Dataset for Mechanistic Insights into Mixing of LNP with Biomembranes.
Authors/Creators
- 1. Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc: Olomouc, CZ
- 2. Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc: Olomouc, CZ; IT4Innovations, VŠB – Technical University of Ostrava, CZ
Description
This repository contains data from the manuscript:
Čechová, P., Paloncýová, M., Šrejber, M., Otyepka, M. Mechanistic Insights into Mixing of LNP with Biomembranes
> 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 > input_files : *.mdp files used for simulations (for details see Systems_and_simulations_Detailed_SI.xlsx)
> 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)
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)