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16 results for “lipid binding”
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
<p>Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?:</p> <p><br>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. </p> <p>1) ConfocalMicroscopy</p> <p> 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 </p> <p> 1b) GUVs_Statistics<br> - GUVs_Statistics.txt explains how we generated the bar plot shown in Fig. 1E</p> <p> 1c) Final_Graph<br> - Figure_1B_1D.png is the figure representing figure 1B and 1D<br> - 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) <br> - Where_To_Find_Representative_Images.txt states the folders where the raw images chosen for figure 1 can be found </p> <p>2) FCS<br> <br> 2a) Raw_Data: <br> - 1_points: .ptu files <br> - 2_points: .ht3 files <br> - Raw_Data_Description.docx which compositions and conditions correspond to which point in the two data sets<br> <br> 2b) Final_Graphs:<br> - Figure_2A.xlsx contains the x-y source file for figure 2A</p> <p> 2c) Analysis: <br> - 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)<br> - Notes_for_FCS_Analysis.docx contains a brief description of the analysis of the autocorrelation curves</p> <p>3) GPLaurdan<br> <br> 3a) Raw Data: all the spectra are stored in folders named by date (yymmdd_lipidcomposition_Laurdan) and are in both .FS and .txt formats </p> <p> 3b) GP calculations: contains all the .xlsx files calculating the GP values from the raw emission and excitation spectra</p> <p> 3c) Final_Graphs<br> - 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<br> - Figure_2C_2D.xlsx contains the x-y source file for the figure 2C and 2D</p> <p>4) LiveCellsImaging </p> <p> 3a) Intensity_Protrusions_vs_Cell_Body: <br> - contains all the .xlsx files calculating the intensity of the various images. File renamed by date (yymmdd) <br> - All data in all excel sheets gathered in another Excel file to create a final graph </p> <p> 3b) Final_Graphs<br> - Figure_S2B.xlsx contains the x-y source file for the figure S2B</p> <p>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.</p> <p> </p> <p>6) 211124_BioCev_Imaging_1 folder has the .jpg files of the time laps, these are shown in fig 1A and S2.</p> <p>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. </p> <p><br>9) SPR</p> <p> 9a) Raw Data: <br> - SPR_Raw_Data.xlsx x/y exported sensorgrams <br> - the .jpg files of the software are also reported and named by lipid composition</p> <p> 9b) Final_Graph: <br> - Fig.2B.xlsx contains the x-y source file for the figure 2B</p> <p> 9c) Analysis<br> - 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)<br> - Analysis of SPR data_notes.docx: read me for detailed explanation</p>
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain
Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"
<p><strong>Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"</strong></p> <p>The dataset contains the following folders:</p> <p>- number_of_contacts: files with the number of contacts between the rim domains of LukF and Hlg2 and the membrane, for different bilayer compositions (Fig. 2).</p> <p>- binding_events: files with the duration of the time interavals in which LukF and Hlg2 are bound to the membrane, and the scripts used to compute for each system the number of binding/unbinding events and the average membrane residence time (Fig. 3).</p> <p>- electrostatic_potential: files of the surface electrostatic potential produced with the adaptive Poisson-Boltzmann solver and used for visualization with Chimera (Fig. 4).</p> <p>- angles: files with the angle values computed between the protein axis and the z-axis of the simulation box (Fig. 5).</p> <p>- contacts_per_residue: files with the number of frames in which each protein residue is in contact with the membrane, with respect to the total number of frames in which the rim domain interacts with the bilayer (Fig. 5).</p> <p>- distance_protein_membrane: files with the minimum distance between the protein and the membrane (Fig. 6).</p> <p>- binding_sites: file produced by PyLipid with relevant information on the main DOPC binding sites identified in LukF.</p> <p>- min_distance_per_residue: files with the minimum distance between each protein residue and the membrane, computed at the binding steps (Fig. S5).</p>
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes? - additional data
<p>CaM_Data_Repository_Revision:<br>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. </p> <p>1) ConfocalMicroscopy</p> <p> 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 </p> <p> 1b) Final_Graph<br> - 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<br> <br>2) DLS</p> <p> 2a) Raw Data: <br> - 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 <br> - 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 </p> <p> 2b) Final_Graph: <br> - Fig.S4B.xlsx contains the x-y source file for the figure S4B<br> - Fig.S5A.xlsx contains the x-y source file for the figure S5A </p> <p>3) Z-potential</p> <p> 3a) Raw Data: <br> - 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 <br> - 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 </p> <p> 3b) Final_Graph: <br> - Fig.S4C.xlsx contains the x-y source file for the figure S4C<br> - Fig.S5B.xlsx contains the x-y source file for the figure S5B </p> <p> </p> <p> </p>
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>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 <em>Arabidopsis thaliana </em>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.</p>
Data from: Force transduction and lipid binding in MscL: a continuum-molecular approach
The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, and identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10–13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.
Data from: Force transduction and lipid binding in MscL: a continuum-molecular approach
Open the record for dataset details and reuse information.
The kinase GSK-3 alters the repertoire of RNA binding proteins present on lipid metabolism transcripts leading to altered expression in the C. elegans nervous system
GEO Series GSE286246. Caenorhabditis elegans. 8 samples. Type: Other.
Identification of lipid-binding lncRNAs in triple-negative breast cancer
GEO Series GSE92414. Homo sapiens. 2 samples. Type: Expression profiling by array.
The kinase GSK-3 alters the repertoire of RNA binding proteins present on lipid metabolism transcripts leading to altered expression in the C. elegans nervous system
GEO Series GSE286247. Caenorhabditis elegans. 6 samples. Type: Expression profiling by high throughput sequencing.
Loss of G protein pathway suppressor 2 in human adipocytes triggers lipid remodeling through upregulation of ATP binding cassette subfamily G member 1
GEO Series GSE152517. Homo sapiens. 60 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Suppression of asthmatic phenotype and altered lipid metabolism in mice lacking zona pellucida binding protein 2
GEO Series GSE98513. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease associated variant that regulates PPAP2B expression through altered C/EBP-beta binding
GEO Series GSE54975. Homo sapiens. 31 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array.
DNA G-quadruplex structure participates in regulation of lipid metabolism through Acyl-CoA binding protein
GEO Series GSE201939. Homo sapiens. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Senotoxins target senescence via lipid binding specificity, ion imbalance and lipidome remodelling.
GEO Series GSE290509. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Chemicals targeting Lipid binding domain (LBD) of 38γ
GEO Series GSE182484. Homo sapiens. 4 samples. Type: Expression profiling by array.
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