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Table 3 Predicted penetration depths (D) and binding energies (ΔG calc ) of peripheral proteins, whose orientations with respect to the membrane have been previously suggested based on their 3D structures

From: The role of hydrophobic interactions in positioning of peripheral proteins in membranes

Protein PDB id ΔG calc (kcal/mol) D(Å) References
Lipid clamps
GRK2 kinase -βγ complex 2bcj -5.5 5.0 [131]
Seminal plasma protein 1h8p -12.3 9.2 [132]
Myotubularin-related protein 1zvr -2.3 2.9 [133]
Other proteins
Fatty acid amine hydrolase 1mt5 -30.8 10.0 [134]
Signal peptidase 1kn9 -4.5 4.5 [135]
Lanosterol synthase 1w6k -19.9 6.5 [136]
Monoamine oxidase 1o5w -19.9 6.5 [137]
Prostaglandin E synthase 1z9h -13.1 4.4 [49]
Carnitine O-palmitoyltransferase 2 2h4t -8.3 3.6 [138]
Major envelope glycoprotein E 1ok8 -9.9 4.9 [139]
Ferrochelatase 1hrk -9.2 7.2 [140]
Sphingomyelinase C 1zwx -6.2 6.0 [141]
α-Toxin (bacterial phospholipase C) 1olp -4.8 3.3 [142]
β-glycosidase 1vff -6.5 3.3 [143]
Hydroxysteroid dehydrogenase 1y5m -14.9 3.0 [144]
Carotenoid oxygenase 2biw -12.7 5.1 [145]
α-Tocopherol transfer protein 1oiz -20.7 8.4 [146]
Phosphatidylinositol transfer protein 1aua -14.0 7.8 [147]
Ganglioside GM2 activator 1pub -7.8 5.2 [148]
Oxysterol-binding protein 1zi7 -5.9 3.0 [149]
Viscotoxin A3 1okh -4.0 5.8 [150]
  1. aOther examples include phospholipases A2 and C, microbial and mammalian lipases, annexins, mammalian cytochromes P450, and fatty acid binding proteins [5, 11, 48].
  2. bStructures with removed transmembrane helices.
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