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| Format: | Recurso digital |
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Zenodo
2026
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| Accès en ligne: | https://doi.org/10.5281/zenodo.18637692 |
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Table des matières:
- <p>Trajectory for MD simulation on EGFR TM-JM sequence in the ordered membrane with GM3</p> <p><span lang="EN-US">Protein:</span></p> <p><span lang="EN-US">- Source: PDB entry (EGFR transmembrane-juxtamembrane domain structure)</span></p> <p><span lang="EN-US">- Number of copies: 4</span></p> <p><span lang="EN-US">- Chains labeled A, B, C, D</span></p> <p><span lang="EN-US">- Conversion: martinize2 version 2.6 with elastic network constraints</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Membrane:</span></p> <p><span lang="EN-US">- Box dimensions: 40 × 40 × 10 nm³</span></p> <p><span lang="EN-US">- Total lipid molecules: ~5300</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Upper leaflet (analyzed):</span></p> <p><span lang="EN-US">- DIPC: 33 mol%</span></p> <p><span lang="EN-US">- CHOL: 33 mol%</span></p> <p><span lang="EN-US">- DPSM (sphingomyelin): 33 mol%</span></p> <p><span lang="EN-US">- DPG3 (GM3): 1 mol%</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Lower leaflet (not analyzed):</span></p> <ul> <li><span lang="EN-US">DIPC: 33 mol%</span></li> <li><span lang="EN-US">CHOL: 33 mol%</span></li> <li><span lang="EN-US">DOPS (dilinoleoyl phosphatidylserine): 33 mol%</span></li> </ul> <p> </p> <p><span lang="EN-US">Force field: MARTINI 2.2 with MARTINI protein model</span></p> <p><span lang="EN-US">Electrostatics:</span></p> <p><span lang="EN-US">- Method: Reaction-field</span></p> <p><span lang="EN-US">- Cutoff: 1.2 nm</span></p> <p><span lang="EN-US">- Relative dielectric constant (</span><span lang="EN-US">ε</span><span lang="EN-US">ᵣ</span><span lang="EN-US">): 15 (MARTINI standard)</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Van der Waals:</span></p> <p><span lang="EN-US">- Method: Shifted potential</span></p> <p><span lang="EN-US">- Cutoff: 1.2 nm</span></p> <p><span lang="EN-US">- Switch: 1.0 nm (shifted to zero at cutoff)</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Constraints:</span></p> <p><span lang="EN-US">- Protein elastic network: Enabled (maintains secondary structure)</span></p> <p><span lang="EN-US">- Cutoff: 0.9 nm (backbone beads)</span></p> <p><span lang="EN-US">- Force constant: 500 kJ mol</span><span lang="EN-US">⁻</span><span lang="EN-US">¹ nm</span><span lang="EN-US">⁻</span><span lang="EN-US">²</span></p> <p><span lang="EN-US">- Bond constraints: None (MARTINI uses harmonic bonds)</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Lipid parameters:</span></p> <p><span lang="EN-US">- DIPC: MARTINI lipid type "C1A" headgroup, "C1" tail beads</span></p> <p><span lang="EN-US">- DOPS/DIPS: MARTINI lipid type "C1A" headgroup with charge</span></p> <p><span lang="EN-US">- CHOL: MARTINI cholesterol model (4 beads)</span></p> <p><span lang="EN-US">- DPSM: MARTINI sphingomyelin model</span></p> <p><span lang="EN-US"> </span></p> <p><strong><span lang="EN-US">S2.3 Simulation Protocols</span></strong></p> <p><span lang="EN-US">S2.3.1 Energy Minimization</span></p> <p><span lang="EN-US">- Algorithm: Steepest descent</span></p> <p><span lang="EN-US">- Convergence criterion: Maximum force < 10 kJ mol</span><span lang="EN-US">⁻</span><span lang="EN-US">¹ nm</span><span lang="EN-US">⁻</span><span lang="EN-US">¹</span></p> <p><span lang="EN-US">- Typical steps: 5,000-10,000</span></p> <p><span lang="EN-US">- Purpose: Remove steric clashes from initial structure</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">S2.3.2 Equilibration</span></p> <p><span lang="EN-US">Duration: 100 ns</span></p> <p><span lang="EN-US">Ensemble: NPT (constant number, pressure, temperature)</span></p> <p><span lang="EN-US">Temperature control:</span></p> <p><span lang="EN-US">- Target: 298 K</span></p> <p><span lang="EN-US">- Thermostat: Velocity-rescale (v-rescale, modified Berendsen)</span></p> <p><span lang="EN-US">- Time constant: 1.0 ps</span></p> <p><span lang="EN-US">- Coupling groups: Protein, lipids, solvent (separately coupled)</span></p> <p><span lang="EN-US">Pressure control:</span></p> <p><span lang="EN-US">- Target: 1 bar</span></p> <p><span lang="EN-US">- Barostat: Semi-isotropic Berendsen</span></p> <p><span lang="EN-US">- Time constant: 5.0 ps</span></p> <p><span lang="EN-US">- Compressibility: 3 × 10</span><span lang="EN-US">⁻⁴</span><span lang="EN-US"> bar</span><span lang="EN-US">⁻</span><span lang="EN-US">¹</span></p> <p><span lang="EN-US">- Semi-isotropic: xy plane coupled, z independent</span></p> <p><span lang="EN-US">Integration:</span></p> <p><span lang="EN-US">- Time step: 20 fs (0.020 ps, standard for MARTINI)</span></p> <p><span lang="EN-US">- Neighbor list update: every 10 steps</span></p> <p><span lang="EN-US">Position restraints:</span></p> <p><span lang="EN-US">- Protein backbone: 1000 kJ mol</span><span lang="EN-US">⁻</span><span lang="EN-US">¹ nm</span><span lang="EN-US">⁻</span><span lang="EN-US">² (first 50 ns)</span></p> <p><span lang="EN-US">- Released gradually over 50-100 ns</span></p> <p><span lang="EN-US">Output:</span></p> <p><span lang="EN-US">- Coordinates: every 1 ns</span></p> <p><span lang="EN-US">- Energies: every 100 ps</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">S2.3.3 Production Run</span></p> <p><span lang="EN-US">Duration: 10 </span><span lang="EN-US">μ</span><span lang="EN-US">s total for all systems</span></p> <p><span lang="EN-US">Ensemble: NPT</span></p> <p><span lang="EN-US">Temperature control:</span></p> <p><span lang="EN-US">- Same as equilibration (298 K, v-rescale, </span><span lang="EN-US">τ</span><span lang="EN-US"> = 1.0 ps)</span></p> <p><span lang="EN-US">Pressure control:</span></p> <p><span lang="EN-US">- Target: 1 bar</span></p> <p><span lang="EN-US">- Barostat: Parrinello-Rahman (more accurate than Berendsen for production)</span></p> <p><span lang="EN-US">- Time constant: 12.0 ps (longer than equilibration to reduce fluctuations)</span></p> <p><span lang="EN-US">- Compressibility: 3 × 10</span><span lang="EN-US">⁻⁴</span><span lang="EN-US"> bar</span><span lang="EN-US">⁻</span><span lang="EN-US">¹</span></p> <p><span lang="EN-US">- Semi-isotropic: xy plane coupled, z independent</span></p> <p><span lang="EN-US">Integration:</span></p> <p><span lang="EN-US">- Time step: 20 fs</span></p> <p><span lang="EN-US">- Neighbor list update: every 10 steps (with Verlet scheme)</span></p> <p><span lang="EN-US">Output frequencies:</span></p> <p><span lang="EN-US">- Coordinates: every 100 ps (5000 steps)</span></p> <p><span lang="EN-US">- Energies: every 100 ps</span></p> <p><span lang="EN-US">- Velocities: not saved (to reduce file size)</span></p> <p><span lang="EN-US">- Forces: not saved</span></p> <p><span lang="EN-US">Periodic boundary conditions: xyz (all dimensions)</span></p> <p><span lang="EN-US">Neighbor searching:</span></p> <p><span lang="EN-US">- Method: Verlet cutoff scheme</span></p> <p><span lang="EN-US">- Cutoff: 1.4 nm</span></p> <p><span lang="EN-US">- Update frequency: automatically determined by GROMACS</span></p>