Table 2 Predicted penetration depths (D) and binding energies (ΔG calc ) of peripheral proteins and peptides, whose overall orientations or penetration depths in the lipid bilayer have been experimentally evaluated.
From: The role of hydrophobic interactions in positioning of peripheral proteins in membranes
Protein | PDB id | ΔG calc (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] |