Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sensing of citrulline modifications in histone peptides by deep cavitand hosts.

ABSTRACT: Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution.

SUBMITTER: Gill AD

PROVIDER: S-EPMC6872487 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sensing of citrulline modifications in histone peptides by deep cavitand hosts.

Gill Adam D AD Hickey Briana L BL Wang Siwen S Xue Min M Zhong Wenwan W Hooley Richard J RJ

Chemical communications (Cambridge, England) 20191001 88

Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution. ...[more]

PMID: 31621759

Similar Datasets

Lipid bilayer environments control exchange kinetics of deep cavitand hosts and enhance disfavored guest conformations.

Project description:The effects on the molecular recognition properties of water-soluble deep cavitand hosts upon embedding them in phosphocholine lipid bilayer environments have been studied by 2D NMR experiments. By employing suitable guests containing 19F or 13C nuclei that can be encapsulated inside the host, 2D EXSY NMR experiments can be used to analyze and compare the in/out guest exchange rates in aqueous solution, isotropically tumbling micelles, or magnetically ordered bicelles. These analyses show that embedding the deep cavitands in lipid bilayers slows the guest exchange rate, due to the lipids acting as a "compression sleeve" around the host, restricting guest egress. This effect also enhances guest conformations in the host that are not observed in free solution, such as axial cyclohexane conformers and ketone hydrates.

| S-EPMC5890788 | biostudies-literature

Selective protein recognition in supported lipid bilayer arrays by tailored, dual-mode deep cavitand hosts.

Project description:Self-folding deep cavitands with variably functionalized upper rims are able to selectively immobilize proteins at a biomimetic supported lipid bilayer surface. The immobilization process takes advantage of the dual-mode binding capabilities of the hosts, combining a defined binding pocket with upper rim charged/H-bonding groups. A variety of proteins can be selectively immobilized at the bilayer interface, either via complementary charge/H-bonding interactions, cavity-based molecular recognition, or a combination of both. The immobilization process can be used to bind unmodified native proteins, epitopes for bioadhesion, or proteins covalently modified with suitable RNMe3+ binding "handles" and charged groups that can either match or mismatch with the cavitand rim. The immobilization process can be monitored in real time using surface plasmon resonance (SPR) spectroscopy, and applied to the construction of cavitand:lipid arrays using the hosts and trehalose vitrified phospholipid vesicles. The selective, dual-mode protein recognition is maintained in the arrays, and can be visualized using SPR imaging.

| S-EPMC6041475 | biostudies-literature

Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms.

Project description:The in vitro deuteroacetylation of histones obtained from biological sources has been used previously in bottom-up mass spectrometry analyses to quantitate the percent of endogenous acetylation of specific lysine sites and/or peptides. In this report, derivatization of unmodified lysine residues on histones is used in combination with high performance mass spectrometry, including combined HPLC MS/MS, to distinguish and quantitate endogenously acetylated isoforms occurring within the same tryptic peptide sequence and to extend this derivatization strategy to other post-translational modifications, specifically methylation, dimethylation and trimethylation. The in vitro deuteroacetylation of monomethylated lysine residues is observed, though dimethylated or trimethylated residues are not derivatised. Comparison of the relative intensities ascribed to the deuteroacetylated and monomethylated species with the deuteroacetylated but unmethylated analog, provides an opportunity to estimate the percent of methylation at that site. In addition to the observed fragmentation patterns, the very high mass accuracy available on the Orbitrap mass spectrometer can be used to confirm the structural isoforms, and in particular to distinguish between trimethylated and acetylated species.

| S-EPMC3289288 | biostudies-literature

Guest recognition in a partially bridged deep cavitand.

Project description:The synthesis of a new deep cavitand partially bridged via disulfide bonds is described. Its thermodynamic and kinetic complexation parameters are compared with those of an unbridged analogue. The disulfide bridges cause deviations in ?H and ?S but result in only small differences in ?G of complexation. The bridges increase the activation barrier for guest dissociation and lead to complexes with enhanced kinetic stability.

| S-EPMC2966534 | biostudies-literature

Deep Cavitand Calixarene-Solubilized Fullerene as a Potential Photodynamic Agent.

Project description:Fullerene has attracted much attention in biomedical research due to its unique physical and chemical properties. However, the hydrophobic nature of fullerene is limited to deploy in the body, given that the biofluids are mainly water. In this study, a water-soluble supramolecular nanoformulation based on a deep cavitand calixarene (SAC4A) and fullerene is developed to overcome the hydrophobicity of fullerene and is used as a potential photodynamic agent. SAC4A solubilizes fullerene very well with a simple grinding method. The significantly increased water solubility of fullerene enables efficient activation of reactive oxygen species. The host-guest strategy to solubilize fullerene can not only provide a new method to achieve water solubility but also expand the biomedical applications of fullerene.

| S-EPMC8327297 | biostudies-literature

Cavitand Decorated Silica as a Selective Preconcentrator for BTEX Sensing in Air.

Project description:The monitoring of benzene and other carcinogenic aromatic volatile compounds at the ppb level requires boosting both the selectivity and sensitivity of the corresponding sensors. A workable solution is the introduction in the devices of preconcentrator units containing molecular receptors. In particular, quinoxaline cavitands (QxCav) resulted in very efficient preconcentrator materials for the BTEX in air to the point that they have been successfully implemented in a commercial sensor. In this work, we report a highly efficient quinoxaline-based preconcentrator material, in which the intrinsic adsorption capacity of the QxCav has been maximized. The new material consists of silica particles covalently coated with a suitable functionalized QxCav derivative (QxCav@SiO2). In this way, all the cavities are exposed to the analyte flux, boosting the performance of the resulting preconcentration cartridge well above that of the pure QxCav. It is noteworthy that the preconcentrator adsorption capacity is independent of the relative humidity of the incoming air.

| S-EPMC9268237 | biostudies-literature

A new, deep quinoxaline-based cavitand receptor for the complexation of benzene.

Project description:We report the synthesis of a new macrocyclic receptor, namely 2,8,14,20-tetra-hexyl-4,24:6,10:12,16:18,22-O,O'-tetra-kis-[2,3-di-hydro-[1,4]dioxino[2,3-g]quinoxalin-7,8-di-yl]resorcin[4]arene, DeepQxCav, obtained by the addition of ethyl-ene glycol di-tosyl-ate to an octa-hydroxy quinoxaline cavitand. A 1:1 supra-molecular complex of this cavitand with benzene has been obtained and analysed through X-ray diffraction analysis. The complex, of general formula C92H88O16N8·C6H6, crystallizes in the space group C2/c, with the cavitand host located about a twofold rotation axis. The benzene guest, which is held inside the cavity by C-H?? inter-actions and dispersion forces, is disordered over two equivalent sites, one in a general position and one lying on a twofold axis. The crystal structure features C-H?O hydrogen bonds and C-H?? inter-actions involving the alkyl chains, the aromatic rings, and the O atoms of the dioxane moiety of the resorcinarene scaffold. The crystal studied was refined as a two-component twin.

| S-EPMC6362646 | biostudies-literature

Spontaneous drying of non-polar deep-cavity cavitand pockets in aqueous solution.

Project description:There are many open questions regarding the hydration of solvent-exposed non-polar tracts and pockets in proteins. Although water is predicted to de-wet purely repulsive surfaces and evacuate crevices, the extent of de-wetting is unclear when ubiquitous van der Waals interactions are in play. The structural simplicity of synthetic supramolecular hosts imbues them with considerable potential to address this issue. To this end, here we detail a combination of densimetry and molecular dynamics simulations of three cavitands, coupled with calorimetric studies of their complexes with short-chain carboxylates. Our results reveal the range of wettability possible within the ostensibly identical cavitand pockets-which differ only in the presence and/or position of the methyl groups that encircle the portal to their non-polar pockets. The results demonstrate the ability of macrocycles to template water cavitation within their binding sites and show how the orientation of methyl groups can trigger the drying of non-polar pockets in liquid water, which suggests new avenues to control guest complexation.

| S-EPMC8170693 | biostudies-literature

A deep cavitand with a fluorescent wall functions as an ion sensor.

Project description:The synthesis and characterization of a deep cavitand bearing a fluorescent benzoquinoxaline wall is reported. Noncovalent host-guest recognition events are exploited to sense small charged molecules including acetylcholine. The cavitand also exhibits an anion dependent change in fluorescence that is used to differentiate halide ions in solution.

| S-EPMC3186209 | biostudies-literature

Readers of histone modifications.

Project description:Histone modifications not only play important roles in regulating chromatin structure and nuclear processes but also can be passed to daughter cells as epigenetic marks. Accumulating evidence suggests that the key function of histone modifications is to signal for recruitment or activity of downstream effectors. Here, we discuss the latest discovery of histone-modification readers and how the modification language is interpreted.

| S-EPMC3131977 | 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