Jan 14, 2026
Atomistic molecular dynamics simulation of ATG13-ATG101-WIPI3/ATG13-ATG101-WIPI3-WIPI2 complex on a membrane bilayer
- Sanjoy Paul1
- 1Max Planck Institute of Biophysics
Protocol Citation: Sanjoy Paul 2026. Atomistic molecular dynamics simulation of ATG13-ATG101-WIPI3/ATG13-ATG101-WIPI3-WIPI2 complex on a membrane bilayer . protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg31o41l25/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: November 12, 2025
Last Modified: January 14, 2026
Protocol Integer ID: 232168
Keywords: molecular dynamics simulations of the atg13, molecular dynamics simulation, atomistic molecular dynamics simulation, protein interface, membrane bilayer, wipi2 complex, atg13, membrane, atg101, wipi3
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-000350
Medical Research Council
Grant ID: MC_UU_00038/2
National Institute of Health
Grant ID: R01 Ns134598
Abstract
This protocol details molecular dynamics simulations of the ATG13-ATG101-WIPI3/ATG13-ATG101-WIPI3-WIPI2 complex on a membrane bilayer and analysis of the stability of the protein-protein interfaces.
Troubleshooting
Model Preparation
Begin with the AlphaFold2-predicted model of the ATG13-ATG101-WIPI3/ ATG13-ATG101-WIPI3-WIPI2 complex as the initial structure for the simulation.
Put this protein complex on a membrane bilayer and remove some lipids near the protein segments that insert into the membrane.
Membrane Composition
Consider the following membrane composition: 65% DOPC, 20% DOPE, 10% DOPS, and 5% PI(3)P.
Simulation Runs
Perform 1 μs production run of the simulation system. Perform minimization and equilibration before carrying out the production run.
Maintain system pressure at 1 Bar and temperature at 303 K using Parrinello-Rahman barostat and Nose-Hoover thermostat.
Electrostatic Interactions
Treat long-range electrostatic interactions using the particle mesh Ewald method.
Analysis
Monitor the time evolution of the distance between ATG13 D217 and WIPI3 K42/K44, along with the RMSD of the ATG13 DHF motif and its interacting WIPI3 residues, as well as the ATG13-WIPI2 interface.