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2,216 results for “membrane”
Data from: Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair
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Maintaining local alkalinity of CO-electroreduction full cell by silica-confined electrocatalysts in membrane electrode assembly
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Data from: Conditional requirement for dimerization of the membrane-binding module for BTK signaling in lymphocyte cell lines
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Data from: Phagolysosomes break down the membrane of a non-apoptotic corpse independent of macroautophagy
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Data from: Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations
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Data from: Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics
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Biomasses, starch content, cell membrane leakage and phenology of established diploids and tetraploids and synthetic neotetraploids of Jasione maritima var. maritima
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Simulations of single-protein membranes
<p>Nine simulations, each with a single copy of a single protein (1–7,A,B) and 400 DPPC lipids per protein per leaflet. The simulations are performed using the coarse-grained Martini model with scaled-down protein–protein interactions. These systems are described carefully in:</p> <p>M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758</p> <p>The topologies for proteins A&B are included in https://doi.org/10.5281/zenodo.3572241, whereas other ones can be obtained from: https://doi.org/10.5281/zenodo.846428</p> <p> </p>
Simulations of crowded membranes
<p>Nine simulations, each with nine copies of a single protein (1–7,A,B) and 50 DPPC lipids per protein per leaflet. The simulations are performed using the coarse-grained Martini model with scaled-down protein–protein interactions. These systems are described carefully in:</p> <p>M. Javanainen, H. Martinez-Seara, R. Metzler, and I. Vattulainen; Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett., 2017, 8 (17), pp 4308–4313, DOI: 10.1021/acs.jpclett.7b01758</p> <p>The topologies for proteins A&B are included in this upload, whereas other ones can be obtained from: https://doi.org/10.5281/zenodo.846428</p>
Simulations of DLPC, DOPC, and DEPC membranes
<p>Simulations of three different lipid bilayers using the CHARMM36 lipid model. The bilayers were built using CHARMM-GUI and simulated for 500 ns using Gromacs 2019. The systems contain 200 lipids (DLPC, DOPC, or DEPC), 50 lipids per water, and 130 mM NaCl. For each simulation, the run input file (tpr), topology (top), index (ndx), trajectory (xtc), log file (log), energy file (edr), continue point (cpt), and the final structure (gro) are given. The topology refers to the Gromacs-compatible CHARMM36 force field, available at http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and to other itp files provided in this upload. The simulation parameters are given in the md.mdp file.</p>
Large membranes crowded with proteins at different temperatures
<p>Simulation data for crowded coarse-grained (Martini) membranes with 36 proteins per system. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 3600 lipids in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. smaller simulations of the same system are uploaded to DOI:10.5281/zenodo.3604282 and DOI:10.5281/zenodo.3604289</p> <p>.</p>
Simulations of a membrane with a dilute concentration of proteins in different system sizes
<p>Simulations of a dilute (400 lipids per protein per leaflet) DPPC membranes with seven types of embedded proteins. The systems are a 50% smaller (S) and 4 times larger (L) versions of the lp400 simulation in the upload: DOI:10.5281/zenodo.846428. Topologies and simulation parameters are identical to those in that upload.</p>
Medium membranes crowded with proteins at different temperatures
<p>Simulation data for crowded coarse-grained (Martini) membranes with 9 proteins per system. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 900 lipids in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller and larger simulations of the same system are uploaded to DOI:10.5281/zenodo.3604282 and DOI:10.5281/zenodo.3604293</p> <p>.</p>
Large membranes with a single protein at different temperatures
<p>Simulation data for coarse-grained (Martini) membranes containing a single protein. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 7200 lipids (3600 per leaflet) in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller simulaions with a single protein and 800 lipids (400 per leaflet) are at 315 K are available at DOI:10.5281/zenodo.3572299 and at other temperatures at 10.5281/zenodo.3604448. Medium simulations with 3200 lipids (1600 per leaflet) are available at DOI:10.5281/zenodo.3604687</p>
Medium membranes with a single protein at different temperatures
<p>Simulation data for coarse-grained (Martini) membranes containing a single protein. Nomenclature follows that in the paper (CITATION TO BE ADDED), where also all simulation details are found. Simulations are performed at 4 temperatures (300, 315, 330, and 345 K), and there are a total of 3200 lipids (1600 per leaflet) in the systems. The topology and index files are common for all simulations. The simulation parameters follow DOI:10.5281/zenodo.846428, and the required topologies can also be obtained from that upload. Smaller simulaions with a single protein and 800 lipids (400 per leaflet) are at 315 K are available at DOI:10.5281/zenodo.3572299 and at other temperatures at 10.5281/zenodo.3604448. Larger simulations with 7200 lipids (3600 per leaflet) are available at DOI:10.5281/zenodo.3604731</p> <p> </p>
Simulation of POPC:POPE 1:1 membrane with the Slipids force field
<p>A POPC:POPE 1:1 bilayer with 100 lipids per leaflet is simulated for 300 ns using the Slipids model and Gromacs simulation engine version 2019.4. The trajectory (.xtc) is saved every 100ps. The simulation parameters (.mdp), the energy file (.edr), the continue point to extend the simulation (.cpt), the run input parameters (.tpr), and the final structure (.gro) are also given. The lipid topologies (.itp) are provided, and the Slipids force field is available at http://www.fos.su.se/~sasha/SLipids/</p>
Suspended photonic crystal membranes in AlGaAs heterostructures for integrated multi-element optomechanics
<p>The figures in [Sushanth Kini Manjeshwar et.al (arXiv:2004.12454)] were produced with the data stored here. The data were produced by the provided scripts. Please read the Readme.txt for the overview of the structure of the data and how to use the scripts to re-generate the data or use it to produce new data.</p>
Data: An ESCRT-III polymerization sequence drives membrane deformation and fission
<p>Raw data to "an ESCRT-III polymerization sequence drives membrane deformation and fission"</p>
Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity
Recently evolved alleles of Apolipoprotein L-1 (APOL1) provide increased protection against African trypanosome parasites while also significantly increasing the risk of developing kidney disease in humans. APOL1 protects against trypanosome infections by forming ion channels within the parasite, causing lysis. While the correlation to kidney disease is robust, there is little consensus concerning the underlying disease mechanism. We show in human cells that the APOL1 renal risk variants have a population of active channels at the plasma membrane, which results in an influx of both Na+ and Ca2+. We propose a model wherein APOL1 channel activity is the upstream event causing cell death, and that the activate-state, plasma membrane-localized channel represents the ideal drug target to combat APOL1-mediated kidney disease.
Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
<p>We report all-atom molecular dynamics simulations of physiologically composed asymmetric bilayers containing phosphoinositides in the presence of monovalent and divalent cations. We have characterized the molecular mechanism by which these divalent cations interact with phosphoinositides. Calcium desolvates more readily, consistent with single-molecule calculations, and forms a network of ionic-like bonds that serve as a "molecular glue'' that allows a single ion to coordinate with up to three phosphatidylinositol-(4,5)-bisphosphate lipids. The phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and neither does PI(4,5)P2 in the presence of Mg. The resulting network of Ca-mediated lipid-lipid bonds grows to span the entire simulation space and therefore has implications for the lateral distribution of phosophoinositides in the bilayer. We observe context-specific differences in lipid diffusion rates, lipid surface densities, and bilayer structure. The molecular-scale delineation of ion-lipid arrangements reported here provides insight into similar nanocluster formation induced by peripheral proteins to regulate the formation of functional signaling complexes on the membrane.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.