Dataset for GM3 ganglioside employs amplified competition and membrane reorganization to control EGFR signaling

# EGFR-GM3 Molecular Dynamics Trajectories ## Dataset Description This dataset contains molecular dynamics simulation trajectories investigating the inhibitory mechanism of GM3 ganglioside on EGFR (Epidermal Growth Factor Receptor) activation. The simulations reveal how GM3 prevents EGFR dimerization through competitive binding and membrane reorganization. ## File Contents ### Trajectory Files - `with_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-containing membrane (8-10 μs) - `without_GM3.xtc` - Trajectory of EGFR TM-JM peptides in GM3-free ordered membrane (8-10 μs) ### Structure Files - `with_GM3.psf` - Protein structure file for GM3-containing system - `without_GM3.psf` - Protein structure file for GM3-free system ## Simulation Details ### System Composition - **Membrane dimensions**: 40 × 40 nm - **Proteins**: 4 EGFR TM-JM peptides (residues 610-659) - **GM3-free system**: CHOL:DLiPC:SM = 33:33:33 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet) - **GM3-containing system**: CHOL:DLiPC:SM:GM3 = 33:33:33:1 mol% (upper leaflet); CHOL:DLiPC:DOPS = 33:33:33 mol% (lower leaflet) ### Simulation Parameters - **Force field**: MARTINI 2.2 coarse-grained - **Software**: GROMACS 2023.3 - **Temperature**: 298 K - **Pressure**: 1 bar (semi-isotropic coupling) - **Salt concentration**: 150 mM NaCl - **Duration**: 8-10 μs per system ## Usage These trajectories can be analyzed using standard molecular dynamics analysis tools: ```bash # Example: Load with MDAnalysis (Python) import MDAnalysis as mda # Load GM3-containing system u_gm3 = mda.Universe('with_GM3.psf', 'with_GM3.xtc') # Load GM3-free system u_free = mda.Universe('without_GM3.psf', 'without_GM3.xtc') # Codes for analyses on the manuscript by Sato and Tamagaki-Asahina Codes for analyses are available on github, https://github.com/takeshi-sato-dev/