Table I.
Overview of the Performed Molecular Dynamics Simulations
| Simulation | CYPOR conformation | P450 2D6 | DPPC | Ions | H2O | Additions | Box dimensions (nm) | Length (ns) |
|---|---|---|---|---|---|---|---|---|
| CC | Closed | No | 0 | 40 Na+ | 18504 | NADPH | x = 7.24 | 10 |
| 15 Cl− | y = 9.30 | |||||||
| z = 9.86 | ||||||||
| CN | Closed | No | 0 | 40 Na+ | 18813 | NADP+ | x = 7.31 | 2 |
| 16 Cl− | y = 9.32 | |||||||
| z = 9.87 | ||||||||
| OC | Open | No | 0 | 40 Na+ | 24157 | None | x = 7.90 | 10 |
| 15 Cl− | y = 8.68 | |||||||
| z = 12.28 | ||||||||
| OM | Open | No | 511 | 50 Na+ | 84223 | None | x = 12.68 | 2 |
| 21 Cl− | y = 12.68 | |||||||
| z = 20.00 | ||||||||
| CO | Open | Yes | 0 | 69 Na+ | 72143 | None | x = 11.58 | 10 |
| 38 Cl− | y = 13.10 | |||||||
| z = 15.78 | ||||||||
| CM | Open | Yes | 509 | 50 Na+ | 82314 | None | x = 12.68 | 10 |
| 16 Cl− | y = 12.68 | |||||||
| z = 20.00 | ||||||||
| PR | Closed/open/closed | No | 0 | 40 Na+ | 33315 | Position restraint FMN domain linearly interpolated to the open conformation | x = 8.90 | 6.2 |
| 15 Cl− | y = 10.93 | |||||||
| z = 11.48 | ||||||||
| SB | Open/closed | No | 0 | 40 Na+ | 24157 | Distance restraints between FAD FMN domain based on salt bridges | x = 7.90 | 2 |
| 15 Cl− | y = 8.68 | |||||||
| z = 12.28 | ||||||||
| HB | Open/closed | No | 0 | 40 Na+ | 24157 | Distance restraints between FAD FMN domain based on hydrogen bonds | x = 7.90 | 4 |
| 15 Cl− | y = 8.68 | |||||||
| z = 12.28 | ||||||||
| PP | Open/closed | No | 0 | 40 Na+ | 24157 | Phi/Psi angle restraints in the hinge region | x = 7.90 | 20 |
| 15 Cl− | y = 8.68 | |||||||
| z = 12.28 |
This tables shows a detailed overview of the different simulations that were performed to study the cytochrome P450 reductase (CYPOR), alone and in complex with cytochrome P450 2D6(2D6). The first column assigns a label to the simulations, CC stands for closed conformation, CN for the closed conformation with NADP+ instead of NADPH, OC for the model in an open conformation, OM for the model in an open conformation in the membrane, CO for the complex with cytochrome P450 2D6 and CM is the complex in the membrane. The abbreviations PR, SB, HB, and PP designate the simulations with positions restraints, restraints on salt bridges, restraints on hydrogen bonds and restraints on the ϕ and ψ angles, respectively. The second column shows the conformation of CYPOR followed by the presence of 2D6. Furthermore, the number of DPPC molecules, ions and water molecules in the system is indicated. Additionally, it is indicated whether any restraints were used and what the size of the simulations box was. The final column indicates the length of the simulation.