Table 1.
List of channels identified in simulations of cytochrome P450cam
| Channel | X ray∗ | Occur.† | rmax ≥ 1.2 Ň | rmax (Å)§ | l (Å) § | Cost§ | Nwp¶ | twp (ns)‖ | pwp-channel(%)∗∗ |
|---|---|---|---|---|---|---|---|---|---|
| Apo-P450cam | |||||||||
| W1 | Y | 48 | 1 | 1.26 | 36.5 | 31.49 | 3 | 3.59 ± 2.52 | 55.7 ± 19.6 |
| W2 | Y | 40 | 1 | 1.23 | 42 | 32.23 | 11 | 12.69 ± 8.22 | 44.6 ± 33.2 |
| S | Y | 140 | 1 | 1.23 | 31.5 | 30.23 | 1 | 3.48 | 16.0 |
| 1a | Y | 17 | 0 | 1.06 | 37 | 45.38 | 0 | — | — |
| 1b | Y | 0 | 0 | — | — | — | — | — | — |
| 1c | N | 3 | 0 | 0.81 | 37.5 | 53.38 | 0 | — | — |
| 1d | N | 1 | 0 | 0.9 | 47 | 55.33 | 0 | — | — |
| 2a | Y | 180 | 2 | 1.27 | 29 | 19.73 | 0 | — | — |
| 2ac | Y | 74 | 0 | 0.99 | 28.5 | 35.66 | 0 | — | — |
| 2b | Y | 10 | 0 | 0.81 | 35.5 | 46.01 | 0 | — | — |
| 2c | N | 29 | 0 | 0.99 | 30.5 | 40.83 | 0 | — | — |
| 2ce | N | 18 | 0 | 0.71 | 33.5 | 52.87 | 0 | — | — |
| 2d | N | 73 | 5 | 1.32 | 53 | 38.16 | 7 | 9.98 ± 5.58 | 54.6 ± 4.5 |
| 2e | Y | 124 | 11 | 1.3 | 23.5 | 18.06 | 27 | 3.25 ± 2.08 | 48.7 ± 23.6 |
| 2f | N | 13 | 2 | 1.39 | 51 | 39.46 | 2 | 4.65 ± 2.60 | 69.5 ± 0.7 |
| 3a | Y | 29 | 0 | 1.01 | 28.5 | 48.65 | 0 | — | — |
| 3b | N | 23 | 0 | 1.09 | 46 | 44.19 | 0 | — | — |
| 4 | N | 33 | 0 | 1.06 | 26 | 37.24 | 0 | — | — |
| 5 | N | 91 | 0 | 1.10 | 46 | 38.66 | 0 | — | — |
| Pdx1 | Y | 27 | 0 | 0.79 | 27.5 | 41.44 | 0 | — | — |
| Pdx2 | Y | 26 | 0 | 1.07 | 32 | 45.8 | 0 | — | — |
| Camphor-bound P450cam | |||||||||
| W1 | Y | 71 | 0 | 0.9 | 35 | 32.06 | 0 | — | — |
| W2 | Y | 74 | 0 | 1.04 | 31.5 | 26.3 | 0 | — | — |
| S | Y | 183 | 0 | 1.07 | 36 | 29.29 | 0 | — | — |
| 1a | Y | 9 | 0 | 0.85 | 38.5 | 48.98 | 0 | — | — |
| 1b | Y | 22 | 0 | 0.83 | 36.5 | 44.32 | 0 | — | — |
| 1c | N | 3 | 0 | 0.89 | 40 | 51.7 | 0 | — | — |
| 1d | N | 0 | 0 | — | — | — | — | — | - |
| 2a | Y | 146 | 5 | 1.29 | 32 | 17.84 | 2 | 0.62 ± 0.37 | 42.5 ± 13.4 |
| 2ac | Y | 63 | 0 | 1.08 | 28.5 | 28.96 | 0 | - | — |
| 2b | Y | 13 | 0 | 1.06 | 39.5 | 46.07 | 0 | — | — |
| 2c | N | 1 | 0 | 0.71 | 24.5 | 48.44 | 0 | — | — |
| 2ce | N | 1 | 0 | 1.06 | 37 | 53.82 | 0 | — | — |
| 2d | N | 0 | 0 | — | — | — | — | — | — |
| 2e | Y | 113 | 0 | 0.96 | 24.5 | 26.75 | 0 | — | — |
| 2f | N | 0 | 0 | — | — | — | 0 | — | — |
| 3a | Y | 116 | 0 | 1 | 31 | 38.03 | 0 | — | — |
| 3b | N | 2 | 0 | 1.11 | 42 | 50.53 | 0 | — | — |
| 4 | N | 4 | 0 | 0.76 | 26.5 | 55.14 | 0 | — | — |
| 5 | N | 36 | 0 | 1.11 | 48 | 43.46 | 0 | — | — |
| Pdx1 | Y | 25 | 0 | 0.93 | 28.5 | 39.82 | 0 | — | — |
| Pdx2 | Y | 160 | 2 | 1.29 | 34.5 | 32.01 | 0 | — | — |
∗
Y, channel appears in the x-ray crystal structure; N, channel is not observed in the crystal structure.
†
Number of channel-appearing occurrences in the CAVER output calculated for the 200 MD trajectory snapshots (i.e., the 100–300-ns time window with one snapshot taken every 1 ns).
‡
Number of appearing occurrences with rmax ≥ 1.2 Å.
§
Maximum probe radius, rmax, and length, l, for channel with the lowest CAVER cost-function value.
¶
Number of water passages.
‖
Water passage time.
∗∗
Percentage probability of finding water in the corresponding CAVER channel during passage.