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4 results for “ionizable lipids”
Dataset for Mechanistic Insights into Interactions Between Ionizable Lipid Nanodroplets and Biomembranes
<p>This repository contains data from the manuscript:</p> <p>Čechová, P., Paloncýová, M., Šrejber, M., Otyepka, M. </p> <p><strong>Mechanistic Insights into Interactions Between Ionizable Lipid Nanodroplets and Biomembranes <br></strong><strong><em>Journal of Biomolecular Structure and Dynamics <br></em></strong></p> <p><strong><a href="https://doi.org/10.1080/07391102.2024.2329307"> https://doi.org/10.1080/07391102.2024.2329307</a> </strong></p> <p>> Data > : contains detail informations about simulated systems;<br>Data_4Zenodo.xlsx (detail properties of simulated systems);<br>Melting_dynamics.xlsx (processed data used in Figure 4);<br>Systems_and_simulations_Detailed_SI.xlsx (molecular composition and simulation parameters for all simulations)</p> <p>> Data > Figures : data used for generation of figures in the article</p> <p>> Data > input_files : *.mdp files used for simulations (for details see Systems_and_simulations_Detailed_SI.xlsx)</p> <p>> Data > PMF_data_share :</p> <p>> Data > scripts : scripts used for data analysis of system properties</p> <p>> Starting_structures > Membrane only : starting structures and topologies files for lipid bilayers</p> <p>> Starting_structures > Pulling : starting structures and topologies for pulling simulations</p> <p>> Starting_structures > Pulling > Post_pulling : final structures after biased pulling later used as starting structures for unbiased simulations</p> <p>> Starting_structures > Stress : snapshots of simulations used as starting points for for simulations used for calculations of lateral pressures</p> <p>> Trajectories_Membrane_only : compressed simulation trajectories (*.xtc) and corresponding run input files (*.tpr) for lipid bilayer</p> <p>> Trajectories_Pulling : compressed trajectories (*.xtc) for pulling simulations and subsequent unbiased runs and corresponding run input files (*.tpr)</p> <p>> Builder_4Zenodo : script for bilayer building and the input file for membrane composition definition</p> <p>> Builder_4Zenodo > lipids : lipid structure, topology and equilibration files used by the Builder.sh script</p> <p>> Builder_4Zenodo > Building_folder_test : folder with a finished building process with a sample bilayer </p> <p> </p> <p>NOMENCLATURE</p> <p>A3D : ALC-0315 ionizable lipid (deprotonated) </p> <p>A3P : ALC-0315 ionizable lipid (protonated)</p> <p>p1-p3 : replicas 1-3 for individual systems (pulling and subsequent unbiased runs)</p> <p>free : replica for given system (unbiased runs)</p> <p>ndisk : denotes simulations used for preparation of nanodisc/LNP</p> <p>tiny : denotes simulations used for long term membrane stability assessment</p> <p>pure : denotes pure lipid bilayer</p> <p>CHL : denotes cholesterol content (35 % of molar ratio) in lipid bilayers</p> <p> </p> <p>NOTE: For more details on simulation setup please see the file Systems_and_simulation_Details_SI.xlsx (in > Data)</p>
MD data for Ionizable cationic lipids and helper lipids synergistically contribute to RNA packing and protection in lipid-based nanomaterials
<p>The data stored in this repository is part of the journal article: Zimmer, D. N., Schmid, F., & Settanni, G. (2024). Ionizable Cationic Lipids and Helper Lipids Synergistically Contribute to RNA Packing and Protection in Lipid-Based Nanomaterials. <em>The Journal of Physical Chemistry B</em> <a href="https://doi.org/10.1021/acs.jpcb.4c05057" target="_blank" rel="noopener">https://doi.org/10.1021/acs.jpcb.4c05057</a></p> <p> </p> <p>Data of multiscale simulations of DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in the presence of RNA. For each formulation, data is provided with different coarse-grained parameterizations (generic, adapted) and differents treatments of the RNA (ELN, noELN). Provided are the first and the final frame of each run, the associated topologies, and the respective gromacs input files.</p> <p><strong>> M_PE, M_PC, P_PE, P_PC</strong></p> <p>DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in presence of a 40mer RNA fragment. </p> <ul> <li>cg_<strong>generic</strong>+aa: <ul> <li>cg: 2 microsecond production run based on a generic MARTINI parametrization <ul> <li>md_0.gro: first frame</li> <li>md_10.gro: final frame </li> <li>cg_rna_bilayer.top: Topology of the system</li> <li>cg_DLD{M/P}_lipid.itp: generic MARTINI topology of DLinDMA/DLinDAP</li> <li>martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1.itp, martini_v2.1-dna.itp: Several MARTINI topology files for molecules not included in MARTINI</li> <li>Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI</li> </ul> </li> <li>aa: 300/600 nanosecond production run based on CHARMM36 <ul> <li>md_0.gro: first frame</li> <li>md_60.gro: final frame </li> <li>backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP)</li> <li>CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36.</li> </ul> </li> <li>ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. </li> <li>cgmdp: Gromacs input files for the cg runs</li> <li>aamdp: Gromacs input files for the aa runs</li> </ul> </li> <li>cg_<strong>adapted</strong>+aa: <ul> <li>cg: starting and ending frame of a 2 microsecond production run based on an adapted MARTINI parametrization <ul> <li>md_0.gro: first frame</li> <li>md_10.gro: final frame </li> <li>cg_rna_bilayer.top: Topology of the system</li> <li>martini_v2.0_DIDMA_20 or martini_v2.0_DIDAP_20: generic MARTINI topology of DLinDMA/DLinDAP</li> <li>martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1-dna_cr1_POL_NACL.itp: Several MARTINI topology files for molecules not included in MARTINI</li> <li>Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI</li> </ul> </li> <li>aa: 300/600 nanosecond production run based on CHARMM36 <ul> <li>md_0.gro: first frame</li> <li>md_60.gro: final frame </li> <li>backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP)</li> <li>CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36.</li> </ul> </li> <li>ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. </li> <li>cgmdp: Gromacs input files for the cg runs</li> <li>aamdp: Gromacs input files for the aa runs</li> </ul> </li> </ul>
Supplementary data for "Comparison of ionizable lipids for lipid nanoparticle mediated DNA delivery"
Open the record for dataset details and reuse information.
Synergistic Effect of Nucleoside Modification and Ionizable Lipid Composition on Translation and Immune Responses to mRNA Vaccines
GEO Series GSE303153. Macaca fascicularis; Homo sapiens. 292 samples. Type: Expression profiling by high throughput sequencing.
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