Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Pronucleotide Probe for Live-Cell Imaging of Protein AMPylation.

ABSTRACT: Conjugation of proteins to AMP (AMPylation) is a prevalent post-translational modification (PTM) in human cells, involved in the regulation of unfolded protein response and neural development. Here we present a tailored pronucleotide probe suitable for in situ imaging and chemical proteomics profiling of AMPylated proteins. Using straightforward strain-promoted azide-alkyne click chemistry, the probe provides stable fluorescence labelling in living cells.

SUBMITTER: Kielkowski P

PROVIDER: S-EPMC7317759 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Pronucleotide Probe for Live-Cell Imaging of Protein AMPylation.

Kielkowski Pavel P Buchsbaum Isabel Y IY Becker Tobias T Bach Kathrin K Cappello Silvia S Sieber Stephan A SA

Chembiochem : a European journal of chemical biology 20200206 9

Conjugation of proteins to AMP (AMPylation) is a prevalent post-translational modification (PTM) in human cells, involved in the regulation of unfolded protein response and neural development. Here we present a tailored pronucleotide probe suitable for in situ imaging and chemical proteomics profiling of AMPylated proteins. Using straightforward strain-promoted azide-alkyne click chemistry, the probe provides stable fluorescence labelling in living cells. ...[more]

PMID: 32027064

Similar Datasets

Pronucleotide probe for in vivo imaging of protein AMPylation.

Project description:Protein AMPylation is a prevalent posttranslational modification in human cells involved in the regulation of unfolded protein response and neural development. Here we present a novel pro-N6azA probe suitable for in vivo imaging and chemical proteomics profilling of AMPylated proteins. The pro-N6azA probe provides stable fluorescent labelling in living cells accesible by straightforward strain-promoted azide-alkyne click reaction. Application of this probe may contribute significantly to the analysis of protein AMPylation during various metabolic processes including neurodevelopment and unfolded protein response.

2019-12-10 | PXD016011 | Pride

Nanoscale live-cell imaging using hopping probe ion conductance microscopy.

Project description:We describe hopping mode scanning ion conductance microscopy that allows noncontact imaging of the complex three-dimensional surfaces of live cells with resolution better than 20 nm. We tested the effectiveness of this technique by imaging networks of cultured rat hippocampal neurons and mechanosensory stereocilia of mouse cochlear hair cells. The technique allowed examination of nanoscale phenomena on the surface of live cells under physiological conditions.

| S-EPMC2702483 | biostudies-literature

NitroxylFluor: A Thiol-Based Fluorescent Probe for Live-Cell Imaging of Nitroxyl.

Project description:Detection of nitroxyl (HNO), the transient one-electron reduced form of nitric oxide, is a significant challenge owing to its high reactivity with biological thiols (with rate constants as high as 109?M-1 s-1). To address this, we report a new thiol-based HNO-responsive trigger that can compete against reactive thiols for HNO. This process forms a common N-hydroxysulfenamide intermediate that cyclizes to release a masked fluorophore leading to fluorescence enhancement. To ensure that the cyclization step is rapid, our design capitalizes on two established physical organic phenomena; the alpha-effect and the Thorpe-Ingold effect. Using this new trigger, we developed NitroxylFluor, a selective HNO-responsive fluorescent probe. Treatment of NitroxylFluor with an HNO donor results in a 16-fold turn-on. This probe also exhibits excellent selectivity over various reactive nitrogen, oxygen, and sulfur species and efficacy in the presence of thiols (e.g., glutathione in mM concentrations). Lastly, we successfully performed live cell imaging of HNO using NitroxylFluor.

| S-EPMC7414788 | biostudies-literature

Ultrahigh affinity Raman probe for targeted live cell imaging of prostate cancer.

Project description:Precise visualization of tumor margins with characterization of microscopic tumor invasion are unmet needs in prostate oncology that demand approaches with high sensitivity and specificity. To address those needs we report surface-enhanced Raman scattering (SERS) based optical imaging for prostate cancer using a combination of live cell Raman microscopy, optimally engineered SERS tags and a urea-based small-molecule inhibitor of prostate-specific membrane antigen (PSMA) as a targeting moiety. We develop gold nanostar based SERS agents that offer ultrahigh binding affinity to PSMA with nearly four orders of magnitude lower IC50 values in relation to existing clinical imaging agents. This combination enables selective recognition of prostate cancer cells, and facilitates quantitative and photostable Raman measurements. Using Raman microscopy to analyze phenotypically similar prostate cancer cell lines differing only in PSMA expression, we demonstrate facile, site-selective recognition using as low as 20 pM of the SERS agent for imaging, opening the door for spectroscopic detection of prostate and other PSMA-expressing tumors in vivo.

| S-EPMC5356002 | biostudies-literature

Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins.

Project description:Conditional fluorescence imaging is a powerful technique for precise spatiotemporal analysis of proteins in live cells upon administration of a synthetic probe. To be applicable to various biological phenomena, probes must be membrane-permeable, have a high signal-to-noise ratio, and work quickly. To date, few probes meet all of these requirements. Here, we designed a fluorogenic probe (AcFCANB) that could label intracellular proteins fused to the photoactive yellow protein (PYP) tag in live cells within 30 min and used it to image heterochromatin protein 1 localization in nuclei. AcFCANB is based on a modular platform consisting of fluorophore, ligand and quencher. We accelerated the labeling reaction by strategic mutations of charged residues on the surface of PYP. A simple model based on molecular dynamics simulations quantitatively reproduced the cooperative effect of multiple mutations on labeling rate.

| S-EPMC5952543 | biostudies-literature

Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence "Turn-On" Probe.

Project description:Messenger RNA (mRNA) plays a critical role in cellular growth and development. However, there have been limited methods available to visualize endogenous mRNA in living cells with ease. We have designed RNA-based fluorescence "turn-on" probes that target mRNA by fusing an unstable form of Spinach with target-complementary sequences. These probes have been demonstrated to be selective, stable, and capable of targeting various mRNAs for live E. coli imaging.

| S-EPMC5460623 | biostudies-literature

A nature-inspired betalainic probe for live-cell imaging of Plasmodium-infected erythrocytes.

Project description:A model betalainic dye was semisynthesized from betanin, the magenta pigment of the red beet, and was effective for live-cell imaging of Plasmodium-infected red blood cells. This water-soluble fluorescent probe is photostable, excitable in the visible region and cell membrane-permeable, and its photophysical properties are not notably pH-sensitive. Fluorescence imaging microscopy of erythrocytes infected with Plasmodium falciparum, a causative agent of malaria in humans, showed that only the parasite was stained. Z-stacking analysis suggested that the probe accumulates proximal to the nucleus of the parasite. Indicaxanthin, one of the natural fluorescent betalains found in the petals of certain flowers, did not stain the parasite or the red blood cell.

| S-EPMC3547039 | biostudies-literature

New Highly Sensitive and Specific Raman Probe for Live Cell Imaging of Mitochondrial Function.

Project description:For Raman hyperspectral detection and imaging in live cells, it is very desirable to create novel probes with strong and unique Raman vibrations in the biological silent region (1800-2800 cm-1). The use of molecular probes in Raman imaging is a relatively new technique in subcellular research; however, it is developing very rapidly. Compared with the label-free method, it allows for a more sensitive and selective visualization of organelles within a single cell. Biological systems are incredibly complex and heterogeneous. Directly visualizing biological structures and activities at the cellular and subcellular levels remains by far one of the most intuitive and powerful ways to study biological problems. Each organelle plays a specific and essential role in cellular processes, but importantly for cells to survive, mitochondrial function must be reliable. Motivated by earlier attempts and successes of biorthogonal chemical imaging, we develop a tool supporting Raman imaging of cells to track biochemical changes associated with mitochondrial function at the cellular level in an in vitro model. In this work, we present a newly synthesized highly sensitive RAR-BR Raman probe for the selective imaging of mitochondria in live endothelial cells.

| S-EPMC10897933 | biostudies-literature

Ratiometric Polymer Probe for Detection of Peroxynitrite and the Application for Live-Cell Imaging.

Project description:Peroxynitrite (ONOO-) is one of the sources of oxidation stress involved in many biological signaling pathways. The role of ONOO- being a double-edged sword in biological systems drives the development of effective detection tools. In this work, a boronate-based polymeric fluorescent probe PB-PVA was synthesized and the probe performance was evaluated. The probe exhibits ratiometric sensing of ONOO- in a range of 0-6 µM. There is good linear relationship between the probe fluorescence intensity ratio and ONOO- concentration. The probe also displays moderate selectivity towards ONOO- over other ROS. Moreover, it is water-soluble and possesses good biocompatibility which aids the imaging of ONOO- in living cells. These properties could make the probe a promising tool in in vitro study related to ONOO-.

| S-EPMC6804088 | biostudies-literature

A Near-Infrared Fluorogenic Pyrrole-Imidazole Polyamide Probe for Live-Cell Imaging of Telomeres.

Project description:Telomeres are closely associated with cellular senescence and cancer. Although some techniques have been developed to label telomeres in living cells for study of telomere dynamics, few biocompatible near-infrared probes based on synthetic molecules have been reported. In this study, we developed a near-infrared fluorogenic pyrrole-imidazole polyamide probe (SiR-TTet59B) to visualize telomeres by conjugating a silicon-rhodamine (SiR) fluorophore with a tandem tetramer pyrrole-imidazole polyamide targeting 24 bp in the telomeric double-stranded (ds) DNA. SiR-TTet59B was almost nonfluorescent in water but increased its fluorescence dramatically on binding to telomeric dsDNA. Using a peptide-based delivery reagent, we demonstrated the specific and effective visualization of telomeres in living U2OS cells. Moreover, SiR-TTet59B could be used to observe the dynamic movements of telomeres during interphase and mitosis. This simple imaging method using a synthetic near-infrared probe could be a powerful tool for studies of telomeres and for diagnosis.

| S-EPMC7683039 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data