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2,216 results for “membrane”
NMR data in 'Ca2+-dependent release of Synaptotagmin-1 from the SNARE complex on phosphatidylinositol 4,5-bisphosphate-containing membranes' by Voleti, Jaczynska and Rizo, eLife 2020
<p>The Ca<sup>2+</sup> sensor synaptotagmin-1 and the SNARE complex cooperate to trigger neurotransmitter release. Structural studies elucidated three distinct synaptotagmin-1-SNARE complex binding modes involving 'polybasic', 'primary' and 'tripartite' interfaces of synaptotagmin-1. We investigated these interactions using NMR and fluorescence spectroscopy. Synaptotagmin-1 binds to the SNARE complex through the polybasic and primary interfaces in solution. Ca<sup>2+</sup>-free synaptotagmin-1 binds to SNARE complexes anchored on PIP<sub>2</sub>-containing nanodiscs. R398Q/R399Q and E295A/Y338W mutations at the primary interface, which strongly impair neurotransmitter release, disrupt and enhance synaptotagmin-1-SNARE complex binding, respectively. Ca<sup>2+</sup> induces tight binding of synaptotagmin-1 to PIP<sub>2</sub>-containing nanodiscs, releasing synaptotagmin-1-SNARE interactions. Specific effects of mutations in the polybasic region on Ca<sup>2+</sup>-dependent synaptotagmin-1-PIP<sub>2</sub>-membrane interactions correlate with their effects on release. Our data suggest that synaptotagmin-1 binds to the SNARE complex through the primary interface and that Ca<sup>2+</sup> releases this interaction, inducing PIP<sub>2</sub>/membrane binding and allowing cooperation between synaptotagmin-1 and the SNAREs in membrane fusion to trigger release.</p>
RNA-Seq - membrane-type 1 matrix metalloproteinase
<p>Membrane-type 1 matrix metalloproteinase (MT1-MMP, MMP-14), a transmembrane proteinase with a short cytoplasmic tail, is a major effector of extracellular matrix (ECM) remodeling. Genetic silencing of MT1-MMP in mouse (<i>Mmp14<sup>-/-</sup></i>) and man causes dwarfism, osteopenia, arthritis and lipodystrophy, abnormalities ascribed to defective collagen turnover. We have previously shown non-proteolytic functions of MT1-MMP mediated by its cytoplasmic tail, where the unique tyrosine (Y573) controls intracellular signaling. The Y573D mutation blocks TIMP2/MT1-MMP-induced Erk and Akt signaling without affecting proteolytic activity. Here we report that a mouse with the MT1-MMP Y573D mutation (<i>Mmp14<sup>Y573D/Y573D</sup></i>) shows abnormalities similar to, but also different from those of <i>Mmp14<sup>-/-</sup></i> mice. Skeletal stem cells (SSC) of <i>Mmp14<sup>Y573D/Y573D</sup></i> mice show defective differentiation consistent with the mouse phenotype, which is rescued by wild-type SSC transplant. These results provide the first <i>in vivo</i> demonstration that MT1-MMP modulates bone, cartilage and fat homeostasis by controlling SSC differentiation through a mechanism independent of proteolysis.</p>
SIRAH-CoV2 initiative: Membrane embedded SARS-CoV-2 ORF3a (PDB id:6XDC)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the SARS-CoV2 ORF3a dimeric transmembrane protein (PDB id: 6XDC, Bioassembly 1) embedded in a membrane patch containing POPE, POPC, and POPS phospholipids in a 2:1:1 proportion. Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00435">Barrera et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The files contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com. Additionally, </p> <p>The files 6xdc_SIRAHcg_rawdata_0-2us.tar, 6xdc_SIRAHcg_rawdata_2-4us.tar, 6xdc_SIRAHcg_rawdata_4-6us.tar, 6xdc_SIRAHcg_rawdata_6-8us.tar, and 6xdc_SIRAHcg_rawdata_8-10us.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6XDC_SIRAHcg_10us_prot-memb_skip10ns.tar contains only the protein and phospholipids´ coordinates, with one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6xdc_SIRAHcg_10us_prot-memb_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6xdc_SIRAHcg_prot-memb.prmtop 6xdc_SIRAHcg_prot-memb.ncrst 6xdc_SIRAHcg_10us_prot-memb_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Results from: Angiogenic property of silk fibroin scaffolds with adipose-derived stem cells on chick chorioallantoic membrane
<p>Angiogenesis is a key step in tissue regeneration and repair. Biomaterials that allow or promote angiogenesis are thus beneficial. In this study, angiogenic properties of salt-leached silk fibroin (SF) scaffolds seeded with human adipose stem cells (hADSCs) were studied using chick chorioallantoic membrane (CAM) as a model. The hADSC-seeded SF scaffolds (SF-hADSC) with porosity of 77.34 ± 6.96 % and pore diameter of 513.95 ± 4.99 µm were implanted on CAM of chick embryos that were on embryonic day 8 (E8) of development. The SF-hADSC scaffolds induced a spoke-wheel pattern of capillary network indicative of angiogenesis, which was evident since E11. Moreover, ingrowth of blood vessels into the scaffolds was seen in histological sections. The unseeded scaffolds induced the same extent of angiogenesis later on E14. In contrast, the control group could not induce angiogenesis to the same extent even as late. <i>In vitro</i> cytotoxicity tests and <i>in vivo</i> angioirritative study reaffirmed the biocompatibility of the scaffolds. This work highlighted that the biocompatible SF-hADSC scaffolds accelerates angiogenesis, and hence they can be a promising biomaterial for regeneration of tissues that require angiogenesis.</p>
Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress
<p>The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM's unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin's LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.</p>
Simulations of POPC membranes of various shapes
<p>Simulations of POPC membranes in 1) <strong>budded</strong> shape with Gaussian curvature and 2) <strong>wave</strong> shape with mean curvature but no Gaussian curvature and with two wavelengths ("long" and "short"), and 3) a freely <strong>fluctuating</strong> membrane.</p> <p>Simulations were performed using GROMACS simulation engine (DOI: 10.1016/j.softx.2015.06.001 ) and the Martini 2 force field ( DOI:10.1021/jp071097f ). The budded and wavy geometries generated using BUMPy ( DOI: 10.1021/acs.jctc.8b00765 ) are maintained using restrained dummy particles that repel lipid acyl chains</p> <p>All input and output files are provided for each simulation, and the cpt files allow to extend the simulations. Additionally, topologies (in the TOP.tar archive) and simulation parameters (md.mdp) are provided.</p> <p>Some of the simulations have been used in DOI: 10.1101/2020.09.23.310086 and DOI: 10.26434/chemrxiv-2021-6wksn</p>
FIGURE 5. Pelvic disc anterior membrane A in Checklist of gobies (Teleostei: Gobiidae) of the Mediterranean Sea and a key for species identification
FIGURE 5. Pelvic disc anterior membrane A) absent, B) and C) present. Pelvic disc anterior membrane B) without lateral lobes and C) with lateral lobes. Absence of anterior membrane in A), presence of anterior membrane in B) and lateral lobe in C) marked with grey arrow. Pelvic disc anterior membrane height (a) in midline and the length of spinous ray (b) in red. Drawing by M. Kovačić.
Molecular Simulations of Lipid Membrane Partitioning and Translocation by Bacterial Quorum Sensing Modulators
<p>All simulation data and analysis tools for regenerating results from the journal paper:</p> <p>T. Jin, S. J. Patel, and R. C. Van Lehn. “Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators.” <em>PLOS ONE</em>, <strong>accepted.</strong></p>
Fluorescent Membrane Tension Probes for Early Endosomes
<p><strong>Table of contents</strong></p> <p>1. Synthesis and Characterization</p> <p>1.1. Compounds <strong>1</strong>,<strong> 3</strong>,<strong> 4</strong>,<strong> 6</strong>,<strong> 7</strong>,<strong> 9</strong>,<strong> 10</strong>, <strong>11</strong>,<strong> 12</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> <li>HRMS</li> </ul> <p>1.2. Compounds <strong>15</strong>,<strong> 17</strong>,<strong> 19</strong>,<strong> 24</strong>,<strong> 1’</strong>,<strong> 3’</strong>,<strong> 5’</strong>,<strong> 7’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> <li>ESI-MS</li> </ul> <p>1.3. Compounds <strong>21</strong>,<strong> 23</strong>,<strong> 26</strong>,<strong> 8’</strong>,<strong> 10’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR</li> <li>LC-MS</li> <li>IR</li> </ul> <p>2. p<em>K</em><sub>a</sub> Determination</p> <p>2.1. Titration of <strong>32</strong>,<strong> 35</strong>,<strong> 36</strong> for the determination of the correction function</p> <ul> <li>Lab Book Page</li> <li>NMR</li> </ul> <p>2.2. Titration of Model Compounds <strong>1’</strong> – <strong>10’</strong></p> <ul> <li>Lab Book Page</li> <li>NMR </li> </ul> <p>3. Co-Localization with EGF</p> <p>4. Automated Microscopy</p> <p>5. FLIM Imaging</p> <p>6. FLIM of Early Endosomes</p>
Figures of Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes
<p>Figures of the article "Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes"</p>
Data from: Kin discrimination and outer membrane exchange in Myxococcus xanthus: a comparative analysis among natural isolates
Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer-membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer-membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and inter-strain antagonisms. A large proportion of predicted TraA functional diversity documented among global isolates is contained within the cm-scale population. We find evidence of balancing selection on the PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMI kin discrimination is not generally caused by TraA dissimilarity. Finally, it has been proposed that inter-strain antagonisms might be caused by OME-mediated toxin transfer. However, we find that most strain pairs exhibiting strong antagonisms are predicted to be incapable of OME due to TraA dissimilarity. Overall, our results suggest that documented patterns of kin discrimination in a defined natural population of M. xanthus are not causally related to the degree of TraA relatedness among interactants.
Data from: A double-sided microscope to realize whole-ganglion imaging of membrane potential in the medicinal leech
Studies of neuronal network emergence during sensory processing and motor control are greatly promoted by technologies that allow us to simultaneously record the membrane potential dynamics of a large population of neurons in single cell resolution. To achieve whole-brain recording with the ability to detect both small synaptic potentials and action potentials, we developed a voltage-sensitive dye (VSD) imaging technique based on a double-sided microscope that can image two sides of a nervous system simultaneously. We applied this system to the segmental ganglia of the medicinal leech Hirudo verbana. Double-sided VSD imaging enabled simultaneous recording of membrane potential events from almost all of the identifiable neurons. Using data obtained from double-sided VSD imaging we analyzed neuronal dynamics in both sensory processing and generation of behavior and constructed functional maps for identification of neurons contributing to these processes.
Data from: Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity
Antarctic notothenioid fishes are highly stenothermal, yet their tolerance for warming is species-dependent. Because a body of literature points to the loss of cardiac function as underlying thermal limits in ectothermic animals, we investigated potential relationships among properties of ventricular mitochondrial membranes in notothenioids with known differences in both cardiac mitochondrial metabolism and organismal thermal tolerance. Fluidity of mitochondrial membranes was quantified by fluorescence depolarization for the white-blooded Chaenocephalus aceratus and the red-blooded Notothenia coriiceps. In these same membranes, lipid compositions and products of lipid peroxidation, the latter of which can disrupt membrane order, were analyzed in both species and in a second icefish, Pseudochaenichthys georgianus. Mitochondrial membranes from C. aceratus were significantly more fluid than those of the more thermotolerant species N. coriiceps (P < .0001). Consistent with this, ratios of total phosphatidylethanolamine (PE) to total phosphatidylcholine (PC) were lower in membranes from both species of icefishes, compared to those of N. coriiceps (P < .05). However, membranes of N. coriiceps displayed a greater unsaturation index (P < .0001). No differences among species were found in membrane products of lipid peroxidation. With rising temperatures, greater contents of PC in mitochondrial membranes from ventricles of icefishes are likely to promote membrane hyperfluidization at a lower temperature than for cardiac mitochondrial membranes from the red-blooded notothenioid. We propose that physical and chemical properties of the mitochondrial membranes may contribute to some of the observed differences in thermal sensitivity of physiological function among these species.
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine
<p>Simulation files for POPC lipid membrane with Charmm36 force field without NBFIX for Gromacs MD simulation engine</p> <p>NaCl concentration is 730 mM.</p> <p>The goal was to study the effect of salt on the order <br /> parameters of the lipid head group and the glycerol <br /> backbone for the NMRlipids project, see <br /> http://nmrlipids.blogspot.fi for more information.</p>
Simulation files for DPPC lipid membrane with Slipids force field for Gromacs MD simulation engine
<p>the files denoted with 350 resp 700 resp 1000 have NaCl concentrations of 850 resp 1750 resp 2570 mM.</p> <p> </p> <p>The goal was to study the effect of salt on the order parameters of the lipid head group and the glycerol backbone for the NMRlipids project, see http://nmrlipids.blogspot.fi for more information.</p>
Inputs and outputs for polyamide membrane
<p>LAMMPS input files and modified LAMMPS version for constructing coarse-grained polyamide membranes via interfacial polymerisation. </p> <p>LAMMPS input files for equilibrating atomistic polyamide membranes. Also included are output configurations in LAMMPS data format. </p>
Confined diffusion of nanoparticles inserted into a diblock polymer membrane captured by fluorescence microscopy
<p>The membrane average pore size was 1µm with a standard deviation of 0.25µm. The video was record by 50 FPS. For more information please see </p> <p>Haramagatti CR, Schacher FH, Müller AHE, Köhler J. Diblock copolymer<br> membranes investigated by single-particle tracking. Phys Chem Chem Phys.<br> 2011;13(6):2278–2284. doi:10.1039/c0cp01658f</p>
FIGURES 16–20. Telegeusis spp., membranous wing. 16. T in Five new species of Telegeusis Horn, 1895 (Coleoptera: Telegeusidae) from Mexico, with a key to the species
FIGURES 16–20. Telegeusis spp., membranous wing. 16. T. austellus sp. n.; 17. T. sonorensis sp. n.; 18. T. boreios sp. n.; 19. T. glessun sp. n.; 20. T. granulatus sp. n.
144 NaK channel proteins in a DPPC membrane
<p>144 NaK channels embedded in a DPPC membrane formed by 14400 lipid molecules simulated for 25 microseconds using the protein model by Sansom et al. [1,2] and the Martini lipid model [3]. The membrane is solvated by a total of 294163 water beads, counter ions, and a NaCl concentration of 154 mM. Files are compatible with Gromacs 4.6. and above.</p> <p>[1] Peter Bond and Mark Sansom, Insertion and assembly of membrane proteins via simulation, J. Am. Chem. Soc., 2006, 128 (8), pp 2697–2704</p> <p>[2] Kathryn A. Scott et al., Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly, Structure, 2008, 16 (4), pp 621–630</p> <p>[3] Siewert J. Marrink et al., Coarse Grained Model for Semiquantitative Lipid Simulations, J. Phys. Chem. B, 2004, 108 (2), pp 750–760</p>
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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.