Table 1.
Summary of the template and target proteins.
| Target PDB code |
Secondary structure |
Number of residues |
Target resolution (Å) |
Template PDB code |
Template resolution (Å) |
Sequence indentity (%) |
HL for target (Å) |
HL for homology (Å) |
Lipid type |
|---|---|---|---|---|---|---|---|---|---|
| 1j4n | α-helical | 249 | 2.2 | 1z98 | 2.1 | 44 | 24 | 24 | DMPC |
| 1py6 | α-helical | 227 | 1.8 | 5ahy | 2.2 | 35 | 32 | 29 | DPPC |
| 1qj8 | β-barrel | 148 | 1.9 | 2n2l | - | 44 | 24 | 24 | DMPC |
| 3odu | α-helical | 302 | 2.5 | 4ea3 | 3.0 | 31 | 28 | 27 | DPPC |
| 3vg9 | α-helical | 297 | 2.7 | 4gbr | 4.0 | 32 | 29 | 20 | DLPC |
| 4hyj | α-helical | 258 | 2.3 | 3ddl | 1.9 | 33 | 25 | 23 | DMPC |
| 4kr8 | β-barrel | 340 | 3.1 | 4gcp | 2.0 | 57 | 11 | 10 | DLPC |
| 4n6h | α-helical | 303 | 1.8 | 4ea3 | 3.0 | 60 | 32 | 27 | DPPC |
Resolutions in Å are given for crystal structures as reported from experiment. A resolution value is not available for the solution NMR structure 2n2l. Sequence identities were obtained from the PSI-BLAST Web server. Hydrophobic lengths (HL) were calculated by MEMHLength program for the target protein and homology models after the equilibration in DPPC bilayer. The lipid type indicates the lipids used in the second set of explicit bilayer simulations (see Methods).