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2,216 results for “membrane”
Membrane rigidity regulates E. coli proliferation rates
<p>Combining single cell experiments, population dynamics and theoretical methods of membrane mechanics, we put forward that the rate of cell proliferation in E. coli colonies can be regulated by modifiers of the mechanical properties of the bacterial membrane. Bacterial proliferation was modelled as mediated by cell division through a membrane constriction divisome based on FtsZ, a mechanically competent protein at elastic interaction against membrane rigidity. Using membrane fluctuation spectroscopy in the single cells, we revealed either membrane stiffening when considering hydrophobic long chain fatty substances, or membrane softening if short-chained hydrophilic molecules are used. Membrane stiffeners caused hindered growth under normal division in the microbial cultures, as expected for membrane rigidification. Membrane softeners, however, altered regular cell division causing persistent microbes that abnormally grow as long filamentous cells proliferating apparently faster. We invoke the concept of effective growth rate under the assumption of a heterogeneous population structure composed by distinguishable individuals with different FtsZ-content leading the possible forms of cell proliferation, from regular division in two normal daughters to continuous growing filamentation and budding. The results settle altogether into a master plot that captures a universal scaling between membrane rigidity and the divisional instability mediated by FtsZ at the onset of membrane constriction.</p> <p><br> </p>
Raw data for the article: A Randomized Controlled Trial of Antithrombin Supplementation During Extracorporeal Membrane Oxygenation
<p><strong>Objectives: </strong>Supplementation of antithrombin might decrease the amount of heparin needed to achieve a given anticoagulation target during extracorporeal membrane oxygenation. However, exogenous antithrombin itself may increase the risk of bleeding. We conceived a study to evaluate the effect of antithrombin supplementation in adult patients requiring venovenous extracorporeal membrane oxygenation for respiratory failure on heparin dose, adequacy of anticoagulation, and safety.</p> <p><strong>Design: </strong>Prospective randomized controlled trial.</p> <p><strong>Setting: </strong>ICUs of two Italian referral extracorporeal membrane oxygenation centers.</p> <p><strong>Patients: </strong>Adult patients requiring venovenous extracorporeal membrane oxygenation for severe respiratory failure and unfractionated heparin for systemic anticoagulation.</p> <p><strong>Interventions: </strong>Before extracorporeal membrane oxygenation start, patients were randomized to either receive antithrombin concentrate to maintain a plasmatic level 80-120% (treatment) or not (control) during the extracorporeal membrane oxygenation course.</p> <p><strong>Measurements and main results: </strong>The primary outcome was the total amount of heparin required to maintain activated partial thromboplastin time ratio 1.5-2. Secondary outcomes were anti-factor Xa, the incidence of hemorrhagic and thrombotic events, and the amount of blood products transfused. Twenty-four patients in the treatment group and 24 in the control group were included in the intention-to-treat analysis. Antithrombin was 109.5% (93.0-123.0%) in the treatment group and 84.0% (68.5-98.0%) in the control group (p = 0.001). Supplementation of antithrombin did not decrease heparin dose (13.5 international units/kg/hr [9.6-17.9 international units/kg/hr] vs 15.1 international units/kg/hr [10.7-18.3 international units/kg/hr] in the treatment and control group, respectively; p = 0.33) and anti-Factor Xa levels (0.4 international units/mL [0.3-0.5 international units/mL] vs 0.3 international units/mL [0.2-0.5 international units/mL] in the treatment group and control group respectively; p = 0.65). Bleeding, blood product transfusions, and thrombosis were not different in the two groups.</p> <p><strong>Conclusions: </strong>Antithrombin supplementation may not decrease heparin requirement nor diminish the incidence of bleeding and/or thrombosis in adult patients on venovenous extracorporeal membrane oxygenation.</p>
Input Data for "Assembly and Analysis of Cell-Scale Membrane Envelopes"
<p>Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf protocellmodeling.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*trr" --exclude="*js" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*state_prev.cpt" --exclude="*.o[0-9]*" cgDracula`, which intentionally excludes large files. The full 4.8TB dataset that includes trajectories is available upon request.</p> <p>The data is split into multiple subdirectories and largely undocumented, however here are the highlights:</p> <ul> <li>The <strong>Analysis</strong> subdirectory is where the analysis in the paper lives. All other directories are related to building or running systems.</li> <li><strong>getsources.py</strong> in the main directory is the script that downloads the initial structure from MemProtMD.</li> <li><strong>transform.py</strong> builds the initial protein models from MemProtMD.</li> <li><strong>vesiclebuilder.py</strong> builds the lipid ball.</li> <li><strong>protpatchplacer.py</strong> sets up the ultra-coarse grained simulation, which is in the <strong>supercg</strong> directory.</li> <li><strong>movepatches.py</strong> takes the results from the ultra-coarse grained simulation, and builds the protein ball.</li> <li><strong>gendx.tcl</strong> generates the density maps from the protein ball.</li> <li>This is used in <strong>lipids/picklipids.py</strong>, which cuts out the pieces of the lipid that need to be removed.</li> <li>The water is added to the system with <strong>addwater/quicksolvate.sh</strong></li> <li>The system is ionized by <strong>ionize.py</strong></li> <li>And a topology is written by <strong>writetop.py</strong></li> </ul>
Structural Basis for Membrane Recruitment of ATG16L1 by WIPI2 in Autophagy Raw GUV Data
<p>Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.</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>
Dataset: Carbonate Regeneration Using a Membrane Electrochemical Cell for Efficient CO2 Capture
<p>Dataset for journal publication "Carbonate Regeneration Using a Membrane Electrochemical Cell for Efficient CO2 Capture," published in ACS Sustainable Chemistry & Engineering (DOI: 10.1021/acssuschemeng.2c04175). Data are organized according to figure number.</p>
Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"
<p>Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. <em>PLoS Comput. Biol.</em> <strong>2023</strong>, <em>19</em>, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.</p>
Dataset of paper "Kinetic and mechanistic analysis of membrane fouling in microplastics removal from water by dead-end microfiltration"
<p>Dataset of paper "Kinetic and mechanistic analysis of membrane fouling in microplastics removal from water by dead-end microfiltration":</p> <ul> <li>Microplastics and membrane characterisation: micro-FTIR and ATR spectra.</li> <li>Particle Size Distribution.</li> <li>Identifying the main successive fouling mechanisms using Hermia’s equation.</li> <li>The kinetic constants as a function of the microplastic type and the operating parameters.</li> <li>Permeate flux decline during microplastics filtration.</li> <li>Water contact angle and profilometry measured before and after the filtration of MPs.</li> </ul>
Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures
<p>The thylakoid membrane is in a temperature-sensitive equilibrium that shifts repeatedly during the life cycle in response to ambient temperature or solar irradiance.<br> Plants respond to seasonal temperature by changing their thylakoid lipid composition, while a more rapid mechanism for short-term heat exposure is required.<br> The emission of the small organic molecule isoprene has been postulated as one such possible rapid mechanism.<br> The protective mechanism of isoprene is not known, but some plants emit isoprene during periods of high-temperature stress.<br> In this work, we investigate the dynamics and structure for lipids within a thylakoid membrane at different temperatures and varied isoprene content using classical molecular dynamics simulations.<br> The results are compared with experimental findings from across the literature for temperature-dependent changes in the lipid composition and shape of thylakoids.<br> We find that the surface area, volume, and flexibility of the membrane, as well as the lipid diffusion, increase with temperature, while the membrane thickness decreases.<br> Saturated thylakoid 34:3 glycolipids derived from eukaryotic synthesis pathways exhibit significantly different dynamics than lipids from prokaryotic synthesis paths, which could explain the upregulation of specific lipid synthesis pathways at different temperatures.<br> Increasing isoprene concentration was not observed to have a significant thermoprotective effect on the thylakoid membranes.</p>
Pure POPE membrane simulations with the CHARMM-Drude force field at 310K (OpenMM)
<p>MD simulation data of a pure POPE membrane with the CHARMM-Drude force field generated with the OpenMM simulation engine at 310K.</p> <p>Parameters from CHARMM-GUI.</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: Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair
<p><span>The maintenance of plasma membrane integrity and a capacity for efficiently repairing damaged membranes are essential for cell survival. Large-scale wounding depletes various membrane components at the wound sites, including phosphatidylinositols, yet little is known about how phosphatidylinositols are generated after depletion. Here, working with our <em>in</em> <em>vivo C. elegans</em> epidermal cell wounding model, we discovered phosphatidylinositol 4-phosphate (PtdIns4<em>P</em>) accumulation and local phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)<em>P<sub>2</sub></em>] generation at the wound site. We found that PtdIns(4,5)<em>P<sub>2</sub></em> generation depends on the delivery of PtdIns4<em>P</em>, PI4K, and PI4P 5-kinase PPK-1. In addition, we show that wounding triggers enrichment of the Golgi membrane to the wound site, and that is required for membrane repair. Moreover, genetic and pharmacological inhibitor experiments support that the Golgi membrane provides the PtdIns4<em>P</em> for PtdIns(4,5)<em>P<sub>2</sub></em> generation at the wounds. Our findings demonstrate how the Golgi apparatus facilitates membrane repair in response to wounding and offers a valuable perspective on cellular survival mechanisms upon mechanical stress in a physiological context. </span></p>
La and Mn-doped cobalt spinel oxygen evolution catalyst for proton exchange membrane electrolysis
<p>Finding electrocatalysts using earth-abundant materials as a replacement to iridium for oxygen-evolution reaction (OER) in proton exchange membrane water electrolyzer (PEMWE) represents a critical step in reducing the cost for green hydrogen production. We report here a nanofibrous cobalt spinel catalyst co-doped with lanthanum and manganese prepared from zeolitic imidazolate framework embedded in electrospun polymer fiber. The catalyst demonstrated a low overpotential of 353 millivolts at 10 milliamperes per square centimeter and a low degradation for OER over 360 hours in acidic electrolyte. PEMWE containing this catalyst at anode demonstrated a current density of 2000 milliamperes per square centimeter at 2.47 volts (Nafion® 115 membrane) or 4000 milliamperes per square centimeter at 3.00 volt (Nafion® 212 membrane), and low degradation in accelerated-stress-test. High-resolution electronic microscopy and operando X-ray absorption spectroscopy, combined with computational modeling, revealed the different functions of lanthanum, manganese, and cobalt in enabling enhanced activity, conductivity and acidic tolerance within the OER operating window.</p>
Trajectories of simulated lipid membranes interacting with antimicrobial peptidomimetic AMC-109 and simulation setup files
<p>Trajectories of simulated lipid membranes with antimicrobial peptidomimetic AMC-109.<br> Trajectories are in GROMACS format ".xtc", the frame rate is 10 ns, and water and NaCl ions were omitted from the trajectory deposit to reduce the size to acceptable limits.</p> <p>The molecules are described using MARTINI 3 coarse grained force field.<br> This repository contains a set of simulations with varying ratio of POPC:POPG lipids from<br> 100% POPC, 0% POPG (denoted as "pg000p..") to<br> 0% POPC, 100% POPG (denoted as "pg100p..").<br> Ratios between these two extremes go in steps of 10%,<br> e.g. "pg060p.." denotes 40% POPC, 60% POPG.</p> <p> </p> <p>The files with ".out" or ".xvg" suffix are properties analyzed from the simulation. Namely, they are:<br> - "thickness" : thickness of the membrane<br> - "apl" : area per lipid of the lipid membrane<br> - "numcont" : number of contacts between the peptidomimetic AMC-109 and the lipids<br> - "ordPars" : order parameters of the end tail segments of the sn-1 tail of POPC lipids.</p> <p>More details about how these properties were generated can be found in the attached scripts (".sh" files) in this repository.</p> <p>Sample topology files in GROMACS format (binary ".tpr" and ASCII ".itp") are provided to complete the description of the molecular topologies used to generate the presented simulations.</p> <p> </p> <p>This repository was created as a Supporting Information to a scientific paper at Nature Communications,</p> <p>Lateral membrane organization as target of an antimicrobial peptidomimetic compound, 2023.</p>
Pure POPC membrane simulations with 1000 mM NaCl with the CHARMM-Drude2023 force field (OpenMM)
<p>220.14 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules.</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. Frame saving frequency is 10ps. There are 22014 frames in this trajectory.</p>
Pure POPC membrane simulations with 350 mM CaCl2 with the CHARMM-Drude2023 force field (OpenMM)
<p>219.59 ns MD simulation of pure POPC membrane using Charmm-Drude2023 polarizable force field (</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong></p> <p><strong>)</strong></p> <p>.The system contains 128 POPC lipids, 41 CaCl2, and 6400 SWM4 water molecules.</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. Frame saving frequency is 10ps. There are 21959 frames in this trajectory.</p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
Subset of non-redundant, high resolution multi-pass membrane protein PDB structure files from OPM
<p>A subset of OPM PDB structure files with membrane predictions curated for the MSc thesis project '<strong>Structural characterization of triplets of transmembrane α-helical segments consecutive in sequence in integral membrane proteins: a fragment-based computational pipeline'. </strong>The dataset contains PDB files downloaded from OPM on 22/02/2023. The files are alpha-helical integral membrane proteins with at least three transmembrane regions at better than 2.7 Angtrom resolution. They are non-redundant, with a sequence identity of less than 40% based on clustering with the cd-hit algorithm. </p>
Molecular dynamics simulations of CD59 and CD59-inhibited Membrane Attack Complex
<p>Coarse-grain (CG) trajectories of CD59-C5b8 (last 1,500 ns):</p> <ul> <li>cd59-c5b8_1500ns_rep1.xtc</li> <li>cd59-c5b8_1500ns_rep2.xtc</li> <li>cd59-c5b8_1500ns_rep3.xtc</li> </ul> <p>PyLipID analysis results from CG CD59-C5b8 simulations:</p> <ul> <li>Interactions_CHOL.csv</li> <li>Interactions_DOPC.csv</li> </ul> <p>Atomistic CD59 simulations in DOPC membrane:</p> <ul> <li>cd59_at_rep1_light.trr</li> <li>cd59_at_rep2_light.trr</li> <li>cd59_at_rep3_light.trr</li> </ul> <p>CD59 Euler angles relative to the membrane: </p> <ul> <li>rep1.csv</li> <li>rep2.csv</li> <li>rep3.csv</li> </ul> <p>All xtc and trr files were down-sampled (frames removed) to decrease file size.</p>
Data of the paper Scanning cavity microscopy of a single-crystal diamond membrane
<p>Dataset for all the figures of the paper "Scanning cavity microscopy of a single-crystal diamond membrane"</p> <p>Phys. Rev. Applied 19, 064057</p> <p>10.1103/PhysRevApplied.19.064057</p> <p>https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.19.064057 </p> <p> </p> <p> </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.