FGFR3 Transmembrane–Juxtamembrane Dimer Molecular Dynamics Trajectories

# FGFR3 Transmembrane–Juxtamembrane Dimer Molecular Dynamics Trajectories ## Systems ### 1. FGFR3 Wild-Type — Fluid Membrane - **Protein**: FGFR3 TM–JM peptide (PDB: 2LZL) - **Membrane**: DIPC/DOPS (70:30 mol%), liquid-disordered (Ld) phase - **Box dimensions**: 10 × 10 × 10 nm - **Peptide copies**: 2 - **Production run**: 10 μs - **Force field**: MARTINI 2.2 - **Software**: GROMACS 2023.3 - **Dimer pair analyzed**: Chain A / Chain D (2,215 dimer frames, 5.060–7.579 μs) ### 2. FGFR3 Wild-Type — Ordered Membrane - **Protein**: FGFR3 TM–JM peptide (PDB: 2LZL) - **Membrane**: DIPC/DPSM/CHOL (equimolar upper leaflet), liquid-ordered (Lo) phase - **Box dimensions**: 40 × 40 × 10 nm - **Peptide copies**: 4 - **Production run**: 16 μs - **Force field**: MARTINI 2.2 - **Software**: GROMACS 2023.3 - **Dimer pair analyzed**: Chain A / Chain D (1,451 dimer frames, 13.185–15.268 μs) - **CASCADE analysis window**: 1,451 frames (full dimer period) - **MERIT analysis window**: 1,451 frames (same) ### 3. FGFR3 A391E — Ordered Membrane - **Protein**: FGFR3 TM–JM peptide with A391E mutation (Crouzon syndrome with acanthosis nigricans) - **Membrane**: DIPC/DPSM/CHOL (equimolar upper leaflet) - **Box dimensions**: 40 × 40 × 10 nm - **Peptide copies**: 4 - **Production run**: 10 μs - **Force field**: MARTINI 2.2 - **Software**: GROMACS 2023.3 - **Mutation**: A391E introduced by modifying MARTINI bead types ## Files For each system: - `.psf` — System topology (PSF format) - `.xtc` — Production trajectory (XTC format, every 10 ns) ## Simulation Parameters - **Integration timestep**: 20 fs - **Temperature**: 310 K (velocity rescaling thermostat) - **Pressure**: 1 bar (Parrinello–Rahman barostat, semi-isotropic) - **Electrostatics**: Reaction field (MARTINI default) - **van der Waals cutoff**: 1.1 nm - **Elastic network**: Applied to protein backbone beads (cutoff 0.9 nm, force constant 500 kJ/mol/nm²) - **Water model**: MARTINI polarizable water - **Ion concentration**: 0.15 M NaCl ## Membrane Composition Details **Fluid membrane (WT fluid):** - Upper leaflet: DIPC 100 mol% - Lower leaflet: DIPC 70 mol%, DOPS 30 mol% **Ordered membrane (WT ordered, G380R, A391E):** - Upper leaflet: DIPC 33 mol%, DPSM 33 mol%, CHOL 33 mol% - Lower leaflet: DIPC 33 mol%, CHOL 33 mol%, DOPS 33 mol% ## Analysis SLIDE analysis codehttps://github.com/takeshi-sato-dev/slide CASCADE and MERIT analysis code: https://github.com/takeshi-sato-dev/cascade ## License CC BY 4.0 ## Author Takeshi Sato, Kyoto Pharmaceutical University (takeshi@mb.kyoto-phu.ac.jp)