README

Data and Code Availability

This repository contains the processed datasets, analysis scripts, and representative simulation files associated with the manuscript:

Lipid Disorder and PIP2-Regulated Clustering of Syntaxin-1 JMD–TMD Regions Govern Membrane Fusion Competence

The repository is intended to facilitate reproduction of all analyses and figures presented in the manuscript.

Directory Structure

figures_for_paper/
mb_self_assembly/
Palm_Stx1A/
Stx1A/
Stx1A_noP2/
Palm_Stx1B/
Stx1B/
Stx1B_noP2/

mb_self_assembly/

All source files for making the figure of the paper.

Supporting_Figures/

All source files for reproducing the membrane self-assembly of all the simulations.

Supporting_Tables/

Supporting Tables S1–S4 in CSV format.

Palm_Stx1A/, Palm_Stx1B/, Stx1A/, Stx1A_noP2/, Stx1B/, Stx1B_noP2/

These folders contain the simulation input files, representative trajectories, processed data, and analysis results for each simulation system.

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.

Trajectory Files

The complete production trajectories (*.xtc) are not included because of their large file sizes.

Instead, other files necessary to reproduce simulations are provided for all simulation systems. 

The complete trajectories are available from the corresponding author upon reasonable request.

Reproducibility

All figures presented in the manuscript can be reproduced using the notebook:

• cal_stx_jmd-tmd_data_stats.ipynb

Simulation data are extracted from the trajectories using:

• stx_jmd_tmd_da.ipynb

The simulations were performed using GROMACS with the MARTINI coarse-grained force field as described in the Materials and Methods section of the manuscript.

All simulations are performed in Bridges-2 supercomputer funded by NSF ACCESS Allocation BIO250149.

Contact

For questions regarding the datasets or analysis scripts, please contact the corresponding author.

Citation and Data Usage

If you use any datasets, analysis scripts, figures, or other materials from this repository in your own research, please cite the associated publication:

Dong An, et al. Lipid Disorder and PIP2-Regulated Clustering of Syntaxin-1 JMD–TMD Regions Govern Membrane Fusion Competence. (Journal information will be updated upon publication.)

Citation of the associated publication helps acknowledge the original work and supports continued development and sharing of reproducible computational tools and datasets with the scientific community.