumentation, however may suffer from high false negative rates and background signals or, may involve complex schemes for the introduction of fluorophore pairs. Herein, we present the synthesis and application of fluorescent nucleoside analogues as the foundation for directed approaches for competitive binding analyses. The general approach describes s...
Source: Chembiochem - November 10, 2019 Category: Biochemistry Authors: Seebald L, Madec A, Imperiali B Tags: Chembiochem Source Type: research
Rapid biophysical characterization and NMR structural analysis of small proteins from bacteria and archaea.
Abstract Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins were overlooked for a long time and are becoming discovered only recently. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure-function-relation. Here, we present a method for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable ...
Source: Chembiochem - November 9, 2019 Category: Biochemistry Authors: Kubatova N, Pyper DJ, Jonker HRA, Saxena K, Remmel L, Richter C, Brantl S, Evguenieva-Hackenberg E, Hess W, Klug G, Marchfelder A, Soppa J, Streit W, Mayzel M, Orekhov VY, Fuxreiter M, Schmitz-Streit R, Schwalbe H Tags: Chembiochem Source Type: research
Simultaneous Detection of Multiple Pathogenic Targets with Novel Stem-tagged Primer Sets.
Abstract Simultaneous multiple gene detection is indispensable for the detection of various genes in a small sample obtained by an invasive method. A typical detection method is probe-based fluorescence melting curve analysis using real time PCR. It is very limited because a probe sequence must be designed with at least a different T m for each target. To overcome this limitation, we developed a novel simultaneous multiple gene detection method based on a giant amplicon molecular beacon. PCR was performed by attaching stem sequences with different T m s to each primer set, and the melting T m was measured by hybri...
Source: Chembiochem - November 9, 2019 Category: Biochemistry Authors: Kim YT, Moon J, Hong IS Tags: Chembiochem Source Type: research
Ruthenium(II)-Arene Thiocarboxylates: Identification of a Stable Dimer Selectively Cytotoxic to Invasive Breast Cancer Cells.
Abstract Ru(II)-arene complexes provide a versatile scaffold for novel anti-cancer drugs. A new series of Ru(II)-arene-thiocarboxylato dimers 1-7 were synthesized and characterized. Three of the complexes (2a,b and 5) showed promising anti-proliferative activities in MDA-MB-231 (human invasive breast cancer) cells, and were further tested in a panel of fifteen cancerous and non-cancerous cell lines. Complex 5 showed moderate but remarkably selective activity in MDA-MB-231 cells (IC50 = 39 ± 4 mM Ru). Real-time proliferation studies showed that 5 induced apop...
Source: Chembiochem - November 8, 2019 Category: Biochemistry Authors: Stephens L, Levina A, Trinh I, Blair V, Werrett M, Lay P, Andrews P Tags: Chembiochem Source Type: research
Development of polyamine substituted triphenylamine ligands with high affinity and selectivity for G-quadruplex DNA.
González-García J, Vilar R Abstract Currently significant efforts are devoted to designing small molecules able to bind selectively to guanine-quadruplexes (G4s). These non-canonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, we reported a series of triphenylamine(TPA)-based compounds including macrocyclic polyamines, which display high affinity towards G4 DNA. Following from this initial work, herein we present a series of second-generation compounds, in which the central TPA has been functi...
Source: Chembiochem - November 8, 2019 Category: Biochemistry Authors: García-España EV, Pont I, Martínez-Camarena Á, Galiana-Roselló C, Tejero R, Albelda MT, González-García J, Vilar R Tags: Chembiochem Source Type: research
Hybridization of Oligonucleotides with Hydrophobic Peptide Nucleic Acids Assists Their Cellular Uptake via Aggregate Formation.
Abstract We applied hybridization of hydrophobic peptide nucleic acids (PNA) with oligodeoxynucleotides (ODNs) to their cellular uptake without transfection reagents. We employed a pyrene unit as a hydrophobic functional group and introduced it to the terminal of the PNA strand. The pyrene-tethered PNA (Py PNA) strongly bound with its complementary ODNs to generate amphiphiles; the resulting hybrid formed aggregates that showed efficient cellular uptake and high biological stability. The aggregates, which consisted of a functional DNA aptamer that bound to the Py PNA, penetrated the cell membrane smoothly and exer...
Source: Chembiochem - November 8, 2019 Category: Biochemistry Authors: Misu S, Kurihara R, Nishihara T, Tanabe K, Kainuma R, Sato R Tags: Chembiochem Source Type: research
Real-time BODIPY-binding assay to screen inhibitors of the early oligomerization process of A β 1-42 peptide.
Real-time BODIPY-binding assay to screen inhibitors of the early oligomerization process of Aβ 1-42 peptide. Chembiochem. 2019 Nov 08;: Authors: Tonali N, Dodero VI, Kaffy J, Hericks L, Ongeri S, Sewald N Abstract Misfolding and aggregation of amyloid-β 1-42 peptide (Aβ1-42) play a central role in the pathogenesis of Alzheimer's disease (AD). Targeting the highly cytotoxic oligomeric species formed during the early stages of the aggregation process represents a promising therapeutic strategy to reduce the toxicity associated with Aβ1-42. Currently, the Thioflavin T (ThT) assay is t...
Source: Chembiochem - November 8, 2019 Category: Biochemistry Authors: Tonali N, Dodero VI, Kaffy J, Hericks L, Ongeri S, Sewald N Tags: Chembiochem Source Type: research
Regulation of Immune Activation by Optical Control of TLR1/2 Dimerization.
Abstract The activation of toll like receptors (TLRs) plays important roles in the immune response. The ability to control the activities of TLRs could be used as a switch for immune response. Herein, we rationally designed and synthesized a photoswitchable Pam3CSK4 derivative (P10) to control the activation of TLR1/2. The ground state trans-P10 could stimulate and activate antigen-presenting cells (APCs) through promoting the TLR1/2 dimerization. However, the cis-P10, derived from UV irradiation of trans-P10, reduced the activities of APCs by impeding the TLR1/2 dimerization. In the absence of UV radiation, the c...
Source: Chembiochem - November 8, 2019 Category: Biochemistry Authors: Hu HG, Chen PG, Wang G, Wu JJ, Zhang BD, Li WH, Davis RL, Li YM Tags: Chembiochem Source Type: research
Site-Specific Isotopic Labeling (SSIL) - Access to High-Resolution Structural and Dynamic Information in Low Complexity Proteins.
ado P Abstract Remarkable technical progress in the area of structural biology has paved the way to study previously inaccessible targets. For example, large protein complexes can now be easily investigated by cryo-electron microscopy, and modern high-field NMR magnets have challenged the limits of high-resolution characterization of proteins in solution. However, the structural and dynamic characteristics of certain proteins with important functions still cannot be probed by conventional methods. These proteins in question contain low complexity regions (LCRs), compositionally biased sequences where only a limite...
Source: Chembiochem - November 7, 2019 Category: Biochemistry Authors: Urbanek A, Elena-Real CA, Popovic M, Morató A, Fournet A, Allemand F, Delbecq S, Sibille N, Bernado P Tags: Chembiochem Source Type: research
Advances in DNA Origami-Cell Interfaces.
Abstract The nascent field of DNA nanotechnology has undergone rapid growth since its inception. By using DNA as a biologically "safe" material, DNA nanotechnology shows great promise in applications such as drug-delivery systems. Further progress, however, relies on understanding the different ways in which DNA nanostructures behave in and interact with cells, tissues and even whole organisms. Moreover, this knowledge must then be harnessed in innovative ways to improve existing DNA nanostructures and design new ones, so that they can perform more diverse functions more effectively. There have been many...
Source: Chembiochem - November 6, 2019 Category: Biochemistry Authors: Mishra S, Feng Y, Endo M, Sugiyama H Tags: Chembiochem Source Type: research
Structure and activity of the thermophilic tryptophan-6 halogenase BorH.
Abstract Flavin-dependent halogenases carry out regioselective aryl halide synthesis in aqueous solution at ambient temperature and neutral pH using benign halide salts, making them attractive catalysts for green chemistry. BorH and BorF, two proteins encoded by the biosynthetic gene cluster for the chlorinated bisindole alkaloid borregomycin A, are the halogenase and flavin reductase subunits of a tryptophan-6-halogenase. Quantitative conversion of L-tryptophan (Trp) to 6-chlorotryptophan could be achieved using 1.2 mol% BorH and 2 mol% BorF. The optimal reaction temperature for Trp chlorination is 45 °C, and...
Source: Chembiochem - November 6, 2019 Category: Biochemistry Authors: Lingkon K, Bellizzi J Tags: Chembiochem Source Type: research
Applying a thermostable and organic solvent tolerant ene-reductase for the asymmetric reduction of (R)-carvone.
Paul CE Abstract Ene-reductases allow regio- and stereoselective reduction of activated C=C double bonds at the expense of nicotinamide adenine dinucleotide cofactors (NAD(P)H). Biological NAD(P)H can be replaced by synthetic mimics to facilitate enzyme screening and process optimization. The ene-reductase FOYE-1, originating from an acidophilic iron oxidizer, has been described as a promising candidate and is now explored for applied biocatalysis. Biological and synthetic nicotinamide cofactors were evaluated to fuel FOYE-1 to produce valuable compounds. A maximum activity of 319.7 ± 3.2 U mg-1 with NADPH ...
Source: Chembiochem - November 6, 2019 Category: Biochemistry Authors: Tischler D, Gädke E, Eggerichs D, Gomez Baraibar A, Mügge C, Scholtissek A, Paul CE Tags: Chembiochem Source Type: research
Validation of slow off-kinetics of Sirtuin Rearranging Ligands (SirReals) by means of the label-free electrically switchable nanolever technology.
Abstract We have discovered the sirtuin rearranging ligands (SirReals) as highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase Sirt2. Using a biotinylated SirReal in combination with biolayer interferometry, we previously observed a slow dissociation rate of the inhibitor-enzyme complex, which had been postulated to be the key to the high affinity and selectivity of SirReals. However, for the attachment of biotin to the SirReal core, we introduced a triazole as a linking moiety, which was shown by X-ray co-crystallography to interact with Arg97 of the cofactor binding loop. Herein, we ai...
Source: Chembiochem - November 6, 2019 Category: Biochemistry Authors: Schiedel M, Daub H, Itzen A, Jung M Tags: Chembiochem Source Type: research
Chemical methods for N- and O-sulfation of small molecules, amino acids and peptides.
Abstract Sulfation of the amino acid residues of proteins is an emerging post-translational modification, the functions of which are yet to be fully understood. Current sulfation methods are limited mainly to O -tyrosine (sY) which requires negatively charged species around the desired amino acid residue and a specific sulfotransferase enzyme. Alternatively, for solid phase peptide synthesis a de novo protected sY is required. Therefore, synthetic routes are required to go beyond O -sulfation. We have developed a novel route to N -sulfamation and can dial-in/out O -sulfation (without S -sulfurothiolation), mimicki...
Source: Chembiochem - November 6, 2019 Category: Biochemistry Authors: Benedetti AM, Gill DM, Tsang CW, Jones AM Tags: Chembiochem Source Type: research
5-Benzylidene-4-Oxazolidinones are Synergistic with Antibiotics for the Treatment of Staphylococcus aureus Biofilms.
Abstract The failure of frontline antibiotics in the clinic is one of the most serious threats to human health and requires a multitude of novel therapeutics and innovative treatment approaches to curtail the growing crisis. In addition to traditional resistance mechanisms resulting in the lack of efficacy of many antibiotics, most chronic and recurring infections are further made tolerant to antibiotic action by the presence of biofilms. Herein, we report an expanded set of 5-benzylidene-4-oxazolidinones that are able to inhibit the formation of Staphylococcus aureus biofilms, disperse preformed bi...
Source: Chembiochem - November 5, 2019 Category: Biochemistry Authors: Frohock BH, Gilbertie JM, Daiker JC, Schnabel LV, Pierce JG Tags: Chembiochem Source Type: research
Taming the reactivity of monoterpene synthases to guide regioselective product hydroxylation.
Abstract Monoterpenoids are industrially important natural products with applications in the flavours, fragrances, fuels and pharmaceutical industries. Most monoterpenoids are produced by plants, but recently two bacterial monoterpene synthases have been identified, including a cineole synthase (bCinS). Unlike plant cineole synthases, bCinS is capable of producing nearly pure cineole from geranyl diphosphate in a complex cyclisation cascade that is tightly controlled. Here we have used a multidisciplinary approach to show that Asn305 controls water attack on the α-terpinyl cation and subsequent cyclisat...
Source: Chembiochem - November 4, 2019 Category: Biochemistry Authors: Scrutton N Tags: Chembiochem Source Type: research
Oxidative DNA Cleavage with Clip-Phenanthroline Triplex Forming Oligonucleotide Hybrids.
We report a systematic study of several new types of hybrids of Cu-chelated Clip-phenanthroline artificial metallonuclease (AMN) with triplex forming oligonucleotides (TFO) for sequence-specific cleavage of double stranded DNA. The synthesis of these AMN-TFO hybrids is based on application of the alkyne-azide cycloaddition click reaction (CuAAC) in the key step. The AMN was attached through different linkers at either the 5'- or 3'-end or in the middle of the TFO stretch. The diverse hybrids efficiently formed triplexes with the target purine-rich sequence and their Cu-complexes were studied for their ability to cleave dsD...
Source: Chembiochem - November 3, 2019 Category: Biochemistry Authors: Panattoni A, El-Sagheer AH, Brown T, Kellett A, Hocek M Tags: Chembiochem Source Type: research
Evaluating the Catalytic Potential of a General RNA-Cleaving FANA Enzyme.
Abstract The discovery of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that natural genetic polymers are not unique in their ability to function as enzymes. However, all known examples of in vitro selected XNA enzymes function with reduced activity relative to their natural counterparts, suggesting that XNAs may be limited in their ability to fold into structures with high catalytic activity. To explore this problem, we evaluated the catalytic potential of FANAzyme 12-7, an RNA-cleaving catalyst composed entirely of 2'-fluoroarabino nucleic acid (FANA) that was evolved to cleave RNA at a ...
Source: Chembiochem - November 3, 2019 Category: Biochemistry Authors: Chaput JC, Wang Y, Vorperian A, Shehabat M Tags: Chembiochem Source Type: research
Lipidated stapled peptides targeting the acyl binding protein UNC119.
TN Abstract The acyl binding UNC119 proteins mediate activation and transport of various N-myristoylated proteins. In particular, UNC119a plays a crucial role in the completion of cytokinesis. Here, we report the use of a lipidated peptide originating from the UNC119 binding partner Gnat1 as basis for the design of lipidated stabilized a-helical peptides that target UNC119a. Using the hydrocarbon peptide stapling approach, cell-permeable binders of UNC119a were generated that induced the accumulation of cytokinetic and binucleated cells suggesting UNC119a as a potential target for the inhibition of cytokinesis. ...
Source: Chembiochem - November 3, 2019 Category: Biochemistry Authors: Chromm P, Adihou H, Kapoor S, Vazquez-Chantada M, Davey P, Longmire D, Hennes E, Hofer W, Küchler P, Chiarparin E, Waldmann H, Grossmann TN Tags: Chembiochem Source Type: research
Analysis and Modelling of Large and Heterogeneous Populations of DNA Using a PCR-Based Method.
Abstract The study of populations of large size and high diversity is limited by the capability of collecting data. Moreover, for a pool of individuals, each associated with a unique characteristic feature, as the pool size grows, the possible interactions increase exponentially, quickly beyond the limit of computation and experimental studies. Herein, we present designs of DNA libraries with various diversity. Using a facile analytic method based on real time PCR, we can evaluate the diversity of a pool of DNA allowing extraordinarily high heterogenicity (e.g.> 1 trillion). We demonstrated that these DNA libra...
Source: Chembiochem - November 1, 2019 Category: Biochemistry Authors: Andrade H, Thomas AK, Lin W, Reddavide FV, Zhang Y Tags: Chembiochem Source Type: research
Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation.
Abstract The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small-molecule triggers that turn on proteins through a Staudinger reduction/self-immolation cascade with substantially improved kinetics and yields. We achieved this through site-specific incorporation of a new set of azidobenzyloxycarbonyl lysine derivatives in mammalian cells. This approach allowed us to activate proteins by adding a nontoxic, bioorthogonal phosphine trigger. We applied this methodology to control a post-translational modification (SUMOylati...
Source: Chembiochem - October 30, 2019 Category: Biochemistry Authors: Wesalo JS, Luo J, Morihiro K, Liu J, Deiters A Tags: Chembiochem Source Type: research
NHS-modified ethynylphosphonamidates enable the synthesis of configurationally defined protein conjugates.
Abstract Herein, we describe the application of N-hydroxy-succinimide-(NHS-)-modified phosphonamidate building blocks for the incorporation of Cysteine-selective ethynylphosphonamidates to lysine residues of proteins followed by thiol addition with small molecules and proteins. We demonstrate that our building blocks significantly lower undesired homo-crosslinking side-products that can occur with commonly applied succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) under physiological pH. The previously demonstrated stability of the phosphonamidate moiety additionally solves the problem of premature...
Source: Chembiochem - October 29, 2019 Category: Biochemistry Authors: Kasper MA, Gerlach M, Schneider AFL, Groneberg C, Ochtrop P, Boldt S, Schumacher D, Helma J, Leonhardt H, Christmann M, Hackenberger C Tags: Chembiochem Source Type: research
The Construction and Characterization of Mirror-imaged L-DNA i-Motif.
Abstract The first thermal stable and pH-responsive tetraplex i-motif structure formed by L -DNA is presented. Although this L -type i-motif exhibits the same physiochemical properties as its D -isomer, its inverted chirality and good enzymatic resistance opens the way to the development of new DNA materials of pharmaceutical and biological interest. PMID: 31659823 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - October 28, 2019 Category: Biochemistry Authors: Sun Y, Yang B, Hua Y, Dong Y, Ye J, Wang J, Xu L, Liu D Tags: Chembiochem Source Type: research
Isoindoline-Based Nitroxides as Bioresistant Spin Labels for Protein Labeling via Cysteines and Alkyne Bearing Noncanonical Amino Acids.
er M Abstract Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful tool in protein structural research. Nitroxides are highly suitable spin labeling reagents, but suffer from limited stability in particular in cellular environment. Here, we present the synthesis of a maleimid- and an azide-modified tetraethyl-shielded isoindoline-based nitroxide (M- and Az-TEIO) for labeling of cysteines or the noncanonical amino acid para -ethynyl-l-phenylalanine ( p ENF). We demonstrate high stability of TEIO site-specifically attached to the protein thiore...
Source: Chembiochem - October 28, 2019 Category: Biochemistry Authors: Braun TS, Widder P, Osswald U, Groß L, Williams L, Schmidt M, Helmle I, Summerer D, Drescher M Tags: Chembiochem Source Type: research