Table 3.
Conformational frequency of the RNA simulations determined by cluster analysis.
| rGACC Conformational Frequency (%) | ||||
|---|---|---|---|---|
| Simulation ID | Intercalated | NMR Minor | NMR Major | Inverted |
|
| ||||
| RNA-NPT1 | 16.0 (0.3) | 12.9 (0.7) | 9.2 (0.4) | 8.4 (0.1) |
| RNA-3982 | 6.2 (0.4) | 3.5 (0.3) | 3.1 (0.1) | 7.1 (0.5) |
| RNA-REMD-GB | -- -- | -- -- | -- -- | 92.9 (0.7) |
| RNA-REMD-1 | 24.5 (0.9) | 15.9 (0.7) | 11.8 (0.6) | 7.6 (0.0) |
| RNA-REMD-2 | 24.2 (1.2) | 10.5 (1.0) | 8.8 (0.5) | 9.9 (0.1) |
| RNA-REMD-3 | 18.8 (0.9) | 16.3 (1.0) | 13.1 (0.5) | 7.3 (0.1) |
| RNA-rREMD-S | 29.4 (0.1) | 28.3 (1.1) | 12.0 (0.2) | -- -- |
| RNA-rREMD-1 | 18.7 (0.3) | 15.5 (0.7) | 13.1 (0.4) | 11.3 (0.1) |
| RNA-rREMD-2 | 18.5 (0.1) | 15.3 (1.0) | 13.6 (0.1) | 10.9 (0.0) |
| RNA-rREMD-3 | 18.7 (0.5) | 14.6 (0.7) | 14.0 (0.4) | 10.2 (0.1) |
The four conformational categories are structurally depicted in Figure 6. Data shown is for the 277 K temperature level, except for the RNA-NPT and RNA-398 simulations, for which the temperature is indicated (below). Data at 299 K and 328 K are given in Table S2. An error estimate is given in parentheses which corresponds to the standard deviation of five independent clustering calculations.1 Simulation performed at 300 K.2 Simulation performed at 398 K. The “-- --” indicates that the conformation was not observed in the top fifteen most populated clusters.