Dataset for Mechanistic Insights into Interactions Between Ionizable Lipid Nanodroplets and Biomembranes

This repository contains data from the manuscript: Čechová, P., Paloncýová, M., Šrejber, M., Otyepka, M. Mechanistic Insights into Interactions Between Ionizable Lipid Nanodroplets and Biomembranes Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2024.2329307 > Data > : contains detail informations about simulated systems;Data_4Zenodo.xlsx (detail properties of simulated systems);Melting_dynamics.xlsx (processed data used in Figure 4);Systems_and_simulations_Detailed_SI.xlsx (molecular composition and simulation parameters for all simulations) > Data > Figures : data used for generation of figures in the article > Data > input_files : *.mdp files used for simulations (for details see Systems_and_simulations_Detailed_SI.xlsx) > Data > PMF_data_share : > Data > scripts : scripts used for data analysis of system properties > Starting_structures > Membrane only : starting structures and topologies files for lipid bilayers > Starting_structures > Pulling : starting structures and topologies for pulling simulations > Starting_structures > Pulling > Post_pulling : final structures after biased pulling later used as starting structures for unbiased simulations > Starting_structures > Stress : snapshots of simulations used as starting points for for simulations used for calculations of lateral pressures > Trajectories_Membrane_only : compressed simulation trajectories (*.xtc) and corresponding run input files (*.tpr) for lipid bilayer > Trajectories_Pulling : compressed trajectories (*.xtc) for pulling simulations and subsequent unbiased runs and corresponding run input files (*.tpr) > Builder_4Zenodo : script for bilayer building and the input file for membrane composition definition > Builder_4Zenodo > lipids : lipid structure, topology and equilibration files used by the Builder.sh script > Builder_4Zenodo > Building_folder_test : folder with a finished building process with a sample bilayer NOMENCLATURE A3D : ALC-0315 ionizable lipid (deprotonated) A3P : ALC-0315 ionizable lipid (protonated) p1-p3 : replicas 1-3 for individual systems (pulling and subsequent unbiased runs) free : replica for given system (unbiased runs) ndisk : denotes simulations used for preparation of nanodisc/LNP tiny : denotes simulations used for long term membrane stability assessment pure : denotes pure lipid bilayer CHL : denotes cholesterol content (35 % of molar ratio) in lipid bilayers NOTE: For more details on simulation setup please see the file Systems_and_simulation_Details_SI.xlsx (in > Data)