Table 2.
Native TMH docking tests
| Protein | Docked residues |
Zlrms |
|
|---|---|---|---|
| Full | No weak/bif HB | ||
| Glycophorin A | All | 3.26 | 1.02 |
| Glycerol channel | 39–55 | 2.56 | 1.89 |
| Glycerol channel | 234–245 | 3.59 | 2.87 |
| PsaL subunit of PSI | 5–15 | 2.22 | 1.82 |
| Halorhodopsin | 1–29 | 2.37 | 1.73 |
| Halorhodopsin | 204–232 | 1.71 | 1.66 |
| Calcium ATPase | 764–775 | 2.35 | 1.97 |
| Cytochrome c oxidase | 76–89 | 2.87 | 2.63 |
| Photosynthetic reaction center | 572–582 | 2.22 | 2.01 |
| Photosynthetic reaction center | 659–672 | 2.3 | 1.89 |
| Mean ± SD | — | 2.55 ± 0.55 | 1.95 ± 0.51 |
The energy gap among native, near-native (N), and nonnative (NN) docked complexes was assessed by using Zlrms = (〈E〉NN − 〈E〉N)/σENN (see Materials and Methods). The contribution of the membrane-specific hbonding term to the energy gap between native and nonnative docked complexes was analyzed: full membrane potential (Full), potential without membrane-specific side-chain–backbone bifurcated and side-chain–side-chain, backbone–side-chain weak hbonds (no weak/bif HB). ΔZlmrs is the difference between the Z score values obtained with and without the weak/bif HB potential. Successful discrimination is defined as a Z score >1. PSI, Photosystem I; —, not applicable.