Table 2. List of simulations.
| simulation namea,b | length[ns] |
|---|---|
| Fox-1(complex)_12_1 | 10 000 |
| Fox-1(complex)_12_2 | 1000 |
| Fox-1(complex)_12_3 | 1000 |
| Fox-1(complex)_12_4 | 1000 |
| Fox-1(free)_99_1 | 1000 |
| Fox-1(free)_99_2 | 500 |
| Fox-1(free)_12_1 | 8000 |
| Fox-1(free)_12_2 | 500 |
| Fox-1(free)_14_1 | 500 |
| Fox-1(free)_12_frozenc | 300 |
| Fox-1(free)_12_NaCld | 1000 |
| Fox-1(free*)_99_1b | 1000 |
| Fox-1(free*)_99_2b | 500 |
| Fox-1(free*)_12_1b | 7000 |
| Fox-1(free*)_12_2b | 500 |
| Fox-1(free*)_14_1b | 500 |
| Fox-1(free*)_12_frozenb,c | 300 |
| Fox-1(complex)_12_S155Ae | 1000 |
| Fox-1(complex)_14_S155Ae | 1000 |
| Fox-1(complex)_12_S155A_TIe,f | 54 × 200 |
| Fox-1(complex)_12_S122Ae | 500 |
| Fox-1(complex)_12_S122A_2e | 1000 |
| Fox-1(complex)_14_S122Ae | 1000 |
| Fox-1(complex)_12_S122A_TIe,f | 54 × 200 |
aThe numerals ‘14’, ‘12’ and ‘99’ in the simulation name indicate ff14SB, ff12SB and ff99SB protein force-field versions, respectively. For the RNA, the ff99bsc0χOL3 force field was used in all simulations.
bThe “Fox-1(free*)” simulations were based on the Fox-1 protein/RNA complex structure (PDB: 2err) with the RNA removed.
cThe solute was restrained in its initial conformation by positional restraints.
dNaCl was used in the simulation instead of KCl.
eThe S155A and S122A mutations, respectively, were introduced into the system by molecular modeling. The structure from the 1000 ns time point of the Fox-1(complex)_12_1 simulation was used as the starting structure.
fThe TI (thermodynamics integration) calculations consisted of 54 independent simulations, each lasting 200 ns.