Browse
Submit Data
Databases
API
Help

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two rapid catalyst-free click reactions for in vivo protein labeling of genetically encoded strained alkene/alkyne functionalities.

ABSTRACT: Detailed kinetic analyses of inverse electron-demand Diels–Alder cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition reactions were conducted and the reactions were applied for rapid protein bioconjugation. When reacted with a tetrazine or a diaryl nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics. To apply these “click” reactions for site-specific protein labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pair. Proteins bearing these noncanonical amino acids were successively labeled with a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro and in living cells.

SUBMITTER: Kurra Y

PROVIDER: S-EPMC4166034 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Fluorogenic protein labeling using a genetically encoded unstrained alkene.

Project description:We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels-Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene-tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.

| S-EPMC5369545 | biostudies-literature

GEN-Click: Genetically Encodable Click Reactions for Spatially Restricted Metabolite Labeling.

Project description:Chemical reactions for the in situ modification of biomolecules within living cells are under development. Among these reactions, bio-orthogonal reactions such as click chemistry using copper(I) and Staudinger ligation are widely used for specific biomolecule tracking in live systems. However, currently available live cell copper(I)-catalyzed azide/alkyne cycloaddition reactions are not designed in a spatially resolved manner. Therefore, we developed the "GEN-Click" system, which can target the copper(I)-catalyzed azide/alkyne cycloaddition reaction catalysts proximal to the protein of interest and can be genetically expressed in a live cell. The genetically controlled, spatially restricted, metal-catalyzed biorthogonal reaction can be used for proximity biotin labeling of various azido-bearing biomolecules (e.g., protein, phospholipid, oligosaccharides) in living cell systems. Using GEN-Click, we successfully detected local metabolite-transferring events at cell-cell contact sites.

| S-EPMC10450880 | biostudies-literature

A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling.

Project description:Bioorthogonal chemistry allows rapid and highly selective reactivity in biological environments. The copper-catalyzed azide-alkyne cycloaddition (CuAAC) is a classic bioorthogonal reaction routinely used to modify azides or alkynes that have been introduced into biomolecules. Amber suppression is an efficient method for incorporating such chemical handles into proteins on the ribosome, in which noncanonical amino acids (ncAAs) are site specifically introduced into the polypeptide in response to an amber (UAG) stop codon. A variety of ncAA structures containing azides or alkynes have been proven useful for performing CuAAC chemistry on proteins. To improve CuAAC efficiency, biologically incorporated alkyne groups can be reacted with azide substrates that contain copper-chelating groups. However, the direct incorporation of copper-chelating azides into proteins has not been explored. To remedy this, we prepared the ncAA paz-lysine (PazK), which contains a picolyl azide motif. We show that PazK is efficiently incorporated into proteins by amber suppression in mammalian cells. Furthermore, PazK-labeled proteins show improved reactivity with alkyne reagents in CuAAC.

| S-EPMC8632528 | biostudies-literature

A genetically encoded alkyne directs palladium-mediated protein labeling on live mammalian cell surface.

Project description:The merging of site-specific incorporation of small bioorthogonal functional groups into proteins via amber codon suppression with bioorthogonal chemistry has created exciting opportunities to extend the power of organic reactions to living systems. Here we show that a new alkyne amino acid can be site-selectively incorporated into mammalian proteins via a known orthogonal pyrrolysyl-tRNA synthetase/tRNACUA pair and directs an unprecedented, palladium-mediated cross-coupling reaction-driven protein labeling on live mammalian cell surface. A comparison study with the alkyne-encoded proteins in vitro indicated that this terminal alkyne is better suited for the palladium-mediated cross-coupling reaction than the copper-catalyzed click chemistry.

| S-EPMC4340352 | biostudies-literature

Cu(ii)-alginate-based superporous hydrogel catalyst for click chemistry azide-alkyne cycloaddition type reactions in water.

Project description:A novel sustainable hydrogel catalyst based on the reaction of sodium alginate naturally extracted from brown algae Laminaria digitata residue with copper(ii) was prepared as spherical beads, namely Cu(ii)-alginate hydrogel (Cu(ii)-AHG). The morphology and structural characteristics of these beads were elucidated by different techniques such as SEM, EDX, BET, FTIR and TGA analysis. Cu(ii)-AHG and its dried form, namely Cu(ii)-alginate (Cu(ii)-AD), are relatively uniform with an average pore ranging from 200 nm to more than 20 μm. These superporous structure beads were employed for the copper catalyzed [3 + 2] cycloaddition reaction of aryl azides and terminal aryl alkynes (CuAAC) via click chemistry at low catalyst loading, using water as a solvent at room temperature and pressure. The catalytic active copper(i) species was generated by the reduction of copper(ii) by terminal alkyne via the oxidative alkyne homocoupling reaction. The prepared catalysts were found to be efficient (85-92%) and regioselective by affording only 1,4-disubstituted-1,2,3-triazoles. They were also recoverable and reused in their dried form for at least four consecutive times without a clear loss of efficiency. A mechanistic study was performed through density functional theory (DFT) calculations in order to explain the regioselectivity outcome of Cu(ii)-alginate in CuAAC reactions. The analysis of the local electrophilicity (ω k) at the electrophilic reagent and the local nucleophilicity (N k) at the nucleophilic confirms the polar character of CuAAC. This catalyst has the main advantage of being sustainably ligand-free and recyclable.

| S-EPMC9056610 | biostudies-literature

Click Organocatalysis: Acceleration of Azide-Alkyne Cycloadditions with Mutually Orthogonal Click Reactions.

Project description:"Click organocatalysis" uses mutually orthogonal click reactions to organocatalyze a click reaction. We report the development of an isobenzofuran organocatalyst that increases the rate and regioselectivity of an azide-alkyne cycloaddition. The organocatalytic cycle consists of (1) a Diels-Alder reaction of an alkyne with a diarylisobenzofuran to form a benzooxanorbornadiene, (2) a 1,3-dipolar cycloaddition with an azide to form a 4,5-dihydro-1,2,3-triazole, and (3) a retro-Diels-Alder reaction that releases the triazole product and regenerates the diarylisobenzofuran organocatalyst. The diarylisobenzofuran organocatalyst was computationally designed to catalyze the reaction of perfluorophenyl azide and methyl propiolate to selectively form a 1,4-triazole product. Experimental validation of the designed organocatalyst was obtained with methyl 4-azido-2,3,5,6-tetrafluorobenzoate and methyl propiolate.

| S-EPMC10922906 | biostudies-literature

Cellulose Acetate-Supported Copper as an Efficient Sustainable Heterogenous Catalyst for Azide-Alkyne Cycloaddition Click Reactions in Water.

Project description:A new sustainable heterogeneous catalyst for copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC) was investigated. The preparation of the sustainable catalyst was carried out through the complexation reaction between the polysaccharide cellulose acetate backbone (CA) and copper(II) ions. The resulting complex [Cu(II)-CA] was fully characterized by using different spectroscopic methods such as Fourier-transform infrared spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray (EDX), Ultraviolet-visible (UV-vis), and Inductively Coupled Plasma (ICP) analyses. The Cu(II)-CA complex exhibits high activity in the CuAAC reaction for substituted alkynes and organic azides, leading to a selective synthesis of the corresponding 1,4-isomer 1,2,3-triazoles in water as a solvent and working at room temperature. It is worth noting that this catalyst has several advantages from the sustainable chemistry point of view including no use of additives, biopolymer support, reactions carried out in water at room temperature, and easy recovery of the catalyst. These characteristics make it a potential candidate not only for the CuAAC reaction but also for other catalytic organic reactions.

| S-EPMC10253314 | biostudies-literature

A manganese(i)tricarbonyl-catalyst for near room temperature alkene and alkyne hydroarylation.

Project description:Developing more efficient catalytic processes using abundant and low toxicity transition metals is key to enable their mainstream use in synthetic chemistry. We have rationally designed a new Mn(i)-catalyst for hydroarylation reactions that displays much improved catalytic activity over the commonly used MnBr(CO)5. Our catalyst, MnBr(CO)3(MeCN)2, avoids the formation of the off-cycle manganacycle-(CO)4 species responsible for low catalyst activity, allowing near room temperature hydroarylation of alkenes and alkynes with broad functional group tolerance including late stage functionalisation and diversification of bioactive molecules.

| S-EPMC9667916 | biostudies-literature

Remarkable Alkene-to-Alkene and Alkene-to-Alkyne Transfer Reactions of Selenium Dibromide and PhSeBr. Stereoselective Addition of Selenium Dihalides to Cycloalkenes.

Project description:The original goal of this research was to study stereochemistry of selenium dihalides addition to cycloalkenes and properties of obtained products. Remarkable alkene-to-alkene and alkene-to-alkyne transfer reactions of selenium dibromide and PhSeBr were discovered during this research. The adducts of selenium dibromide with alkenes or cycloalkenes easily exchange SeBr2 with other unsaturated compounds, including acetylenes, at room temperature, in acetonitrile. Similar alkene-to-alkene and alkene-to-alkyne transfer reactions of the PhSeBr adducts with alkenes or cycloalkenes take place. The supposed reaction pathway includes the selenium group transfer from seleniranium species to alkenes or alkynes. It was found that the efficient SeBr2 and PhSeBr transfer reagents are Se(CH2CH2Br)2 and PhSeCH2CH2Br, which liberate ethylene, leading to a shift in equilibrium. The regioselective and stereoselective synthesis of bis(E-2-bromovinyl) selenides and unsymmetrical E-2-bromovinyl selenides was developed based on the SeBr2 and PhSeBr transfer reactions which proceeded with higher selectivity compared to analogous addition reactions of SeBr2 and PhSeBr to alkynes under the same conditions.

| S-EPMC6983007 | biostudies-literature

Extensions of the icosahedral closomer structure by using azide-alkyne click reactions.

Project description: Not available

| S-EPMC3532044 | biostudies-literature