Oct 30, 2025
Coarse-grained simulations of the C-terminus of ATG2A in a buckled bilayer
- Ainara Claveras Cabezudo1,2
- 1Max Planck Institute of Biophysics;
- 2IMPRS on cellular biophysics
Protocol Citation: Ainara Claveras Cabezudo 2025. Coarse-grained simulations of the C-terminus of ATG2A in a buckled bilayer. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl468jogo5/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: October 29, 2025
Last Modified: October 30, 2025
Protocol Integer ID: 231117
Keywords: ASAPCRN, terminal region of the lipid transport protein atg2a, lipid transport protein atg2a, grained molecular dynamics simulation, terminus of atg2a, buckled popc bilayer, atg2a, buckled bilayer this protocol detail, popc bilayer, grained simulation
Abstract
This protocol details coarse-grained molecular dynamics simulations of the C-terminal region of the lipid transport protein ATG2A on a buckled POPC bilayer.
Troubleshooting
Generation of buckled membrane
Make a POPC bilayer using the insane method.
Solvate with 150 mM NaCl.
Run a 10 ns simulation to compress the membrane into a buckled shape.
Use the Berendsen barostat anisotropically coupled to the Y and Z directions. Set the compressibility to 3 × 10−4 bar−1 in these dimensions, and to 0 in all others. Set the pressure to 12 bar in Y and 1 bar in Z.
Use the Verlet scheme with a cut-off distance of 1.418 nm for the short-range neighbor list. Update this list every 20 steps.
Cut off Coulomb and van-der Waals interactions at 1.2 nm.
Set the relative dielectric constant to 15.
Docking of ATG2A C-terminus to buckled membrane
Place the buckled membrane in a simulation box. Place the C-terminus of ATG2A at a random position of the same simulation box. Add Martini 3 water and solvate with 150 mM NaCl.
Run a 1 µs membrane simulation.
To fix the lateral axes, couple the Parrinello-Rahman barostat only to the Z dimension with a compressibility of 3 × 10−4 bar−1 and a coupling constant of 1 ps. Set the compressibility to 0 in all other dimensions.
Simulation of ATG2A C-terminus bound to the buckled membrane
Use the membrane-bound configuration as a starting point for 10 independent replicas.
Draw initial velocities according to the Maxwell-Boltzmann distribution at 310 K.
Run all simulations for 1 µs with the lateral axes fixed as described in the previous section.