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2,697 results for “Lipids”
Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"
<p><strong>Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"</strong></p> <p>The dataset contains the following folders:</p> <p>- number_of_contacts: files with the number of contacts between the rim domains of LukF and Hlg2 and the membrane, for different bilayer compositions (Fig. 2).</p> <p>- binding_events: files with the duration of the time interavals in which LukF and Hlg2 are bound to the membrane, and the scripts used to compute for each system the number of binding/unbinding events and the average membrane residence time (Fig. 3).</p> <p>- electrostatic_potential: files of the surface electrostatic potential produced with the adaptive Poisson-Boltzmann solver and used for visualization with Chimera (Fig. 4).</p> <p>- angles: files with the angle values computed between the protein axis and the z-axis of the simulation box (Fig. 5).</p> <p>- contacts_per_residue: files with the number of frames in which each protein residue is in contact with the membrane, with respect to the total number of frames in which the rim domain interacts with the bilayer (Fig. 5).</p> <p>- distance_protein_membrane: files with the minimum distance between the protein and the membrane (Fig. 6).</p> <p>- binding_sites: file produced by PyLipid with relevant information on the main DOPC binding sites identified in LukF.</p> <p>- min_distance_per_residue: files with the minimum distance between each protein residue and the membrane, computed at the binding steps (Fig. S5).</p>
Source molecular simulation data for calculating energy and friction profiles and permeability coefficients through model lipid membranes
<p>Energy files from GROMACS molecular dynamics simulations with enhanced free energy sampling contain time-dependent evolution of the free energy profiles and friction profiles (and other energies and simulation properties) that were used for calculating permeability coefficients in the publication https://www.biorxiv.org/content/10.1101/2021.07.16.452599v1</p> <p>Simulation system contains a lipid POPC or DPPC bilayer with a varying amount of cholesterol (specified as mol% in the file name). Hydrophobic level of the permeating particle is specified as "level-I", "level-II" etc. When unspecified in the file name, the particle is hydrophobic level "III". Lipids D-C14-PC denote PC lipids with both tails monounsaturated of length 14 carbon atoms. DOPC is equivalent to D-C18-PC. (Detailed description in the publication)</p> <p>Adaptive Weighted Histogram (AWH) method was used to sample the free energy profile of translocating small molecule through the lipid bilayer.</p> <p>GROMACS tool `gmx awh` reads the files and provides the described profiles.</p> <p>Files were generated by GROMACS `mdrun` simulation engine version 2019.3.</p> <p> </p> <p>Coarse-grained MARTINI 3.0 model was used for modeling the biomolecular interactions.</p> <p>Scripts to perform the simulations and the files with initial configurations and simulation settings are stored in a public GitHub repository depozited on Zenodo.org: <a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p> <p> </p> <p>Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).</p> <p>Lindahl, V., Lidmar, J. & Hess, B. Accelerated weight histogram method for exploring free energy landscapes. J. Chem. Phys. 141, 044110 (2014).</p> <p>Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods 18, 382–388 (2021).</p> <p>Melcr, J. Git repository with analysis scripts for MD simulations of permeability through lipid membranes. (2021) doi:<a href="https://doi.org/10.5281/zenodo.5082249">https://doi.org/10.5281/zenodo.5082249</a>.</p>
Raw data to "Opioid sequestration by intravenous lipid emulsion – comparison of lipophilicity in a cell-free system and cellular model"
<p>Data that resulted from the conduction of the in vitro part of the project: Intravenous lipid emulsions as a treatment in acute opioid poisoning - pharmacokinetic and pharmacodynamic evaluation in the rabbit model. It served as raw data for the publication Opioid sequestration by intravenous lipid emulsion – comparison of lipophilicity in a cell-free system and cellular model (draft title). </p>
Raw data for Hancock-Cerutti et. al. "ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling"
<p>Blot images and tabular data for Hancock-Cerutti et. al. "ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling"</p>
Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)
<p><em>Research conducted:</em> The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of <em>Lantana strigocamara</em> and compare it to a previously described origin in <em>Viburnum tinus</em>.</p> <p><em>Methods:</em> We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure in<em> L. strigocamara</em>. We also examine the development of the structure during maturation.</p> <p><em>Key results:</em> We find that the structural color derives from a disordered, multilayered reflector consisting of lipid droplets of ~105 nm that form a plate-like structure in 3D. This structure begins to form early in development and reflects blue wavelengths of light with increasing intensity over time as the structure develops. The lipids used are likely polymers of lipid monomers.</p> <p><em>Main conclusions:</em> <em>Lantana strigocamara</em> is the second origin of a lipid-based photonic structure, convergently evolved with the structure in <em>Viburnum tinus</em>. Chemical differences between the lipids in<em> L. strigocamara</em> and those of <em>V. tinus</em> suggest a distinct evolutionary trajectory with implications for the signaling function of structural colors in fruits.</p>
Research Data Supporting "Coupling Lipid Nanoparticle Structure and Automated Single Particle Composition Analysis to Design Phospholipase Responsive Nanocarriers"
<p>Raw research data supporting Barriga, Pence, et al. 2022, Advanced Materials. <a href="https://doi.org/10.1002/adma.202200839">https://doi.org/10.1002/adma.202200839</a></p>
Hyperactive antifreeze protein from the beetle Rhagium mordax stabilizes model lipid membranes during temperature dependent phase transition
<p>Data from the study submitted in the paper Hyperactive antifreeze protein from the beetle Rhagium mordax stabilises model lipid membranes during temperature-dependent phase transition</p> <p>Data Includes;</p> <p>1. DSC results of RmAFPs interactions with liposomes showing Tm, ΔHcal and Full width at half maximum (FWHM) as well as Phase transitions thermographs by DSC on 1.5mg/ml SUV liposomes either with 60μM (or 0.75mg/ml) RmAFPs or without RmAFPs as control.</p> <p>2. fluorescence spectroscopy data, a complete compilation</p>
mRNA lipid nanoparticle phase transition
<p>The repository contains input files and data from the manuscript:</p> <p>Trollmann, Marius F.W. and Böckmann, Rainer A. "mRNA lipid nanoparticle phase transition", Biophysical Journal (2022) <a href="https://doi.org/10.1016/j.bpj.2022.08.037">https://doi.org/10.1016/j.bpj.2022.08.037</a></p> <p> </p> <p><strong>> Periodic membrane patches</strong></p> <p>Equilibrated structures, .mdp and .top files for the simulations of the periodic Comirnaty membrane patches. (microsecond = us)</p> <p>>> periodic_patches/low_ph/single_patch: </p> <p>~ System A: Three replicas (4.1 us, 3.0 us and 3.0 us) of the self-assembled Comirnaty lipid mixture with the protonated aminolipid</p> <p>>> periodic_patches/low_ph/quad_patch: </p> <p>System B: A quadruplicated system A patch simulated for 1.0 us</p> <p>>> periodic_patches/dspc_chol:</p> <p>System C: Binary membrane including DSPC and 43mol% cholesterol</p> <p>>> periodic_patches/neutral_ph:</p> <p>System D: A deprotonated system B patch simulated for 0.633 us</p> <p>>> periodic_patches/mrna_selfassembly:</p> <p>System E: Structures of the self-assembled Comirnaty lipid mixture with the modified mRNA strand</p> <p>+ periodic_patches/mrna_selfassembly/selfassembly: Structures of the mRNA-lipid mixture after self-assembly with protonated aminolipids</p> <p>+ periodic_patches/mrna_selfassembly/set1: Quadruplicated simulation systems after deprotonation of distant aminolipids (set 1, see paper)</p> <p> + periodic_patches/mrna_selfassembly/set2: Quadruplicated simulation systems after deprotonation of random aminolipids (set 2, see paper)</p> <p>+ periodic_patches/mrna_selfassembly/set3: Simulation systems after deprotonated of all aminolipids (systems were not quadruplicated) (set 3, see paper)</p> <p> </p> <p><strong>> Lipid nanoparticles</strong></p> <p>Equilibrated structures, .mdp and .top files for the simulations of the lipid nanoparticles. (microsecond = us)</p> <p>>> nanoparticles/lnp_nopegs:</p> <p>System F: Structures of the lipid nanoparticles with capped PEGylated lipids</p> <p>>> nanoparticles/lnp_pegs:</p> <p>System G: Structure of the lipid nanoparticle with complete PEGylated lipids</p> <p> </p> <p><strong>> Topologies</strong></p> <p>- topology/DSPC.top - Parameters for the standard phospholipid from the CHARMM36 forcefield</p> <p>- topology/CHOL.top - Parameters for cholesterol from the CHARMM36 forcefield</p> <p>- topology/alc.itp, topology/alc.prm - Parametrization files of the PEG-ylated lipid ALC-0159 obtained from the CGenFF-Webserver</p> <p>- topology/alc_neutral.itp - Parameters for the neutral aminolipid ALC-0315 obtained from the CGenFF-Webserver</p> <p>- topology/alc_protonated.itp - Parameters for the protonated aminolipid ALC-0315 obtained from the CGenFF-Webserver</p> <p>- topology/modRNA.top - Parameters for the short modified mRNA strand. Uridine was replaced with N1-Methylpseudouridine. The parameters were not included in the standard CHARMM36 forcefield (version July 2020) and were manually added to the forcefield.</p> <p>- topology/ALC_SHORT_CORRECT_IDX.itp - Parameters for the capped PEG-ylated lipid ALC-0159 -> Parameters were manually adapted to fit the shortened structure.</p> <p>- topology/charmm36-jul2020.ff - CHARMM36 forcefield parameters (version July 2020) with included parameters for N1-Methylpseudouridine.</p> <p>- topology/cgenff_output - Output from the CGenFF-Webserver to parametrize the aminolipid (ALC-0315) and the PEGylated-lipid (ALC-0159)</p> <p> </p> <p> </p>
Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments
<p>This dataset contains molecular dynamics (MD) trajectories used for preparation of the following manuscript: <br> "Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments". </p>
Lipid droplet quantification datasheet of different MIGA2 constructs expressing cells
<p>Lipid droplet quantification datasheet of different MIGA2 constructs expressing Hela cells: WT, MIGA2 KO, MIGA2 KO cells transfected with WT MIGA2, MIGA2 KO cells transfected with MIGA2 mutants.</p>
Data from: Multiple origins of lipid-based structural colors contribute to a gradient of fruit colors in Viburnum (Adoxaceae)
<p>Structural color is poorly known in plants relative to animals. In fruits, only a handful of cases have been described, including in <em>Viburnum</em> <em>tinus</em> where the blue color results from a disordered multilayered reflector made of lipid droplets. Here, we examine the broader evolutionary context of fruit structural color across the genus <em>Viburnum</em>. We obtained fresh and herbarium fruit material from 30 <em>Viburnum</em> species spanning the phylogeny and used transmission electron microscopy, optical simulations, and ancestral state reconstruction to (1) identify the presence/absence of photonic structures in each species, (2) understand the mechanism producing structural color in newly identified species, (3) relate the development of cell wall structure to reflectance in <em>V</em>. <em>dentatum</em>, and (4) describe the evolution of cell-wall architecture across <em>Viburnum</em>. We identify at least two (possibly three) origins of blue fruit color in <em>Viburnum</em>, both of which produce large photonic structures made of lipid droplets embedded in the cell wall and which reflect blue light. Examining species that may exhibit structural color in combination with anthocyanin and carotenoid pigments, rather than focusing on the most extreme examples, will yield further insights into the diversity, ecology and evolution of fruit color.</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 715 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 72 Ca2+, 112 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 919 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 716mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 716 mM CaCl2 (128 POPC, 26 POPS, 4308 WAT, 56 Ca2+, 112 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 102 mM CaCl2 (104 POPC, 24 POPS, 26 POPS, 4306 WAT, 24 Ca2+, 16 Cl-). Additional Ca2+ cations added to neutralize the negative charge of POPS (leading to total Ca2+ concentration of 306 mM). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 300 ns trajectories were calculated with the last 100 ns stored here.</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
MD simulation trajectory of a POPC bilayer with 100mM CaCl2, Berger force field for lipids, scaled charges for Ca2+ and Cl-
<p>MD simulation trajectory of a POPC bilayer with 100 mM CaCl2 (128 POPC, 26 POPS, 4452 WAT, 8 Ca2+, 16 Cl-). Berger force field for lipids, scaled charges employed for calcium and chloride ions. Gromacs 4.5.5, T=310K, 200 ns trajectories were calculated with the last 100 ns stored here).</p> <p>Used in (see therein also a detailed description of ion scaling):</p> <p>A. Melcrova, S. Pokorna, S. Pullanchery, M. Kohagen, P. Jurkiewicz, M. Hof, P. Jungwirth, P. S. Cremer, L. Cwiklik, The complex nature of calcium cation interactions with phospholipid bilayers<br> Scientific Reports 2016, 6, 38035.<br> DOI: 10.1038/srep38035</p>
Simulations DSPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DSPC (512 lipids) bilayers in gromacs using the charmm36 force field. Temperatures of 333 and 338 K are included. The list of systems can be found below:</p> <p>1) DSPC_512_NaCl_150mM_333K (620ns)<br> 2) DSPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Simulations DPPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DPPC (512 lipids) bilayers in gromacs using the charmm36 force field. Several temperatures between 315 and 338 K are included. The list of systems can be found below where the several parameter are:</p> <p>1) DPPC_512_NaCl_150mM_315K_v-rescale (500ns)<br> 2) DPPC_512_NaCl_150mM_320K (700ns)<br> 3) DPPC_512_NaCl_150mM_320K_v-rescale (500ns)<br> 4) DPPC_512_NaCl_150mM_322K_v-rescale (700ns)<br> 5) DPPC_512_NaCl_150mM_325K (500ns)<br> 6) DPPC_512_NaCl_150mM_325K_v-rescale (500ns)<br> 7) DPPC_512_NaCl_150mM_325K_cutoff09 (500ns)<br> 8) DPPC_512_NaCl_150mM_325K_MEMB_338K (500ns)<br> 9) DPPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Set simulations small pure bilayers (72 lipids) using charmm36 ff in gromacs (DPPC, POPC)
<p>Collection simulations of DPPC and POPC bilayers in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <p>1) DPPC_72_325K (500ns)<br> 2) DPPC_72_310K_rmcomm_leaflets (500ns)<br> 3) DPPC_72_310K_rmcomm_leaflets_low_hydration (500ns)<br> 4) POPC_72_310K (500ns)<br> 5) POPC_72_310K_rmcomm_leaflets (500ns)<br> 6) POPC_72_310K_rmcomm_leaflets_low_hydration (550ns)<br> 7) POPC_72_303K_rmcomm_leaflets_low_hydration (550ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids
<p>The native MS data for paper <strong>"Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids"</strong></p>
Hairpin protein partitioning from the ER to Lipid Droplets involves major structural rearrangements
<div> <p>The project includes dataset from MD simulations and EPR measurements.</p> <p>Description of the MD simulation dataset:<br>-Data type: MD simulations of UBXD8 peptide at varying depths/conformations in POPC bilayer, POPC/Triolein:Cholesteryl oleate monolayer, and in Bilayer-Lipid droplet setup. <br>-Force fields: All-atom simulations were carried out using Charmm36 force field. The parameters for Triolein and Cholesteryl oleate are derived from Olarte et al., 2020 and were obtained from the corresponding authors of that publication. Coarse-grained simulations were carried out using Martini force field. <br>-Simulation Package: All simulations were carried out using GROMACS 2021 simulation package.<br>-File types: The uploaded files include structure files in PDB format, input parameter files (.mdp), topology (topol.top), and force field files.</p> </div> <div>Description of the EPR dataset:<br>- Data type: Experimental spectroscopic measurements, Easyspin simulation and analysis<br>- Files are with filename extensions: DSC, DAT<br>- Information on origin of the data:<br>- EPR spectroscopic measurements with filename extensions DSC and DTA.<br>- EPR spectroscopic simulation and analyses with filename extension m.<br>- EPR simulations were generated using Easyspin version 5.2.36 and Matlab version 23.2.0.2428915.<br>- X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with ER4123D cavity produced by Bruker.</div>
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