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22 results for “plasma 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>
The state-of-the-art machine learning model for Plasma Protein Binding Prediction: computational modeling with OCHEM and experimental validation
<p><span>Institute of Materia Medica, Chinese Academy of Medical Sciences purchased 10,000 ChemDiv databases.</span></p>
Binding and sequestration of poison frog alkaloids by a plasma globulin
<p><span>Alkaloids are important bioactive molecules throughout the natural world, and in many animals, they serve as a source of chemical defense against predation. Dendrobatid poison frogs bioaccumulate alkaloids from their diet to make themselves toxic or unpalatable to predators. Despite the proposed roles of plasma proteins as mediators of alkaloid trafficking and bioavailability, the responsible proteins have not been identified. We use chemical approaches to show that a ~50 kDa plasma protein is the principal alkaloid binding molecule in blood from poison frogs. Proteomic and biochemical studies establish this plasma protein to be liver-derived alkaloid-binding globulin (ABG) that is a member of the serine-protease inhibitor (serpin) family. In addition to alkaloid binding activity, ABG sequesters and regulates the bioavailability of "free" plasma alkaloids <em>in vitro</em>. Unexpectedly, ABG is not related to saxiphilin or albumin but instead exhibits sequence and structural homology to mammalian hormone carriers and amphibian biliverdin binding proteins. Alkaloid-binding globulin (ABG) represents a new small molecule binding functionality in serpin proteins, a novel mechanism of plasma alkaloid transport in poison frogs, and more broadly points towards serpins acting as tunable scaffolds for small molecule binding and transport across different organisms. </span></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>
Dataset associated with: The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo
<p>mRNA localization and transport are integral in regulating gene expression. In <em>Caenorhabditis</em> <em>elegans'</em> 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.</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>
Low Plasma Mannose Binding Lectin (p-MBL) Level is a Risk Factor for Recurrent Pregnancy Loss (RPL)
ClinicalTrials.gov study NCT04017754. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Dataset associated with: The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo
Open the record for dataset details and reuse information.
Binding and sequestration of poison frog alkaloids by a plasma globulin
Open the record for dataset details and reuse information.
Polypropylene and polystyrene may be less thrombogenic than a commercial non-binding surface under plasma-free conditions
<p>Trained Ilastik model used to quantification of survace coverage by platelets is included along with python scripts and ImageJ macros.</p> <p>Raw data representing platelet coverage are inclued in xls file.</p>
Plasma Protein Binding and PK/PD of Total and Unbound Temocillin Non-ICU Patients
ClinicalTrials.gov study NCT03557840. IPD Sharing: NO. Countries: 1. Publications: 21.
This Study Will Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding In Brain Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT01258751. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Plasma Protein Binding Characteristics of Voriconazole
ClinicalTrials.gov study NCT01812473. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Next generation sequencing of antibody heavy chain genes that bind to the hapten NP in sorted memory cells and long-lived plasma cells isolated from mice immunized orally with NP-CT
GEO Series GSE84698. Mus musculus. 15 samples. Type: Other.
To Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding in Lung Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT02017730. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Effect of Albumin Infusion on Oxidative Albumin Modification, Albumin Binding Capacity and Plasma Thiol Status
ClinicalTrials.gov study NCT03214796. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
To Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding In Brain Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT01253655. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Phase 0 Study in Healthy, Hepatic and Renal Impaired Subjects to Obtain Plasma for Lenvatinib Protein Binding
ClinicalTrials.gov study NCT02998775. IPD Sharing: NO. Countries: 1. Publications: 0.
To Evaluate The Relationship Between Plasma Drug Levels And Receptor Binding In Brain Using PET (Positron Emission Tomography) In Healthy Volunteers
ClinicalTrials.gov study NCT01173757. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Association Between Plasma Level of Mannose Binding Lectin and Human Reproduction
ClinicalTrials.gov study NCT05169541. IPD Sharing: YES. Countries: 1. Publications: 0.
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