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Covalent labeling

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https://www.readbyqxmd.com/read/29311464/-development-and-application-of-catalytic-tyrosine-modification
#1
Shinichi Sato, Michihiko Tsushima, Kosuke Nakamura, Hiroyuki Nakamura
 The chemical labeling of proteins with synthetic probes is a key technique used in chemical biology, protein-based therapy, and material science. Much of the chemical labeling of native proteins, however, depends on the labeling of lysine and cysteine residues. While those methods have significantly contributed to native protein labeling, alternative methods that can modify different amino acid residues are still required. Herein we report the development of a novel methodology of tyrosine labeling, inspired by the luminol chemiluminescence reaction...
2018: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/29310242/competitive-horseradish-peroxidase-linked-aptamer-assay-for-sensitive-detection-of-aflatoxin-b1
#2
Linlin Sun, Qiang Zhao
Aflatoxin B1 (AFB1) is one of highly toxic mycotoxins and a known human carcinogen. The frequent contamination of AFB1 in food products and large health risk of AFB1 have raised global concerns. Sensitive detection of AFB1 is of vital importance and highly demanded. Herein, we reported a competitive horseradish peroxidase (HRP)-linked aptamer assay for AFB1, combining the advantages of aptamer for affinity binding and enzyme label for signal amplification. In this assay, free AFB1 in solution competed with a covalent conjugate of bovine serum albumin-AFB1 (BSA-AFB1) coated on the wells of microplate in binding to the HRP-labeled aptamer probe...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29306572/novel-biotin-linker-with-alkyne-and-amino-groups-for-chemical-labelling-of-a-target-protein-of-a-bioactive-small-molecule
#3
Tomoaki Anabuki, Miu Tsukahara, Masanori Okamoto, Hideyuki Matsuura, Kosaku Takahashi
We synthesized a novel linker (1) with biotin, alkyne and amino groups for the identification of target proteins using a small molecule that contains an azide group (azide probe). The alkyne in the linker bound the azide probe via an azide-alkyne Huisgen cycloaddition. A protein cross-linker effectively bound the conjugate of the linker and an azide probe with a target protein. The covalently bound complex was detected by western blotting. Linker 1 was applied to a model system using an abscisic acid receptor, RCAR/PYR/PYL (PYL)...
December 26, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29306437/covalent-probes-for-carbohydrate-active-enzymes-from-glycosidases-to-glycosyltransferases
#4
Yong Xu, Najib Uddin, Gerd K Wagner
Covalent probes for glycosidases and glycosyltransferases are of great interest as tool compounds for chemical biology. For glycosidases, a sizable number of such probes have been developed from covalent glycosidase inhibitors. We review selected recent examples and highlight different design strategies, including probes based on photoaffinity labels and mechanism-based inhibitors, as well as their applications in biology and for activity-based protein profiling. In contrast to glycosidases, only a limited number of covalent probes have been reported to date for glycosyltransferases...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29303555/an-optical-biosensor-based-quantification-of-microcystin-synthetase-a-gene-early-warning-of-toxic-cyanobacterial-blooming
#5
Jinchuan Liu, Xiaohong Zhou, Hanchang Shi
Monitoring and controlling of toxic cyanobacterial strains, which can produce microcystins, is critical to protect human and ecological health. We herein reported an optical biosensor-based quantification of microcystin synthetase A (mcyA) gene so as to discriminate microcystins-producing from non-producing strains. In this assay, the mcyA-specific ssDNA probes were designed in silico with an online tool and then synthesized to be covalently immobilized on an optical fiber surface. Production of fluorescently modified target DNA fragment amplicons was accomplished through the use of Cy5-tagged deoxycytidine triphosphates (dCTPs) in the polymerase chain reaction (PCR) method, which resulted in copies with internally labelled multiple sites per DNA molecule and delivered the great sensitivity...
January 5, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29301937/cyclipostins-and-cyclophostin-analogs-inhibit-the-antigen-85c-from-mycobacterium-tuberculosis-both-in-vitro-and-in-vivo
#6
Albertus Viljoen, Matthias Richard, Phuong Chi Nguyen, Patrick Fourquet, Luc Camoin, Rishi R Paudal, Giri R Gnawali, Christopher D Spilling, Jean-François Cavalier, Stéphane Canaan, Mickael Blaise, Laurent Kremer
An increasing prevalence of cases of drug-resistant tuberculosis requires the development of more efficacious chemotherapies. We previously reported the discovery of a new class of Cyclipostins and Cyclophostin (CyC) analogs exhibiting potent activity against Mycobacterium tuberculosis both in vitro and in infected macrophages. Competitive labeling/enrichment assays combined with MS have identified several serine or cysteine enzymes in lipid and cell wall metabolism as putative targets of these CyC compounds...
January 4, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29296673/glutathione-responsive-selenosulfide-prodrugs-as-a-platform-strategy-for-potent-and-selective-mechanism-based-inhibition-of-protein-tyrosine-phosphatases
#7
Caroline Chandra Tjin, Kate D Otley, Tyler D Baguley, Pradeep Kurup, Jian Xu, Angus C Nairn, Paul J Lombroso, Jonathan A Ellman
Dysregulation of protein tyrosine phosphorylation has been implicated in a number of human diseases, including cancer, diabetes, and neurodegenerative diseases. As a result of their essential role in regulating protein tyrosine phosphorylation levels, protein tyrosine phosphatases (PTPs) have emerged as important yet challenging therapeutic targets. Here we report on the development and application of a glutathione-responsive motif to facilitate the efficient intracellular delivery of a novel class of selenosulfide phosphatase inhibitors for the selective active site directed inhibition of the targeted PTP by selenosulfide exchange with the active site cysteine...
December 27, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29278328/unpaired-electron-spin-density-distribution-across-reduced-2fe-2s-cluster-ligands-by-13c%C3%AE-cysteine-labeling
#8
Alexander T Taguchi, Yoshiharu Miyajima-Nakano, Risako Fukazawa, Myat T Lin, Amgalanbaatar Baldansuren, Robert B Gennis, Kazuya Hasegawa, Takashi Kumasaka, Sergei A Dikanov, Toshio Iwasaki
Iron-sulfur clusters are one of the most versatile and ancient classes of redox mediators in biology. The roles that these metal centers take on are predominantly determined by the number and types of coordinating ligands (typically cysteine and histidine) that modify the electronic structure of the cluster. Here we map the spin density distribution onto the cysteine ligands for the three major classes of the protein-bound, reduced [2Fe-2S](His)n(Cys)4-n (n = 0, 1, 2) cluster by selective cysteine-13Cβ isotope labeling...
December 26, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29259663/15n-labelling-and-structure-determination-of-adamantylated-azolo-azines-in-solution
#9
Sergey L Deev, Alexander S Paramonov, Tatyana S Shestakova, Igor A Khalymbadzha, Oleg N Chupakhin, Julia O Subbotina, Oleg S Eltsov, Pavel A Slepukhin, Vladimir L Rusinov, Alexander S Arseniev, Zakhar O Shenkarev
Determining the accurate chemical structures of synthesized compounds is essential for biomedical studies and computer-assisted drug design. The unequivocal determination of N-adamantylation or N-arylation site(s) in nitrogen-rich heterocycles, characterized by a low density of hydrogen atoms, using NMR methods at natural isotopic abundance is difficult. In these compounds, the heterocyclic moiety is covalently attached to the carbon atom of the substituent group that has no bound hydrogen atoms, and the connection between the two moieties of the compound cannot always be established via conventional 1H-1H and 1H-13C NMR correlation experiments (COSY and HMBC, respectively) or nuclear Overhauser effect spectroscopy (NOESY or ROESY)...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29241186/strengthening-gastric-cancer-therapy-by-trastuzumab-conjugated-nanoparticles-with-simultaneous-encapsulation-of-anti-mir-21-and-5-fluorouridine
#10
Nan Hu, Jun Feng Yin, Ze Ji, Yidong Hong, Puyuan Wu, Baoxiang Bian, Ziyan Song, Rutian Li, Qin Liu, Fenglei Wu
BACKGROUND/AIMS: MicroRNA-21 is an oncogenic miR (oncomiR) frequently elevated in gastric cancer (GC). Overexpression of miR-21 decreases the sensitivity of GC cells to 5-fluorouridine (5-Fu) and trastuzumab, a humanized monoclonal antibody targeting human epidermal growth factor receptor 2 (HER2). Receptor-mediated endocytosis plays a crucial role in the delivery of biotherapeutics including anti-miRNA oligonucleotides (AMOs). This study is a continuation of earlier findings involving poly(ε-caprolactone) (PCL)-poly (ethylene glycol) (PEG) nanoparticles (PEG-PCL NPs), which were coated with trastuzumab to target GC with HER2 receptor over-expression using anti-miRNA-21 (AMO-21) and 5-Fu...
December 12, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29240412/integration-of-on-column-chemical-reactions-in-protein-characterization-by-lc-ms-cross-path-reactive-chromatography
#11
Jake Pawlowski, Ian Carrick, Igor A Kaltashov
Profiling of complex proteins by means of mass spectrometry (MS) frequently requires that certain chemical modifications of their covalent structure (e.g., reduction of disulfide bonds) be carried out prior to the MS or MS/MS analysis. Traditionally, these chemical reactions take place in the off-line mode to allow the excess reagents (the majority of which interfere with the MS measurements and degrade the analytical signal) to be removed from the protein solution prior to MS measurements. In addition to a significant increase in the analysis time, chemical reactions may result in a partial or full loss of the protein if the modifications adversely affect its stability, e...
December 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29240283/proximal-tubular-epithelial-cells-preferentially-endocytose-covalently-modified-albumin-compared-to-native-albumin
#12
Nguyen D K Ly, Greg H Tesch, David J Nikolic-Paterson, Philip Poronnik
AIM: Albumin can be covalently modified at surface lysine residues and thus the circulation contains a mixture of native albumin (i.e. not modified) and albumin with varying degrees of modification. Uptake and lysosomal degradation of glomerular filtered albumin by proximal tubular cells via the megalin scavenger receptor is considered an important mechanism to limit albumin loss in the urine. However, whether this is a general mechanism of tubular uptake of albumin or if this is restricted to modified albumin is unknown...
December 14, 2017: Nephrology
https://www.readbyqxmd.com/read/29239090/dynamic-covalent-chemistry-within-biphenyl-scaffolds-reversible-covalent-bonding-control-of-selectivity-and-chirality-sensing-with-one-single-system
#13
Cailing Ni, Daijun Zha, Hebo Ye, Yu Hai, Yuntao Zhou, Eric Anslyn, Lei You
Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a universal platform toward binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between open aldehyde and its cyclic hemiaminal within biphenyl derivatives enables the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. The selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli...
December 13, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29237120/ultrafast-time-resolved-studies-on-fluorescein-for-recognition-strands-architecture-in-amyloid-fibrils
#14
Piotr Hanczyc, Alexander A Mikhailovsky, David R Boyer, Michael R Sawaya, Alan J Heeger, David Eisenberg
Protein aggregation is associated with numerous devastating diseases such as Alzheimer's, Parkinson's, and prion diseases. Development of therapeutics would benefit from knowledge of the structural organization of protein molecules in these amyloid aggregates, particularly in their aqueous biological milieu. However, detailed structural studies to date have been mainly on the solid state, and have required large quantities of purified aggregate. Moreover, these conventional methods require the aggregated assembly to remain structurally stable over days or weeks required to perform the experiment, whereas the pathologically relevant species of in vivo aggregates may be shorter lived...
December 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29235040/quantitative-peptidomics-with-five-plex-reductive-methylation-labels
#15
Alexandre K Tashima, Lloyd D Fricker
Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines...
December 12, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29229527/surface-proteins-and-the-formation-of-biofilms-by-staphylococcus-aureus
#16
Sung Joon Kim, James Chang, Binayak Rimal, Hao Yang, Jacob Schaefer
Staphylococcus aureus biofilms pose a serious clinical threat as reservoirs for persistent infections. Despite this clinical significance, the composition and mechanism of formation of S. aureus biofilms are unknown. To address these problems, we used solid-state NMR to examine S. aureus (SA113), a strong biofilm-forming strain. We labeled whole cells and cell walls of planktonic cells, young biofilms formed for 12-24h after stationary phase, and more mature biofilms formed for up to 60h after stationary phase...
December 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29228311/a-new-method-for-post-translationally-labeling-proteins-in-live-cells-for-fluorescence-imaging-and-tracking
#17
M Hinrichsen, M Lenz, J M Edwards, O K Miller, S G J Mochrie, P S Swain, U Schwarz-Linek, L Regan
We present a novel method to fluorescently label proteins, post-translationally, within live Saccharomycescerevisiae. The premise underlying this work is that fluorescent protein (FP) tags are less disruptive to normal processing and function when they are attached post-translationally, because target proteins are allowed to fold properly and reach their final subcellular location before being labeled. We accomplish this post-translational labeling by expressing the target protein fused to a short peptide tag (SpyTag), which is then covalently labeled in situ by controlled expression of an open isopeptide domain (SpyoIPD, a more stable derivative of the SpyCatcher protein) fused to an FP...
December 7, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29222330/discovery-of-stimulator-binding-to-a-conserved-pocket-in-the-heme-domain-of-soluble-guanylyl-cyclase
#18
Jessica A Wales, Cheng-Yu Chen, Linda Breci, Andrzej Weichsel, Sylvie G Bernier, James E Sheppeck, Robert Solinga, Takashi Nakai, Paul A Renhowe, Joon Jung, William R Montfort
Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29218838/intended-and-unintended-targeting-of-polymeric-nanocarriers-the-case-of-modified-poly-glycerol-adipate-nanoparticles
#19
Verena M Weiss, Henrike Lucas, Thomas Mueller, Petr Chytil, Tomáš Etrych, Toufik Naolou, Jörg Kressler, Karsten Mäder
Biodegradable nanoparticles based on stearic acid-modified poly(glycerol adipate) (PGAS) are promising carriers for drug delivery. In order to investigate the impact of the particle interface characteristics on the biological fate, PGAS nanoparticles are covalently and noncovalently coated with N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers. HPMA copolymer-modified PGAS nanoparticles have similar particle sizes, but less negative zeta-potentials. Nanoparticles are double labeled with the fluorescent dyes DiR (noncovalently) and DYOMICS-676 (covalently bound to HPMA copolymer), and their biodistribution is investigated noninvasively by multispectral optical imaging...
December 8, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/29215565/a-miniaturized-impedimetric-immunosensor-for-the-competitive-detection-of-adrenocorticotropic-hormone
#20
Nan Li, Egor M Larin, Kagan Kerman
Adrenocorticotropic hormone (ACTH) plays an essential role in regulating corticosteroid hormone production, which has important functions in a myriad of critical physiological functions. In this proof-of-concept study, a miniaturized immunosensor was developed for the highly sensitive detection of ACTH using electrochemical impedance spectroscopy (EIS) in connection with disposable screen-printed gold electrodes (SPGEs). A film of 3,3'-dithiobis[sulfosuccinimidylpropionate] (DTSSP) was prepared to immobilize anti-ACTH antibodies covalently on the nanostructured SPGE surface...
December 7, 2017: Sensors
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