Table 2.
Predicted penetration depths (D) and binding energies (ΔGcalc) of peripheral proteins and peptides, whose overall orientations or penetration depths in the lipid bilayer have been experimentally evaluated.
| Protein | PDB id | ΔGcalc (kcal/mol) | D (Å) | Methoda | References |
| Lipid clamps | |||||
| C1 domain of protein kinase Cγ | 1tbn | -2.3 | 7.5 | NMR | [114] |
| Annexin 24 | 1dk5 | -1.2 | 1.8 | FL | [115] |
| Blood coagulation factor VIIa | 1dan | -5.7 | 4.8 | FL | [116] |
| Seminal plasma protein | 1h8p | -12.3 | 9.2 | EPR | [117] |
| Other proteins | |||||
| Cardiotoxin III | 1h0j | -13.1 | 6.5 | FTIR | [118] |
| Cytotoxin 1 | 1tgx | -12.4 | 6.8 | FLq | [119] |
| Cardiotoxin II | 1ffj | -18.1 | 8.7 | NMR | [120] |
| Sapecin | 1l4v | -6.6 | 6.1 | NMR | [121] |
| Cytochrome c | 1hrc | -2.0 | 1.9 | SL, NMR | [122, 123] |
| Coagulation factor IXa | 1pfx | -3.8 | 3.2 | FL | [124] |
| Coagulation factor XIV | 1lqv | -4.9 | 3.5 | FL | [125] |
| Peptides | |||||
| Alamethicin | 1amt | -23.7 | 28.1 | NMR, SL | [44–46] |
| Zervamicin IIb | 1ih9 | -14.3 | 9.9 | FL | [47] |
| Antiamoebin I | 1joh | -16.4 | 14.4 | FL | [47] |
| Magainin | 2mag | -14.5 | 10.1 | NMR, FL | [126, 127] |
| Nisin | 1wco | -4.0 | 8.8 | NMR | [128] |
| Neuropeptide Y | 1icy | -9.4 | 9.4 | SL | [129] |
| Mersacidin | 1mqz | -4.9 | 3.5 | NMR | [130] |
aAs in Table 1; FTIR – ATR FTIR spectroscopy.