Table 4 Comparison of calculated binding free energies (ΔGcalc) and maximal experimental (ΔGexp) binding free energies (kcal/mol) to lipid bilayer for different peripheral proteins.
From: The role of hydrophobic interactions in positioning of peripheral proteins in membranes
Protein name | PDB id | ΔGcalc (kcal/mol) | ΔGexp (kcal/mol)a | Reference |
|---|---|---|---|---|
Predominantly nonspecific hydrophobic association | ||||
Cholesterol oxidase (Brevibacterium) | 1coy | -4.1 | -5.9 | [105] |
Cholesterol oxidase (Streptomyces) | 1b4v | -7.1 | -8.7 | [151] |
8R-lipoxygenase | 1zq4 | -5.0 | -6.8 | [104] |
Snake phospholipase A2, group I | 1poa | -5.4 | -11.4 | [98] |
Snake phospholipase A2, group II | 1vap | -10.2 | -10.6c | [98] |
Human phospholipase A2, group II | 1n28 | -6.3 | -6.4 | [57] |
Voltage sensor toxin | 1s6x | -5.2 | -6.8 | [152] |
Kalata B1 | 1nb1 | -5.4 | -6.4 | [153] |
Phospolipase C | 2ptd | -6.0 | -5.6 | [101] |
Insect phospholipase A2 | 1poc | -10.3 | -8.2 | [154] |
Human phospholipase A2, group X | 1le6 | -21.8 | -6.1 | [57] |
Octreotide -2 | 1soc | -5.6 | -5.4 | [155] |
Pancreatic lipase | 1ethA | -16.1 | -11.0 | [156] |
Cytotoxin 1 | 1tgx | -12.4 | -9.6 | [119] |
Sapecin | 1l4v | -6.6 | -9.9 | [121] |
C1 domain of Raf-1 kinase | 1faq | -8.1 | -5.5 | [2] |
Gramicidin S | 1tk2 | -14.1 | -12.1 | [157] |
Specific binding of lipid ligands (lipid clamps) | ||||
C2 domain of cPLA2 | 1rlw | -7.1 | -11.4c | [84] |
cPLA2 holoenzyme | 1cjy | -9.8 | -11.0 | [158] |
Phospholipase Cδ1 | 1djx | -3.2 | -12.0b | [159] |
C2 domain of synaptotagmin IA | 1byn | -4.4 | -6.5 | [160] |
C2 domain of PKCβ | 1a25 | -2.2 | -7.5 | [160] |
C2 domain of PKCα | 1dsy | -0.6 | -12.8c | [161] |
C2 domain of PTEN | 1d5r | -2.6 | -9.7 | [162] |
C2 domain coagulation factor Va | 1sdd | -5.6 | -8.9c | [163] |
C2 domain coagulation factor VIII | 1d7p | -8.1 | -11.2 | [92] |
FYVE domain of Vps27 | 1vfy | -4.0 | -10.3 | [164] |
ENTH domain of epsin | 1h0a | -5.2 | -10.5 | [77] |
PX domain (p40phox) | 1h6h | -4.5 | -12.6 | [39] |
PX domain (p47phox) | 1o7k | -2.7 | -12.1 | [39] |
PH domain of PLC-δ1 | 1mai | -3.2 | -6.2 | [165] |
Equinatoxin II | 1iaz | -2.2 | -11.1 | [166] |
Predominantely nonspecific electrostatic binding | ||||
Charybdotoxin | 2crd | -1.6 | -3.6 | [17] |
Mitochondrial cytochrome c | 1hrc | -2.0 | -5.3 | [76, 167] |
Helix-coil transitions during binding | ||||
Magainin | 2mag | -14.5 | -8.0 | [168] |
Alamethicin | 1amt | -23.7 | -6.2 | [169] |
Zervamicin | 1ih9 | -14.3 | -7.8 | [47] |
Neuropeptide Y | 1icy | -9.4 | -4.7 | [125] |