Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subcellular Dynamic Immunopatterning of Cytosolic Protein Complexes on Microstructured Polymer Substrates.

ABSTRACT: Analysis of protein-protein interactions in living cells by protein micropatterning is currently limited to the spatial arrangement of transmembrane proteins and their corresponding downstream molecules. Here, we present a robust and straightforward method for dynamic immunopatterning of cytosolic protein complexes by use of an artificial transmembrane bait construct in combination with microstructured antibody arrays on cyclic olefin polymer substrates. As a proof, the method was used to characterize Grb2-mediated signaling pathways downstream of the epidermal growth factor receptor (EGFR). Ternary protein complexes (Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified, and we found that EGFR downstream signaling is based on constitutively bound (Grb2:SOS1 and Grb2:Gab1) as well as on agonist-dependent protein associations with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal analysis further revealed significant differences in stability and exchange kinetics of protein interactions. Furthermore, we could show that this approach is well suited to study the efficacy and specificity of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether, this method represents a significant enhancement of quantitative subcellular micropatterning approaches as an alternative to standard biochemical analyses.

SUBMITTER: Hager R

PROVIDER: S-EPMC8630788 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Bioinspired Microstructured Polymer Surfaces with Antireflective Properties.

Project description:Over the years, different approaches to obtaining antireflective surfaces have been explored, such as using index-matching, interference, or micro- and nanostructures. Structural super black colors are ubiquitous in nature, and biomimicry thus constitutes an interesting way to develop antireflective surfaces. Moth-eye nanostructures, for example, are well known and have been successfully replicated using micro- and nanofabrication. However, other animal species, such as birds of paradise and peacock spiders, have evolved to display larger structures with antireflective features. In peacock spiders, the antireflective properties of their super black patches arise from relatively simple microstructures with lens-like shapes organized in tightly packed hexagonal arrays, which makes them a good candidate for cheap mass replication techniques. In this paper, we present the fabrication and characterization of antireflective microarrays inspired by the peacock spider's super black structures encountered in nature. Firstly, different microarrays 3D models are generated from a surface equation. Secondly, the arrays are fabricated in a polyacrylate resin by super-resolution 3D printing using two-photon polymerization. Thirdly, the resulting structures are inspected using a scanning electron microscope. Finally, the reflectance and transmittance of the printed structures are characterized at normal incidence with a dedicated optical setup. The bioinspired microlens arrays display excellent antireflective properties, with a measured reflectance as low as 0.042 ± 0.004% for normal incidence, a wavelength of 550 nm, and a collection angle of 14.5°. These values were obtained using a tightly-packed array of slightly pyramidal lenses with a radius of 5 µm and a height of 10 µm.

| S-EPMC8470586 | biostudies-literature

Reversible Binding Interfaces Made of Microstructured Polymer Brushes.

Project description:The polymer brush architecture of the end-tethered polymer molecules is one of the most widely used efficient methods to regulate interfacial interactions in colloidal systems found in live matter and manufactured materials. Emerging applications of polymer brush structures require solutions to new tasks in the control of interfacial interactions. The rapid development of live cell manufacturing relies on scalable and efficient cell harvesting methods. Stimuli-responsive surfaces made of surface-grafted poly(N-isopropylacrylamide) (PNIPAM) can bind and detach the adherent cell upon changes in temperature and have been used for cell growth and harvesting. The applications are limited by the requirement to satisfy a range of PNIPAM coating characteristics that depend on the dimensions of the integrin complex in the cell membrane and the basal surface. The analysis of the microstructured surfaces, when adhesive and disjoining functions of the microdomains are decoupled, shows that many limitations of PNIPAM one-component coatings can be avoided by using a much broader range of structural characteristics of the microstructured interfaces composed of alternating disjoining PNIPAM domains and adhesive polymeric domains with cell-affinity functional groups. Temperature-controlled reversible adhesion to such microstructured interfaces is studied here experimentally with model systems of solid spherical particles and by employing simulations for solid and soft membranes interacting with the microstructured surfaces to mimic interactions with soft and solid disk-like particles.

| S-EPMC10993409 | biostudies-literature

Revealing Dynamic Protein Acetylation across Subcellular Compartments.

Project description:Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled the cataloging of thousands of sites throughout the cell; however, identifying regulatory acetylation marks have proven to be a daunting task. Knowledge of the kinetics and stoichiometry of site-specific acetylation is an important factor to uncover function. Here, an improved method of quantifying acetylation stoichiometry was developed and validated, providing a detailed landscape of dynamic acetylation stoichiometry within cellular compartments. The dynamic nature of site-specific acetylation in response to serum stimulation was revealed. In two distinct human cell lines, growth factor stimulation led to site-specific, temporal acetylation changes, revealing diverse kinetic profiles that clustered into several groups. Overlap of dynamic acetylation sites among two different human cell lines suggested similar regulatory control points across major cellular pathways that include splicing, translation, and protein homeostasis. Rapid increases in acetylation on protein translational machinery suggest a positive regulatory role under progrowth conditions. Finally, higher median stoichiometry was observed in cellular compartments where active acetyltransferases are well described. Data sets can be accessed through ProteomExchange via the MassIVE repository (ProteomExchange: PXD014453; MassIVE: MSV000084029).

| S-EPMC7427125 | biostudies-literature

Nanotopography Enhances Dynamic Remodeling of Tight Junction Proteins through Cytosolic Liquid Complexes.

Project description:Nanotopographic materials provide special biophysical stimuli that can regulate epithelial tight junctions and their barrier function. Through the use of total internal reflection fluorescence microscopy of live cells, we demonstrated that contact of synthetic surfaces with defined nanotopography at the apical surface of epithelial monolayers increased paracellular permeability of macromolecules. To monitor changes in tight junction morphology in live cells, we fluorescently tagged the scaffold protein zonula occludens-1 (ZO-1) through CRISPR/Cas9-based gene editing to enable live cell tracking of ZO-1 expressed at physiologic levels. Contact between cells and nanostructured surfaces destabilized junction-associated ZO-1 and promoted its arrangement into highly dynamic liquid cytosolic complexes with a 1-5 μm diameter. Junction-associated ZO-1 rapidly remodeled, and we observed the direct transformation of cytosolic complexes into junction-like structures. Claudin-family tight junction transmembrane proteins and F-actin also were associated with these ZO-1 containing cytosolic complexes. These data suggest that these cytosolic structures are important intermediates formed in response to nanotopographic cues that facilitate rapid tight junction remodeling in order to regulate paracellular permeability.

| S-EPMC7606830 | biostudies-literature

Global, quantitative and dynamic mapping of protein subcellular localization.

Project description:Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

| S-EPMC4959882 | biostudies-literature

Rigidity-driven growth and migration of epithelial cells on microstructured anisotropic substrates.

Project description:The physical properties of the cellular environment are involved in regulating the formation and maintenance of tissues. In particular, substrate rigidity appears to be a key factor dictating cell response on culture surfaces. Here we study the behavior of epithelial cells cultured on microfabricated substrates engineered to exhibit an anisotropic stiffness. The substrate consists of a dense array of micropillars of oval cross-section, so that one direction is made stiffer than the other. We demonstrate how such an anisotropic rigidity can induce directional epithelial growth and guide cell migration along the direction of greatest rigidity. Regions of high tractional stress and large cellular deformations within the sheets of cells are concentrated at the edges, in particular at the two poles of the islands along their long axis, in correlation with the orientation of actin stress fibers and focal adhesions. By inducing scattering activity of epithelial cells, we show that isolated cells also migrate along the direction of greatest stiffness. Taken together, these findings show that the mechanical interactions of cells with their microenvironment can be tuned to engineer particular tissue properties.

| S-EPMC1895941 | biostudies-literature

Shape Memory Polyurethane-Based Smart Polymer Substrates for Physiologically Responsive, Dynamic Pressure (Re)Distribution.

Project description:Shape memory polymers (SMPs) are an exciting class of stimuli-responsive smart materials that demonstrate reactive and reversible changes in mechanical property, usually by switching between different states due to external stimuli. We report on the development of a polyurethane-based SMP foam for effective pressure redistribution that demonstrates controllable changes in dynamic pressure redistribution capability at a low transition temperature (?24 °C)-ideally suited to matching modulations in body contact pressure for dynamic pressure relief (e.g., for alleviation or pressure ulcer effects). The resultant SMP material has been extensively characterized by a series of tests including stress-strain testing, compression testing, dynamic mechanical analysis, optical microscopy, UV-visible absorbance spectroscopy, variable-temperature areal pressure distribution, Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray diffraction, differential scanning calorimetry, dynamic thermogravimetric analysis, and 1H nuclear magnetic resonance spectroscopy. The foam system exhibits high responsivity when tested for plantar pressure modulation with significant potential in pressure ulcers treatment. Efficient pressure redistribution (?80% reduction in interface pressure), high stress response (?30% applied stress is stored in fixity and released on recovery), and excellent deformation recovery (?100%) are demonstrated in addition to significant cycling ability without performance loss. By providing highly effective pressure redistribution and modulation when in contact with the body's surface, this SMP foam offers novel mechanisms for alleviating the risk of pressure ulcers.

| S-EPMC6761750 | biostudies-literature

Gold nanoparticle-polymer/biopolymer complexes for protein sensing.

Project description:Nanoparticle-based sensor arrays have been used to distinguish a wide range of biomolecular targets through pattern recognition. Such biosensors require selective receptors that generate a unique response pattern for each analyte. The tunable surface properties of gold nanoparticles make these systems excellent candidates for the recognition process. Likewise, the metallic core makes these particles fluorescence superquenchers, facilitating transduction of the binding event. In this report we analyze the role of gold nanoparticles as receptors in differentiating a diversity of important human proteins, and the role of the polymer/biopolymer fluorescent probes for transducing the binding event. A structure-activity relationship analysis of both the probes and the nanoparticles is presented, providing direction for the engineering of future sensor systems.

| S-EPMC4102399 | biostudies-literature

Three-Dimensional, Bifunctional Microstructured Polymer Hydrogels Made from Polyzwitterions and Antimicrobial Polymers.

Project description:Biofilm-associated infections of medical devices are a global problem. For the prevention of such infections, biomaterial surfaces are chemically or topographically modified to slow down the initial stages of biofilm formation. In the bifunctional material here presented, chemical and topographical cues are combined, so that protein and bacterial adhesion as well as bacterial proliferation are effectively inhibited. Upon changes in the surface topography parameters and investigation of the effect of these changes on bioactivity, structure-property relationships are obtained. The target material is obtained by microcontact printing (μCP), a soft lithography method. The antimicrobial component, poly(oxanorbornene)-based synthetic mimics of an antimicrobial peptide (SMAMP), was printed onto a protein-repellent polysulfobetaine hydrogel, so that bifunctional 3D structured polymer surfaces with 1, 2, and 8.5 μm spacing are obtained. These surfaces are characterized with fluorescence microscopy, surface plasmon resonance spectroscopy, atomic force microscopy, and contact angle measurements. Biological studies show that the bifunctional surfaces with 1 and 2 μm spacing are 100% antimicrobially active against Escherichia coli and Staphylococcus aureus, 100% fibrinogen-repellent, and nontoxic to human gingival mucosal keratinocytes. At 8.5 μm spacing, the broad-band antimicrobial activity and the protein repellency are compromised, which indicates that this spacing is above the upper limit for effective simultaneous antimicrobial activity and protein repellency of polyzwitterionic-polycationic materials.

| S-EPMC7611509 | biostudies-literature

Detecting temporal protein complexes from dynamic protein-protein interaction networks.

Project description:BackgroundProteins dynamically interact with each other to perform their biological functions. The dynamic operations of protein interaction networks (PPI) are also reflected in the dynamic formations of protein complexes. Existing protein complex detection algorithms usually overlook the inherent temporal nature of protein interactions within PPI networks. Systematically analyzing the temporal protein complexes can not only improve the accuracy of protein complex detection, but also strengthen our biological knowledge on the dynamic protein assembly processes for cellular organization.ResultsIn this study, we propose a novel computational method to predict temporal protein complexes. Particularly, we first construct a series of dynamic PPI networks by joint analysis of time-course gene expression data and protein interaction data. Then a Time Smooth Overlapping Complex Detection model (TS-OCD) has been proposed to detect temporal protein complexes from these dynamic PPI networks. TS-OCD can naturally capture the smoothness of networks between consecutive time points and detect overlapping protein complexes at each time point. Finally, a nonnegative matrix factorization based algorithm is introduced to merge those very similar temporal complexes across different time points.ConclusionsExtensive experimental results demonstrate the proposed method is very effective in detecting temporal protein complexes than the state-of-the-art complex detection techniques.

| S-EPMC4288635 | 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