Table 1. Simulation systems.
| Name | Starting structure | Type | Duration [ns] |
|---|---|---|---|
| AllMetO_1,2,3 | All 5 Met→Met(O)a | 300 Kb | 3 x 40 |
| M1495MO_1,2,3 | M1495M(O) | 300 Kb | 3 x 40 |
| M1521MO_1,2,3 | M1521M(O) | 300 Kb | 3 x 40 |
| M1528MO_1,2,3 | M1528M(O) | 300 Kb | 3 x 40 |
| M1606MO_1,2,3 | M1606M(O) | 300 Kb | 3 x 40 |
| AllMetO_pull_1,2,3 | AllMetO_1 (10 ns), AllMetO_2 (10+20 ns) | pulling | 3 x 15 |
| M1495MO_pull_1,2,3 | M1495MO_1 (10 ns), M1495O_2 (10+20 ns) | pulling | 3 x 15 |
| M1521MO_pull_1,2,3 | M1521MO_1 (10 ns), M1521O_2 (10+20 ns) | pulling | 3 x 15 |
| M1528MO_pull_1,2,3 | M1528MO_1 (10 ns), M1528O_2 (10+20 ns) | pulling | 3 x 15 |
| M1495_fep_1,2,3 | WT_1 (10+20 ns), WT_2 (10 ns)c | FEP | 3 x 10 |
| M1521_fep_1,2,3 | WT_1 (10+20 ns), WT_2 (10 ns)c | FEP | 3 x 10 |
| M1528_fep_1,2,3 | WT_1 (10+20 ns), WT_2 (10 ns)c | FEP | 3 x 10 |
| M1606_fep_1,2,3 | WT_1 (10+20 ns), WT_2 (10 ns)c | FEP | 3 x 10 |
aAll five methionine residues at positions 1495, 1521, 1528, 1545 and 1606 were mutated to methionine sulfoxide.
bThese simulations sampled the folded state at room temperature and were not subjected to any perturbation like pulling or FEP.
cThe FEP simulations were started from snapshots sampled during previously published trajectories with the unoxidized wild-type [9]. All simulations were performed in triplicates and labeled with 1, 2 and 3, respectively. The simulations labeled with “300 K” were started after mutating methionine to methionine sulfoxide at the indicated positions in the wild-type structure of the A2 domain with PDB code 3GXB. All other simulations, pulling and FEP, were started from snapshots sampled along the “300 K” runs as indicated.