Electrostatics and Local Aromatic Residues Govern Lipid Binding and Membrane Penetration of Synaptotagmin C2 Domains

C2 Domain Simulations This repository contains the simulation trajectories, analysis scripts, and processed figures associated with the manuscript: **Electrostatics and Local Aromatic Residues Govern Lipid Binding and Membrane Penetration of Synaptotagmin C2 Domains** Directory structure C2_domain_simulations/│├── C2A_PM_actual_runs/│ Molecular dynamics simulation trajectories and processed data for C2A domains.│├── C2B_PM_actual_runs/│ Molecular dynamics simulation trajectories and processed data for C2B domains.│├── Figures_C2_project/│ Figures, and supplementary figures generated from the simulations.│└── cal_c2_pm_interaction_stats.ipynbJupyter notebook used for analyses and figure generation. Simulation data The simulation folders contain independent MARTINI coarse-grained molecular dynamics simulations of isolated synaptotagmin C2 domains interacting with PIP2-containing plasma membranes under different charge states. Due to their large file sizes, membrane self-assembly simulations and the trajectories generated from the production molecular dynamics simulations are not included in this repository. These trajectory files are available from the corresponding author(s) upon reasonable request. Analysis The Jupyter notebook reproduces the quantitative analyses presented in the manuscript, including: - PIP2 binding analysis- Membrane penetration analysis- Linear regression models- Figure generation Software requirements The analyses were performed using: Python 3.8.10 NumPy 1.24.4 SciPy 1.10.1 Pandas 1.5.3 MDTraj 1.10.0 Matplotlib 3.7.5 Seaborn 0.11.2 statannotations 0.6.0 scikit-learn 1.3.2 Additional package requirements are listed in the corresponding analysis scripts where applicable. Correspondence For questions regarding the dataset or analysis, please contact the corresponding author. Citation If you use this dataset or analysis pipeline, please cite the associated publication.