Table 2. Summary of MD simulations on wild type AmtB and His variants, and deduced conductivity compared to that observed in vivo.
Protein | Substrate | t simulation (ns) | t exiting (ns) | Conductivity (fromsimulation) | Conductivity (fromexperiment) | |
A1 | wild-type | CH3NH2 | 20 | 13.950 | Conductive | Conductive |
A2 | wild-type | NH3 | 20 | 1.792 | Conductive | Conductive |
B1 | H168A | CH3NH2 | 100 | – | Nonconductive | Nonconductive |
B2 | H168A | NH3 | 20 | 4.415 | Conductive | Conductive |
C1 | H318A | CH3NH2 | 100 | – | Nonconductive | Nonconductive |
C2 | H318A | NH3 | 20 | 8.860 | Conductive | Conductive |
D1 | H168A/H318A | CH3NH2 | 20 | 5.190 | Exit to periplasm | Nonconductive |
D2 | H168A/H318A | NH3 | 40 | 37.460 | Exit to periplasm | Nonconductive |
D3 | H168A/H318A | CH3NH2 | 100 | 3.700 | Exit to cytoplasm | Nonconductive |
D4 | H168A/H318A | NH3 | 100 | 78.420 | Exit to cytoplasm | Nonconductive |
D5 | H168A/H318A | – | 20 | |||
D6 | H168A/H318A | – | 20 |
The initial location of the substrate is always at site Am2. Simulations D5 and D6 both without substrate are designed to explore the intrinsic dynamic property of the conformations of the Phe gate (F107 and F215).