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2,216 results for “membrane”
Simulations of Na+ and Ca2+ binding to phospholipid membranes
<p>Simulations of various bilayers together with ions. A DOPC bilayer in the liquid disordered phase (310 K) and a DPPC bilayer in the gel phase (293 K), both formed of 200 lipids, were simulated with the presence of either 130 mM of NaCl or 450 mM of CaCl_2. The Slipids model [1–3] is employed for lipids, tip3p model for water, the ion parameters by Smith and Dang for NaCl [4] and the ion parameters by Kohagen et al. for CaCl_2 [5]. Trajectories with NaCl are 200 ns long, while with CaCl_2 they were either 500 ns (DOPC) or 800 ns (DPPC) long.</p> <p>Additionally, a ternary mixture of DPPC, DOPC, and cholesterol was simulated with the presence of 150 mM or 1 M of NaCl [4] at 310 K. The membrane was pre-assembled to contain Ld/Lo coexistence with a well-defined boundary. The Lo side consisted of 205 DPPC and 52 cholesterol molecules, while the Ld side consisted of 166 DOPC molecules. Trajectories are 200 ns long.</p> <p>The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ and the ion parameters are available at https://bitbucket.org/hseara/ions/<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format. Trajectories (.xtc) are saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file except for the varying temperatures (md.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, The Journal of Physical Chemistry B 2012 116 (10), 3164-3179, DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948, DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further. Joakim P. M. Jämbeck and Alexander P. Lyubartsev, Journal of Chemical Theory and Computation 2013 9 (1), 774-784, DOI: 10.1021/ct300777p</p> <p>[4] Computer simulations of NaCl association in polarizable water. David E. Smith and Liem X. Dang, The Journal of Chemical Physics 1994 100, 3757-3766, DOI: 10.1063/1.466363</p> <p>[5] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth, The Journal of Physical Chemistry B 2014 118 (28), 7902-7909, DOI: 10.1021/jp5005693</p>
3D Cryo Soft X-ray Transmission Microscopy data of Intact Thick Cells for Membrane Segmentation and Quantification
<p>The datasets used for evaluation of the proposed method in R. Cárdenes and C. Zhang et al. "3D Membrane Segmentation and Quantification of Intact Thick Cells using Cryo Soft X-ray Transmission Microscopy: A Pilot Study", PloS One, 2017. (DOI: 10.1371/journal.pone.0174324)</p>
Coarse-grained simulations of lipid membranes with various concentrations of embedded proteins
<p>Membranes with a polydisperse set of proteins with lipid/protein ratios of 50 (lp50), 75 (lp75), 100 (lp100), 200 (lp200), and 400 (lp400) are simulated for 100 µs. The protein–protein interactions are scaled down to prevent excessive aggregation. </p> <p>For all simulated lipid/protein ratio, a trajectory (.xtc) file is stored every 10 ns. Note that water beads and ions have been removed for a smaller file size. All beads, including solvent ones, are present in initial and final structures (.gro). Energy terms are stored every 1 ns (.edr). Simulation run input files (.tpr) and checkpoint files (.cpt) enable the rerunning or continuation of the simulations. Topology (.top) and index (.ndx) files for each system are also provided.</p> <p>The topology files for scaled protein–protein interactions work as follows: The bead types of the proteins in their topology files (.itp) are changed to those with a 'p', for example P4–>P4p. The interactions between normal beads are listed in martini_v2.2_standard.itp, while the interactions among 'p' beads as well as the cross terms between 'p' beads and normal beads are given in martini_v2.2_scaled_80.itp. The force constant of the elastic network was increased to enable an integration time step of 20 fs.</p> <p>The lipid head groups are gently restrained in the direction normal to the membrane to prevent excessive fluctuations and they hence simulate the presence of an actin cytoskeleton.</p> <p>The simulation parameters, common for all systems, are listed in the file md.mdp. </p> <p>All files are compatible with Gromacs 5.0.</p> <p>The results extracted from these simulations are presented in the paper</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 Martini topologies are obtained form http://cgmartini.nl</p>
Non-Universal Impact of Cholesterol on Membranes: Mobility, Curvature Sensing, and Elasticity
<p><strong>Dataset repository - Non-Universal Impact of Cholesterol on Membranes: Mobility, Curvature Sensing, and Elasticity</strong></p> <p>==============================</p> <p>The repository contains setup files and parameter files for atomistic molecular dynamics (MD) simulations performed with the GROMACS 2020/2021/2023 series. Modified trajectories for the post-processing analysis are further included. The repositiory corresponds to the following manuscript:</p> <p><strong>Non-Universal Impact of Cholesterol on Membranes: Mobility, Curvature Sensing, and Elasticity</strong></p> <p><strong>Nature Comm. 14, 8038 (2023)</strong></p> <p>Matthias Pöhnl, Marius F.W. Trollmann, and Rainer A. Böckmann<br>Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany<br>Erlangen National High-Perfomance Computing Center (NHR@FAU), Erlangen, Germany<br>*rainer.boeckmann@fau.de</p> <p>Corresponding author:</p> <p>* Rainer A. Böckmann (rainer.boeckmann@fau.de)</p> <p> </p> <p>For each simulation system, the start pdb (<em>'name'_start.pdb</em>), topology (<em>.top</em>), the simulation parameters (<em>.mdp</em>), the final pdb file (<em>'name'_end.pdb</em>) , and the simulation input file (<em>.tpr</em>) are provided in <a href="../api/records/10067080/draft/files/Membrane-Systems.zip/content">Membrane-Systems.zip</a>. The different studied systems are listed in '<a href="../api/records/10067080/draft/files/AA_Systems.pdf/content">AA_Systems.pdf' </a>and <a href="../api/records/10067080/draft/files/CG_Systems.pdf/content">CG_Systems.pdf. </a></p> <p>Additionally, the force field files are provided in <a href="../api/records/10067080/draft/files/FF-Charmm.zip/content">FF-Charmm.zip </a>and <a href="../api/records/10067080/draft/files/FF-Martini.zip/content">FF-Martini.zip.</a></p>
Figs. 5–8 in A Method to Observe Membranous Structures of Female Genitalia in the Inflated Condition (Coleoptera: Cerambycidae)
Figs. 5–8. Comparison of female genital organs in natural and artificial conditions. 5) Oberea sobosana, deflated natural condition, lateral view; 6) O. sobosana, artificially inflated condition, lateral view; 7) Hypocacia fruhstorferi, inflated naturally, lateral view; 8) H. fruhstorferi, artificially inflated condition, lateral view. Scale = 1 mm. Comparisons are made between conditions of the same specimen. The slight differences between Figs. 7–8 are due to the inner pressure of inflation. The genitalia are fully inflated in the artificial condition, but have slightly lower pressure in the natural condition.
Figs. 1–4. The method for inflating the female genital organ. 1 in A Method to Observe Membranous Structures of Female Genitalia in the Inflated Condition (Coleoptera: Cerambycidae)
Figs. 1–4. The method for inflating the female genital organ. 1) Insert nozzle or needle from gonopore to near the distal part of the vagina or bursa copulatrix; 2) Inject petroleum jelly to inflate membranous parts; 3) Clamp median oviduct when jelly flows from oviduct cavity; 4) Carefully extract nozzle from gonopore after inflation.
Figs. 9–18 in A Method to Observe Membranous Structures of Female Genitalia in the Inflated Condition (Coleoptera: Cerambycidae)
Figs. 9–18. Fully inflated female genital organs of Cerambycidae in lateral view. 9) Pidonia shikokensis shikokensis; 10) Leptura regalis; 11) Schwarzerium quadricollis; 12) Xylotrechus villioni; 13) Bumetopia japonica japonica; 14) Eupromus ruber; 15) Mesosa japonica; 16) Agelasta yonaguni subkonoi; 17) Pachyosa cervinopicta; 18) Japanomesosa poecila. bc = bursa copulatrix; ov = oviduct; sp = spermatheca; vg = vagina. Scale = 1 mm.
A New and less corrosive Method for the Activation of Cation Exchange Membranes used in tubular PEM Electrolyzers
<p>Data presented in the article with the same title</p>
Coarse-grained simulations of the Sec61 and TRAP complexes in a multi-component membrane
<p>to be added</p>
Dataset for the paper "Nanostructured Catalyst Layer Allowing Production of Ultralow Loading Electrodes for Polymer Electrolyte Membrane Fuel Cells with Superior Performance" published in ACS Appl. Energy Mater.
<p>The data in this spreadsheet was used to produce the figures in the paper</p><p>Authors:</p><p>Colleen Jackson, Michalis Metaxas, Jack Dawson, Anthony Kucernak</p><p>Title:</p><p>Nanostructured Catalyst Layer Allowing Production of Ultralow Loading Electrodes for Polymer Electrolyte Membrane Fuel Cells with Superior Performance</p><p>Journal:</p><p>ACS Appl. Energy Mater. </p><p>DOI:</p><p>10.1021/acsaem.3c01987</p><p>Please cite the above reference if you wish to use this data</p><p>DOI of data:</p><p>10.5281/zenodo.10256698</p>
SPARCS_test_data_small_membrane
<p>Example images to run the SPARCS computation workflow on.</p>
Molecular Dynamics Simulation Dataset for "Hydrophobic Mismatch Drives Self-Organization of Designer Proteins into Synthetic Membranes"
<p>This repository contains molecular dynamics (MD) simulation data from the study on the self-organization of designer proteins in synthetic membranes. The data includes simulations for different single lipid compositions (DOPC, DPPC, DYPC) denoted as [lipid]-PL* where PL stands for the different TMD constructs. Multi component simulation are named accordingly. The repository provides initial (eqi.gro) and final (prod.gro) coordinates for each simulation. The 'cmd' file in each directory outlines the assembly process of each simulation, and the 'mdp' folder contains all input files for the simulations. </p>
Maternal omega-3 polyunsaturated fatty acids improved accretion of DHA-enriched phosphatidylethanolamines and neuronal membrane lipid-rich domains in C57BL/6 mice fetal brains during gestation
<p>This file contains raw dataset for fetal brain lipidomics and associated fetal neuronal membrane </p>
Simulation Dataset: The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes
<p>The Zenodo repository contains data to the molecular dynamics simulations in the following manuscript: </p> <p><strong>The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes </strong></p> <p>by</p> <p>Dominik Ruppelt, Marius F. W. Trollmann, Taulant Dema, Sebastian N. Wirtz, Hendrik <br>Flegel, Sophia Mönnikes, Stephanie Grond, Rainer A. Böckmann*, Claudia Steinem*</p> <p>0) Lugdunin-parameterization</p> <p>1) Lugdunin-stack-stability</p> <p> - trans_configuration.gro: Artifical lugdunin stack in trans configuration (see SFig. 23 a).</p> <p> - gauche_configuration.gro: Artifical lugdunin stack in gauche configuration (see SFig. 23 b)</p> <p> - DMPC</p> <p> - DOPC</p> <p> - POPC</p> <p> - POPC_CHOL</p> <p>2) Partitioning-of-Lugdunin-in-Membranes</p> <p> - POPC</p> <p> - POPC_CHOL</p> <p> - GRAMPOS</p> <p>3) PMF-calculations</p> <p> - GRAMPOS_WT</p> <p> - POPC_CHOL_MUT</p> <p> - POPC_CHOL_WT</p> <p> - POPC_MUT</p> <p> - POPC_WT</p>
Datasets generated for the manuscript: The basement membrane regulates the cellular localization and the cytoplasmic interactome of Yes-Associated Protein (YAP) in mammary epithelial cells
<p><strong>File proteinGroups-CoIP-Yap1:</strong> Dataset of co-Immunoprecipitation followed of Yes-associated protein (YAP) followed by proteomics to identify YAP interactants.</p> <p><strong>File Gene_set_file_YAP: </strong>Gene sets used for gene set enrichment analysis.</p> <p><strong>Files enrichr_x: </strong>output of the EnrichR tool</p>
Data from: Prebiotic membrane structures mimic the morphology of purported early traces of life on Earth
<p>Original microscopy files used in figures for publication.</p>
Comparative membrane proteomic analysis of Tritrichomonas foetus isolates (non filtered Data Sets)
<p>Tritrichomonas foetus is a flagellated and anaerobic parasite able to infect cattle and felines. Despite its prevalence, there is no effective standardized or legal treatment for T. foetus-infected cattle; the vaccination still has limited success in mitigating infections and reducing abortion risk; and nowadays, the diagnosis of T. foetus presents important limitations in terms of sensitivity and specificity in bovines. Here, we characterize the plasma membrane proteome of T. foetus and identify proteins that are represented in different isolates of this protozoan. Raw proteomics data sets from MALDI-TOF Mass Spectrometry presented here corresponds to six T. foetus isolates (Tf0-Tf5). For Tf2 isolate also five membrane fractions are presented (f1-f5). </p>
Supporting MD trajectories for the paper "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae"
<p>Source data and molecular dynamic trajectories for the article "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae"</p> <p>New compounds with unique mechanisms of action are needed to combat the growing issue of antimicrobial resistance. Supramolecular assemblies, which combine the complex membrane attacking mechanisms of natural host defense peptides with the improved biostability of non-natural compounds offer a promising alternative to current small molecule antibiotics. However, for such membrane-targeting compounds the direct visual insight on the toxic agents in bacteria is still lacking. To this end, we employed a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular peptide structures triggered by bacterial cell surface lipopolysaccharides (LPS). Inspired by the alternating chirality backbone pattern of some effective peptide antimicrobials, we designed lysine-rich heterochiral β3-peptides, termed lamellin-2K and lamellin-3K, with optimal residual spacing for enhanced coordination on the phosphate groups of LPS. Combined molecular dynamics simulations (MD), EM and bacterial assays confirmed that the phosphate-induced conformational change of these lamellins led to the formation of thin, striped lamellar layers, where each stripe represents double arrays of H-bonded peptide molecules that are interconnected by phosphate ions. EM micrographs of Gram-negative bacteria show that the lamellae incised the cell envelope, while leakage and antibacterial activity assays prove that growth inhibition starts already at submicromolar concentrations. Detailed image analysis demonstrated that the lamellae penetrating deep into the bacterial cell have a rather uniform size distribution and, surprisingly, only a few of these supramolecules are sufficient to cause major cell wall damage making them efficient in destroying target cells. Our findings also provide a missing mechanistic link for membrane-targeting agents, connecting how the antibiotic mechanism is built up from individual molecules through on-site formation of the active supramolecules that lead to bactericidal activity.</p> <p>Molecular dynamics trajectories from the production runs of single beta-peptide strands in water + 150 mM NaCl + 50:1 MePO4^(2-):peptide. Altogether 8 runs were performed, each one starting from a different helical conformation (H10, H12 and H14, both positive and negative winding) of the peptide. In the first half (500 ns) of the simulation, the intra-chain hydrogen bonds responsible for the actual helix were kept together by distance restraints. In the second half (again 500 ns), these restraints were instantaneously lifted and the system was left to evolve from the same state. In all cases the helical structure unwound in a very short time (under 100 ns), and did not refold in any helix.</p>
Thin elastic films and membranes under rectangular confinement
<p>Supplementary data for the following manuscript: <span>A. R. Sprenger</span><span>, H. Reinken</span><span>, T. Richter</span> <span>and</span> <span>A. M. Menzel</span>, "<span>Thin elastic films and membranes under rectangular confinement</span>".</p>
Nafion membranes for power generation from physiologic ion gradients
<p>Dataset for the publication: "Nafion membranes for power generation from physiologic ion gradients"</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.
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