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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]
  1. aExperimental values were taken for lipid compositions that provided maximal binding affinity and at the ionic strength close to physiological conditions (~0.1 M of KCl). ΔG exp values were taken from the original publications or calculated from the published molar partition coefficients of the proteins as -RT lnK d .
  2. b Measured for isolated C2 domain of the protein.
  3. c Different binding affinities were determined for these proteins in other studies [8, 160, 170, 171].
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