Table 1:
Simulation Systems
| Name | Starting structure | Type | Duration [ns] |
|---|---|---|---|
| A1_sim_1,2 | PDB code 1AUQ | 300 Ka | 2 × 50 |
| A2_sim_1,2,3 | PDB code 3GXB | 300 Ka | 3 × 40b |
| A1A2_1_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1A2_2_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1A2_3_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1A2_4_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1A2_6_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1A2_6_sim1,2 | complex model | 300 Ka | 2 × 50 |
| A1_M1393_fep_1,2,3 | A1_WT_1 (10+20 ns), A1_WT_2 (10 ns) | FEP | 3 × 10 |
| A2_M1495_fep_1,2,3 | A2_WT_1 (10+20 ns), A2_WT_2 (10 ns) | FEP | 3 × 10c |
| A2_M1545_fep_1,2,3 | A2_WT_1 (10+20 ns), A2_WT_2 (10 ns) | FEP | 3 × 10 |
| A1A2_l_M1495_fep_1,2,3 | A1A2_2met_1 (10+20 ns), A1A2_2met_2 (10 ns) | FEP | 3 × 10 |
| A1A2_2_M1393_fep_1,2,3 | A1A2_2met_1 (10+20 ns), A1A2_2met_2 (10 ns) | FEP | 3 × 10 |
| A1A2_2_M1495_fep_1,2,3 | A1A2_2met_1 (10+20 ns), A1A2_2met_2 (10 ns) | FEP | 3 × 10 |
| A1A2_3_M1545_fep_1,2,3 | A1A2_1met_1 (10+20 ns), A1A2_lmet_2 (10 ns) | FEP | 3 × 10 |
| A1A2_4_M1393_fep_1,2,3 | A1A2_2met_1 (10+20 ns), A1A2_2met_2 (10 ns) | FEP | 3 × 10 |
| A1A2_4_M1495_fep_1,2,3 | A1A2_2met_1 (10+20 ns), A1A2_2met_2 (10 ns) | FEP | 3 × 10 |
| A1lA2_5_M1545_fep_1,2,3 | A1A2_1met_1 (10+20 ns), A1A2_lmet_2 (10 ns) | FEP | 3 × 10 |
| A1A2_6_M1545_fep_1,2,3 | A1A2_1met_1 (10+20 ns), A1A2_lmet_2 (10 ns) | FEP | 3 × 10 |
a
These simulations sampled the unoxidized conformational state of either the isolated domains or the A1A2 complex at room temperature and did not involve FEP.
b
These simulations were performed as part of a previous study.28
c
These simulations were performed as part of a previous study.21 All simulations were performed in either duplicates or triplicates and labeled with indexes (e.g., 1, 2, 3 for triplicates), respectively. The FEP simulations were started from snapshots sampled along the “300 K” runs as indicated.