keyword
MENU ▼
Read by QxMD icon Read
search

Covalent labeling

keyword
https://www.readbyqxmd.com/read/28630348/analysis-of-a-dual-domain-phosphoglycosyl-transferase-reveals-a-ping-pong-mechanism-with-a-covalent-enzyme-intermediate
#1
Debasis Das, Petr Kuzmic, Barbara Imperiali
Phosphoglycosyl transferases (PGTs) are integral membrane proteins with diverse architectures that catalyze the formation of polyprenol diphosphate-linked glycans via phosphosugar transfer from a nucleotide diphosphate-sugar to a polyprenol phosphate. There are two PGT superfamilies that differ significantly in overall structure and topology. The polytopic PGT superfamily, represented by MraY and WecA, has been the subject of many studies because of its roles in peptidoglycan and O-antigen biosynthesis. In contrast, less is known about a second, extensive superfamily of PGTs that reveals a core structure with dual domain architecture featuring a C-terminal soluble globular domain and a predicted N-terminal membrane-associated domain...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28628261/studying-the-conformation-of-a-receptor-tyrosine-kinase-in-solution-by-inhibitor-based-spin-labeling
#2
Dongsheng M Yin, Jeffrey S Hannam, Anton Schmitz, Olav Schiemann, Gregor Hagelueken, Michael Famulok
The synthesis of a spin label based on PD168393, a covalent inhibitor of a major anticancer drug target, the epidermal growth factor receptor (EGFR), is reported. The label facilitates the analysis of the EGFR structure in solution by pulsed electron paramagnetic resonance (EPR) spectroscopy. For various EGFR constructs, including near-full-length EGFR, we determined defined distance distributions between the two spin labels bound to the ATP binding sites of the EGFR dimer. The distances are in excellent agreement with an asymmetric dimer of the EGFR...
June 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28628203/photoactivated-in-vivo-proximity-labeling
#3
David B Beck, Roberto Bonasio
Identification of molecular interactions is paramount to understanding how cells function. Most available technologies rely on co-purification of a protein of interest and its binding partners. Therefore, they are limited in their ability to detect low-affinity interactions and cannot be applied to proteins that localize to difficult-to-solubilize cellular compartments. In vivo proximity labeling (IPL) overcomes these obstacles by covalently tagging proteins and RNAs based on their proximity in vivo to a protein of interest...
June 19, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28625736/use-of-bioconjugation-with-cytochrome-p450-enzymes
#4
REVIEW
Julie Ducharme, Karine Auclair
Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28621541/expanding-the-scope-of-electrophiles-capable-of-targeting-k-ras-oncogenes
#5
Lynn M McGregor, Meredith L Jenkins, Caitlin Kerwin, John E Burke, Kevan M Shokat
There is growing interest in reversible and irreversible covalent inhibitors that target noncatalytic amino acids in target proteins. With a goal of targeting oncogenic K-Ras variants (e.g., G12D) by expanding the types of amino acids that can be targeted by covalent inhibitors, we survey a set of electrophiles for their ability to label carboxylates. We functionalized an optimized ligand for the K-Ras switch II pocket with a set of electrophiles previously reported to react with carboxylates and characterized the ability of these compounds to react with model nucleophiles and oncogenic K-Ras proteins...
June 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28618223/covalent-protein-labeling-and-improved-single-molecule-optical-properties-of-aqueous-cdse-cds-quantum-dots
#6
Sara M Wichner, Victor R Mann, Alexander S Powers, Maya A Segal, Mustafa Mir, Jigar N Bandaria, Mark A DeWitt, Xavier Darzacq, Ahmet Yildiz, Bruce E Cohen
Semiconductor quantum dots (QDs) have proven to be superior probes for single-molecule imaging compared to organic or genetically encoded fluorophores, but they are limited by difficulties in protein targeting, their larger size, and on-off blinking. Here, we report compact aqueous CdSe/CdS QDs with significantly improved bioconjugation efficiency and superior single-molecule optical properties. We have synthesized covalent protein labeling ligands (i.e., SNAP tags) that are optimized for nanoparticle use, and QDs functionalized with these ligands label SNAP-tagged proteins ∼10-fold more efficiently than existing SNAP ligands...
June 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28615413/breaking-the-color-barrier-a-multi-selective-antibody-reporter-offers-innovative-strategies-of-fluorescence-detection
#7
Eugenio Gallo, Jonathan W Jarvik
A novel bi-partite fluorescence platform exploits the high affinity and selectivity of antibody scaffolds to capture and activate small molecule fluorogens. In this report we investigated the property of multi-selectivity activation from a single antibody against diverse cyanine-family fluorogens. Our fluorescence screen identified three cell impermeant fluorogens; each with unique emission spectra (blue, green, and red) and nanomolar affinities. Most importantly, as a protein fusion-tag to G-protein-coupled receptors the antibody biosensor retained full activity - displaying bright fluorogen signals with minimal background on live cells...
June 14, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28614699/a-signal-amplification-probe-enhances-sensitivity-of-antibodies-and-aptamers-based-immuno-diagnostic-assays
#8
Ofer Nussbaum, Michal Bar Oz, Tal Tilayov, Helly Atiya, Shlomo Dagan
One major unmet need is improving the sensitivity of immune-diagnostic assays. This is particularly important in the field of biomarker discoveries and monitoring. We have established a novel signal amplification probe system enabling a highly sensitive target detection platform to be used in immuno-assays. The probe consists of a double stranded DNA that can carry a large number of signaling elements such as biotin or fluorescent molecules. The DNA probe anchors to the recognition unit, whether an antibody or an aptamer, by covalent conjugation or by a simple and rapid molecular association process...
June 11, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28613814/2-chloropropionamide-as-a-low-reactivity-electrophile-for-irreversible-small-molecule-probe-identification
#9
Dharmaraja Allimuthu, Drew J Adams
Resurgent interest in covalent target engagement in drug discovery has demonstrated that small molecules containing weakly reactive electrophiles can be safe and effective therapies. Several recently FDA-approved drugs feature an acrylamide functionality to selectively engage cysteine side chains of kinases (Ibrutinib, Afatinib, and Neratinib). Additional electrophilic functionalities whose reactivity is compatible with highly selective target engagement and in vivo application could open new avenues in covalent small molecule discovery...
June 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28609214/the-potyvirus-particle-recruits-the-plant-translation-initiation-factor-eif4e-by-means-of-the-vpg-covalently-linked-to-the-viral-rna
#10
Geneviève Tavert-Roudet, Agnès Anne, Amandine Barra, Arnaud Chovin, Christophe Demaille, Thierry Michon
The VPg of potyviruses is a protein covalently linked to the 5' end of viral RNA. It interacts with eIF4E, a component of the cellular translation initiation complex. It has been suggested that the 5' RNA linked VPg could mimic the cellular mRNA cap, promoting synthesis of viral proteins. We report here evidences for evidence for recruitment of the plant eIF4E by Lettuce mosaic virus (LMV, potyvirus) particles via the 5' RNA linked VPg. Analysis of the viral population was performed by ELISA-based tests, either with crude extracts of LMV-infected tissues or purified viral particles...
June 13, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28580113/methyltransferase-directed-covalent-coupling-of-fluorophores-to-dna
#11
Milena Helmer Lauer, Charlotte Vranken, Jochem Deen, Wout Frederickx, Willem Vanderlinden, Nathaniel Wand, Volker Leen, Marcelo H Gehlen, Johan Hofkens, Robert K Neely
We report an assay for determining the number of fluorophores conjugated to single plasmid DNA molecules and apply this to compare the efficiency of fluorophore coupling strategies for covalent DNA labelling. We compare a copper-catalyzed azide-alkyne cycloaddition reaction, amine to N-hydroxysuccinimidyl ester coupling reaction and strain-promoted azide-alkyne cycloaddition reaction for fluorescent DNA labelling. We found increased labelling efficiency going from the amine to N-hydroxysuccinimidyl ester coupling reaction to the copper-catalyzed azide-alkyne cycloaddition and found the highest degree of DNA labelling with the strain-promoted azide-alkyne cycloaddition reaction...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28558174/sers-and-serrs-detection-of-the-dna-lesion-8-nitroguanine-a-self-labeling-modification
#12
Steven E J Bell, Susan Dick, Katie Alexander, Ian O'Neil, Richard Cosstick
Rapid and sensitive methods to detect DNA lesions are essential in order to understand their role in carcinogenesis and for potential diagnosis of cancers. The 8-nitroguanine DNA lesion, which is closely associated with inflammation-induced cancers, has been characterised for the first time by surface-enhanced Raman spectroscopy (SERS). This lesion has been studied as the free base, as well as part of a dinucleotide and oligodeoxynucleotides (ODNs) at 5 different excitation wavelengths in the range 785-488 nm...
May 30, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28552820/avidin-conjugated-calcium-phosphate-nanoparticles-as-a-modular-targeting-system-for-the-attachment-of-biotinylated-molecules-in-vitro-and-in-vivo
#13
Selina Beatrice van der Meer, Torben Knuschke, Annika Frede, Nina Schulze, Astrid M Westendorf, Matthias Epple
Avidin was covalently conjugated to the surface of calcium phosphate nanoparticles, coated with a thin silica shell and terminated by sulfhydryl groups (diameter of the solid core about 50 nm) with a bifunctional crosslinker connecting the amino groups of avidin to the sulfhydryl group on the nanoparticle surface. This led to a versatile nanoparticle system where all kinds of biotinylated (bio-)molecules can be easily attached to the surface by the non-covalent avidin-biotin-complex formation. It also permits the attachment of different biomolecules on the same nanoparticle (heteroavidity), creating a modular system for specific applications in medicine and biology...
May 25, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28544959/effect-of-different-mineralization-processes-on-in-vitro-and-in-vivo-bone-regeneration-and-osteoblast-macrophage-cross-talk-in-co-culture-system-using-dual-growth-factor-mediated-non-mulberry-silk-fibroin-grafted-poly-%C3%B0-caprolactone-nanofibrous-scaffold
#14
Promita Bhattacharjee, Tapas K Maiti, Debasis Bhattacharya, Samit Kumar Nandi
This study evaluates mineralized nanofibrous polymeric scaffolds at supporting in vitro osteogenic differentiation of human mesenchymal stem cells (hMSCs) and in vivo bone tissue regeneration. Co-electrospin, alternative soaking, and electrodeposition were used to introduce hydroxyapatite in non-mulberry silk fibroin grafted poly(Є-caprolactone) nanofibrous scaffolds. Bone morphogenic protein-2 and Transforming growth factor-β, at a potency ratio of 1:1, are covalently coupled onto the scaffolds. hMSCs proliferation and interactions are studied through MTT and Alamar blue assay and scanning electron and confocal microscopy...
May 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28542243/covalent-dye-attachment-influences-the-dynamics-and-conformational-properties-of-flexible-peptides
#15
Manuel P Luitz, Anders Barth, Alvaro H Crevenna, Rainer Bomblies, Don C Lamb, Martin Zacharias
Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP)...
2017: PloS One
https://www.readbyqxmd.com/read/28538738/solid-phase-synthesis-cyclization-and-site-specific-functionalization-of-aziridine-containing-tetrapeptides
#16
Benjamin K W Chung, Christopher J White, Andrei K Yudin
Cyclic tetrapeptides comprise a potent and selective class of molecules with a wide range of biological activities, including the phytotoxic activity of tentoxin and the histone deacetylase (HDAC) inhibitory effects of chlamydocin. The incorporation of a functional aziridine group within cyclic peptides enables their conformational control and allows for late-stage and site-selective functionalization of these molecules, thereby creating the potential for covalent protein labeling. This protocol describes the solid-phase synthesis, cyclization, and site-specific structural modification of aziridine-containing tetrapeptides...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28537071/clmsvault-a-software-suite-for-protein-cross-linking-mass-spectrometry-data-analysis-and-visualization
#17
Mathieu Courcelles, Jasmin Coulombe-Huntington, Émilie Cossette, Anne-Claude Gingras, Pierre Thibault, Mike Tyers
Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach...
June 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28530188/simple-assay-for-screening-phytoestrogenic-compounds-using-the-oestrogen-receptor-immobilised-magnetite-nanoparticles
#18
Pimchanok Busayapongchai, Sineenat Siri
With increasing interests of phytoestrogens for their potential applications, a rapid and simple tool for screening these phytochemicals is still required. In this study, a simple assay to detect phytoestrogens was developed based on the competition binding between the tested samples and the fluorescently labelled oestrogen (E2) to the human ligand binding domain of oestrogen receptor (LBD-ER) that was immobilised on the magnetite nanoparticles (MNPs). The 40-kDa LBD-ER peptide was produced in an Escherichia coli system...
June 2017: IET Nanobiotechnology
https://www.readbyqxmd.com/read/28525848/an-amplified-comparative-fluorescence-resonance-energy-transfer-immunosensing-of-ca125-tumor-marker-and-ovarian-cancer-cells-using-green-and-economic-carbon-dots-for-bio-applications-in-labeling-imaging-and-sensing
#19
Somayeh Hamd-Ghadareh, Abdollah Salimi, Fardin Fathi, Saman Bahrami
CA125, is a marker in the clinical diagnosis of several cancers and currently is the best serum-based tumor marker for ovarian cancer. Here, we developed an ultrasensitive antibody-ssDNA aptamer sandwich-type fluorescence immunosensor for CA125 detection. Based on a novel signal amplification strategy the carbon dots (CDs) functionalized with aptamer (CD-aptamer) used as detection probe and PAMAM-Dendrimers/AuNPs was used for covalent attachment of CA125-antibody and completing the sandwich assay method. By measuring of fluorescence resonance energy transfer (FRET) signals between CDs and AuNPs as nanoquenchers, the fluorescence signal quenched during sandwich complex formed between anti-CA125, CA125 and CDs-Aptamer and decreasing of fluorescence response signal is related to CA125 concentrations...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28522327/measurement-of-bacterial-capture-and-phagosome-maturation-of-kupffer-cells-by-intravital-microscopy
#20
Bas G J Surewaard, Paul Kubes
It is central to the field of bacterial pathogenesis to define how bacteria are killed by phagocytic cells. During phagocytosis, the microbe is localized to the phagolysosome where crucial defense mechanisms such as acidification and production of reactive oxygen species (ROS) are initiated. This process has extensively been studied in vitro, however many resident tissue phagocytes will phenotypically change upon isolation from their natural environment. Therefore, interrogation of phagocytosis and phagosomal function of cells in the context of their natural tissue environment enhances our understanding of the biological process in vivo...
May 15, 2017: Methods: a Companion to Methods in Enzymology
keyword
keyword
56238
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"