Table 1. Percentage of simulation time that Arg58 or Lys56 are involved in hydrogen bonds with the backbone of aa-tRNA, determined from short time scale explicit solvent simulations.
Hydrogen bond donors and acceptors have to be within 3.0Å and form a 40° angle between the donor-H-acceptor atoms. Eleven simulations were performed for 25ns at intervals along the RswI-DIII reaction coordinate to measure stability of switch I aa-tRNA interactions, for an aggregate sampling of 275 ns. Arg 58 has two potential hydrogen bonding nitrogens on the guanidinium group.
| RswI-DIII (Å) | % of frames side chain nitrogen is hydrogen bonded to aa-tRNA backbone |
||
|---|---|---|---|
| Arg 58 (NH2 1) | Arg 58 (NH2 2) | Lys 56 (NH3) | |
| 11 | 0 | 0 | 13 |
| 13 | 0 | 0 | 0 |
| 15 | 28 | 22 | 37 |
| 18 | 68 | 56 | 3 |
| 20 | 22 | 22 | 3 |
| 22 | 29 | 20 | 2 |
| 23 | 3 | 55 | 10 |
| 25 | 0 | 0 | 23 |
| 27 | 11 | 23 | 0 |
| 29 | 0 | 0 | 3 |
| 32 | 0 | 0 | 0 |