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 the 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/
Stx1A_L/
Stx1B_dL/
Stx1A_IFTLL/
Stx1B_TLIF/

figures_for_paper/

Contains all source files used to generate the figures and movies presented in the manuscript.

mb_self_assembly/

Contains the source files required to reproduce the membrane self-assembly used to generate the initial configurations for the production simulations of Palm Stx1A, Palm Stx1B, Stx1A, Stx1A_noP2, Stx1B, and Stx1B_noP2.

Note: During system preparation, the membrane self-assembly for the 2–8 copy palmitoylated Stx1B systems was inadvertently performed using a palmitoylated Stx1B-ΔL construct because of a sequence-building issue. The missing C-terminal leucine was identified and restored before the production simulations were initiated. Consequently, all production simulations, analyses, and results reported in the manuscript correspond to the correct palmitoylated wild-type Stx1B sequence.

Palm_Stx1A/, Palm_Stx1B/, Stx1A/, Stx1A_noP2/, Stx1B/, Stx1B_noP2/, Stx1A_L/, Stx1B_dL/, Stx1A_IFTLL/, Stx1B_TLIF/

These directories contain the simulation input files, processed datasets, and analysis results for each simulation system.

For the mutant systems, the initial membrane configurations were reused from previously equilibrated wild-type systems. Specifically, Stx1A-L and Stx1B-ΔL were initialized from their corresponding wild-type systems, whereas the reciprocal mutants Stx1A-IFTLL and Stx1B-TLIF were initialized from the wild-type Stx1B and Stx1A systems, respectively.

Supporting Tables S1–S7 are in xlsx format.

Supporting Movie S1–S3 are in MP4 format.

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, all simulation input files together with the processed datasets and analysis scripts are provided.

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

Note: The filenames of the original figure panel files do not correspond to the panel labels in the final published figures, as the figures were reorganized during manuscript revision. Therefore, the original filenames should not be used to infer the identities or ordering of the panels in the final figures. 

This revised Jupyter notebook contains minor formatting corrections and should replace the corresponding notebook file in the compressed archive.

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 production simulations were performed on the Bridges-2 supercomputer through NSF ACCESS Allocation BIO250149, whereas part of the membrane self-assembly was performed on the Triton supercomputer at the University of Miami.

Contact

The datasets have been organized to correspond as closely as possible to the final manuscript following peer review.

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. IJMS

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.