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opencc-by-sa-4.0Mar 2024View details →

Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?

Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?: This data set contains all the experimental raw data, analysis and source files for the final figures reported in the manuscript: "Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?". It is divided into five (1-5) zipped folders, named as the technique used to obtain the data. Each of them, where applicable, consists of three different subfolders (raw data, analysed data, final graph). Read below for more details.   1) ConfocalMicroscopy    1a) Raw_Data: the raw images are reported as .dat and .tif formats, divided into folders (according to date first yymmdd, and within the same day according to composition). Each folder contains a .txt file reporting the experimental details       1b) GUVs_Statistics        - GUVs_Statistics.txt explains how we generated the bar plot shown in Fig. 1E    1c) Final_Graph        - Figure_1B_1D.png is the figure representing figure 1B and 1D        - Figure1E_%ofGUVswithCaMAdsorbptions.csv is the source file x-y of the bar plot shown in figure 1E (% of GUVs which showed adsorption of CaM over the total amount of measured GUVs)         - Where_To_Find_Representative_Images.txt states the folders where the raw images chosen for figure 1 can be found  2) FCS        2a) Raw_Data:         - 1_points: .ptu files         - 2_points: .ht3 files         - Raw_Data_Description.docx which compositions and conditions correspond to which point in the two data sets        2b) Final_Graphs:        - Figure_2A.xlsx contains the x-y source file for figure 2A    2c) Analysis:         - FCS_Fits.xlsx outcome of the global fitting procedure described in the .docx below (each group of points represents a certain composition and calcium concentration, read the Raw_Data_Description.docx in the FCS > Raw_Data)        - Notes_for_FCS_Analysis.docx contains a brief description of the analysis of the autocorrelation curves 3) GPLaurdan        3a) Raw Data: all the spectra are stored in folders named by date (yymmdd_lipidcomposition_Laurdan) and are in both .FS and .txt formats     3b) GP calculations: contains all the .xlsx files calculating the GP values from the raw emission and excitation spectra    3c)  Final_Graphs        - Data_Processing_For_Fig_2D.csv contains the data processing from the GP values calculated from the spectra to the DeltaGP (GP with- GP without CaM) reported in fig. 2D        - Figure_2C_2D.xlsx contains the x-y source file for the figure 2C and 2D 4) LiveCellsImaging     3a) Intensity_Protrusions_vs_Cell_Body:         - contains all the .xlsx files calculating the intensity of the various images. File renamed by date (yymmdd)         - All data in all excel sheets gathered in another Excel file to create a final graph          3b)  Final_Graphs        - Figure_S2B.xlsx contains the x-y source file for the figure S2B 5) LiveCellImaging_Raw_Data: it contains some of the images, which are given in .tif. They are divided by date (yymmdd) and each contains subfolders renamed by sample name, concentration of ionomycin. Within the subfolders, the images are divided into folders distinguishing the data acquired before and after the ionomycin treatment and the incubation time.   6)  211124_BioCev_Imaging_1 folder has the .jpg files of the time laps, these are shown in fig 1A and S2. 7) 211124_BioCev_Imaging_2 and 8) 211124_BioCev_Imaging_3 contain the images of HeLa cells expressing EGFP-CaM after treatment with ionomycin 200 nM (A1) and 1 uM (A2), respectively.  9) SPR    9a) Raw Data:         - SPR_Raw_Data.xlsx x/y exported sensorgrams         - the .jpg files of the software are also reported and named by lipid composition    9b) Final_Graph:         - Fig.2B.xlsx contains the x-y source file for the figure 2B    9c)  Analysis        - SPR_Analysis.xlsx: excel file containing step-by-step (sheet by sheet) how we processed the raw data to obtain the final figure (details explained in the .docx below)        - Analysis of SPR data_notes.docx: read me for detailed explanation

opencc-by-4.0Nov 2021View details →

Reference data and analysis software for "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane"

Reference data set for the single molecule co-tracking analysis presented in "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane". Corresponding author for further inquiries: Prof. Dr. Jacob Piehler University of Osnabrück, Department of Biology/Chemistry, Division of Biophysics, Barbarastr. 11, 49076 Osnabrück, Germany https://www.biophysik.uni-osnabrueck.de/

opencc-by-4.0Jun 2022View details →

A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane

This upload contains files documented in a preprint and a publication. Preprint: https://doi.org/10.1101/2022.03.30.486314 Publication: <a href="https://doi.org/10.1073/pnas.2205425119">https://doi.org/10.1073/pnas.2205425119</a> The files uploaded here are: - Alphafold predictions for VPS13A N-term (a.a. 1-2100) and C-term (a.a. 1021-3174). The .pse file is the pymol structure alignment of the two predicted VPS13A portions, join at aminoacid position D14 with the different representations presented throughout the paper stored as pymol "scenes".  - AlphaFold-Multimer prediction for the interaction between XK and the C-term region of VPS13A is also included. - An excel file containing the tabular data for the graphs in Figures 1G, S2E and 4D.

opencc-by-4.0May 2023View details →

Revealing the lipidome and proteome of Arabidopsis thaliana plasma membrane

This table contains peaks aera values from GC-MS, TLC-GC-MS and LC-MS for characterization of Arabidopsis thaliana plasma membrane. These data were used for Fig. 6, 7, 8, 9 and S1, S2, S3 and S4 of Bahammou et al. 2023: Revealing the lipidome and proteome of Arabidopsis thaliana plasma membrane

opencc-zeroDec 2023View details →

Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein

Here we present NMR and MS data used in article A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein. NMR data contain full set of assignment experiments used to partially assign signals of non-myristoylated wt M-PMV MAPPHis, H-N HSQC spectra or myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and results from TALOS+ program used to calculate the secondary structure of C-terminal part of both mristoylated and non-myristoylated wt MAPPHis. The MS data contain MS data measured both for non-labeled samples of myristoylated M-PMV MAPPHis wt, A79V and I51A mutants and non-myristoylated MAPPHis, as well as data measured on these proteins after deuterium exchange.

opencc-zeroNov 2021View details →

Vesicles clustering around Wdr35-/- cilia lack electron dense decorations although electron-dense clathrin coated vesicles are still observed budding from the mutant plasma membrane (Figure 7- source data 1)

Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits, and demonstrate an accumulation of 'coat-less' vesicles which fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in-situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.

opencc-by-sa-4.0Jul 2024View details →

Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes? - additional data

CaM_Data_Repository_Revision: This folder contains the experimental raw data, analysis and source for the final figures reported in the paper after revision (Open Biology): "Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?". It is divided into five (1-3) folders, named as the technique used to obtain the data. Each of them, where applicable, consists of three different subfolders (raw data, analysed data, final graph). Read below for more details.   1) ConfocalMicroscopy    1a) Raw_Data: the raw images are reported as .dat and .bmp formats, divided into folders (according date first yymmdd, and within the same day according to    composition). Each folder contains a .txt file reporting the experimental details       1b) Final_Graph        - Figure_1E.csv is the new source file x-y of the bar plot shown in figure 1E (% of GUVs which showed adsorption of CaM over the total amount of        measured GUVs) in the revised version of the manuscript        2) DLS    2a) Raw Data:         - DLS_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt          file stored in the same folder         - DLS_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt          file stored in the same folder     2b) Final_Graph:         - Fig.S4B.xlsx contains the x-y source file for the figure S4B        - Fig.S5A.xlsx contains the x-y source file for the figure S5A   3) Z-potential    3a) Raw Data:         - ZetaPotential_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental         details.txt file stored in the same folder         - ZetaPotential_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental         details.txt file stored in the same folder     3b) Final_Graph:         - Fig.S4C.xlsx contains the x-y source file for the figure S4C        - Fig.S5B.xlsx contains the x-y source file for the figure S5B

opencc-by-4.0Nov 2019View details →

Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane

This Dataset contains primary data used for the publication "Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane" published online on 04. November 2019 doi:10.3390/cells8111388 Abstract: T cell activation is immediately followed by internalization of the T cell receptor (TCR). TCR endocytosis is required for T cell activation, but the mechanisms supporting removal of TCR from the cell surface remain incompletely understood. Here we report that TCR endocytosis is linked to the clathrin-independent carrier (CLIC) and GPI-enriched endocytic compartments (GEEC) endocytic pathway. We show that unlike the canonical clathrin cargo transferrin or the adaptor protein Lat, internalized TCR accumulates in tubules shaped by the small GTPase Cdc42 and the Bin/amphiphysin/Rvs (BAR) domain containing protein GRAF1 in T cells. Preventing GRAF1-positive tubules to mature into endocytic vesicles by expressing a constitutively active Cdc42 impairs the endocytosis of TCR, while having no consequence on the uptake of transferrin. Together, our data reveal a link between TCR internalization and the CLIC/GEEC endocytic route supported by Cdc42 and GRAF1.   Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication. Programs we recommend to view the files are: .fcs files:     FlowJo software v10 (Tree Star, Ashland, OR, USA) .lif files:       LAS X v3 (Leica Microsystems, Wetzlar, Germany) .pzfx files:   Prism v7 software (GraphPad, San Diego, CA, USA)   In case this Dataset is updated, new version will be available with doi:10.5281/zenodo.3545842

opencc-by-4.0Aug 2024View details →

N-glycosylation acts as a switch for FGFR1 trafficking between the plasma membrane and nuclear envelope - yet unpublished supplementary data regarding Fig. 1C

Fibroblast growth factor receptor 1 (FGFR1) is a heavily N-glycosylated cell surface receptor tyrosine kinase that transmits signals across the plasma membrane, in response to fibroblast growth factors (FGFs). Balanced FGF/FGFR1 signaling is crucial for the development and homeostasis of the human body, and aberrant FGFR1 is frequently observed in various cancers. In addition to its predominant localization to the plasma membrane, FGFR1 has also been detected inside cells, mainly in the nuclear lumen, where it modulates gene expression. However, the exact mechanism of FGFR1 nuclear transport is still unknown. In this study, we generated a glycosylation-free mutant of FGFR1, FGFR1.GF, and demonstrated that it is localized primarily to the nuclear envelope. We show that reintroducing N-glycans into the D3 domain cannot redirect FGFR1 to the plasma membrane or exclude the receptor from the nuclear envelope. Reestablishment of D2 domain N-glycans largely inhibits FGFR1 accumulation in the nuclear envelope, but the receptor continues to accumulate inside the cell, mainly in the ER. Only the simultaneous presence of N-glycans of the D2 and D3 domains of FGFR1 promotes efficient transport of FGFR1 to the plasma membrane. We demonstrate that while disturbed FGFR1 folding results in partial FGFR1 accumulation in the ER, impaired FGFR1 secretion drives FGFR1 trafficking to the nuclear envelope. Intracellular FGFR1.GF displays a high level of autoactivation, suggesting the presence of nuclear FGFR1 signaling, which is independent of FGF. Using mass spectrometry and proximity ligation assay, we identified novel binding partners of the nuclear envelope-localized FGFR1, providing insights into its cellular functions. Collectively, our data define N-glycosylation of FGFR1 as an important regulator of FGFR1 kinase activity and, most importantly, as a switchable signal for FGFR1 trafficking between the nuclear envelope and plasma membrane, which, due to spatial restrictions, shapes FGFR1 interactome and cellular function.   These data are raw data of Fig. 1C generated by Aleksandra Chorążewska. These data are not present in supplementary data od publication

opencc-zeroNov 2022View details →

Dataset associated with: The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo

mRNA localization and transport are integral in regulating gene expression. In Caenorhabditis elegans' embryos, the maternally inherited mRNA erm-1 (Ezrin/Radixin/Moesin) becomes concentrated in anterior blastomeres. erm-1 mRNA localizes within those blastomeres to the plasma membrane where the essential ERM-1 protein, a membrane-actin linker, is also found. We demonstrate that the localization of erm-1 mRNA to the plasma membrane is translation dependent and requires its encoded N-terminal, membrane-binding (FERM) domain. By perturbing translation through multiple methods, we found that erm-1 mRNA localization at the plasma membrane persisted only if the nascent peptide remained in complex with the translating mRNA. Indeed, re-coding the erm-1 mRNA coding sequence while preserving the encoded amino acid sequence did not disrupt erm-1 mRNA localization, corroborating that the information directing mRNA localization resides within its membrane-binding protein domain. A single-molecule inexpensive fluorescence in situ hybridization screen of 17 genes encoding similar membrane-binding domains identified three plasma membrane-localized mRNAs in the early embryo. Ten additional transcripts showed potential membrane localization later in development. These findings point to a translation-dependent pathway for localization of mRNAs encoding membrane-associated proteins.

opencc-by-4.0Apr 2023View details →

PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid

Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from Arabidopsis thaliana is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.

opencc-zeroMay 2023View details →

Data from: Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair

The maintenance of plasma membrane integrity and a capacity for efficiently repairing damaged membranes are essential for cell survival. Large-scale wounding depletes various membrane components at the wound sites, including phosphatidylinositols, yet little is known about how phosphatidylinositols are generated after depletion. Here, working with our in vivo C. elegans epidermal cell wounding model, we discovered phosphatidylinositol 4-phosphate (PtdIns4P) accumulation and local phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] generation at the wound site. We found that PtdIns(4,5)P2 generation depends on the delivery of PtdIns4P, PI4K, and PI4P 5-kinase PPK-1. In addition, we show that wounding triggers enrichment of the Golgi membrane to the wound site, and that is required for membrane repair. Moreover, genetic and pharmacological inhibitor experiments support that the Golgi membrane provides the PtdIns4P for PtdIns(4,5)P2 generation at the wounds. Our findings demonstrate how the Golgi apparatus facilitates membrane repair in response to wounding and offers a valuable perspective on cellular survival mechanisms upon mechanical stress in a physiological context.

publicNov 2022View details →

Dataset associated with: The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo

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publicDec 2023View details →

Data from: A myristoyl switch at the plasma membrane triggers cleavage and oligomerization of Mason-Pfizer monkey virus matrix protein

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publicNov 2021View details →

Vesicles clustering around Wdr35-/- cilia lack electron dense decorations although electron-dense clathrin coated vesicles are still observed budding from the mutant plasma membrane (Figure 7- source data 1)

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