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Table 1 Comparison of membrane-bound residues in peripheral proteins according to experimental studies and calculations peripheral proteins.

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

   Experimenta Calculationb
Protein name PDB id Residues buried from water or important for membrane binding Method References Δ G calc (kcal/mol) D (Å) Residues penetrating the hydrocarbon membrane core
Lipid clamps (specific binding of lipid ligands)
C2 domain of phospholipase A2 1rlw A34, F35, G36, M38, L39, Y96, V97, M98 Bn, SL [6, 84, 85] -7.1 5.3 A34, F35, G36, M38, L39, Y96, V97, M98
C2A domain of synaptotagmin I 1byn M173, G174, F234 Bn, SL [7, 86] -4.4 3.7 M173, G174, F234
C2 domain of protein knase Cα 1dsy N189, R249, R252 SL [8] -2.0 1.5 P188, N189, T250
C2B domain of synaptotagmin I 1uov G305, I367 SL [9] -4.3 2.4 V304, G305, I367, G368
C2 domain of protein kinase Cε 1gmi I89, Y91 Bn [87] -5.1 2.4 V29, P31, I89
PX domain (p40phox) 1h6h F35, Y94, V95 Bn [39] -4.5 3.2 F35, Y94, V95
PX domain (p47phox) 1o7k W80 Bn [39] -1.9 1.4 W80
FYVE domain of EEA1 1hyi V21, T22 NMR [40] -2.9 2.5 V21, T22
FYVE domain of Vps27p 1vfy L185, L186 Bn [88] -4.0 2.9 L185, L186
C1 domain of protein kinase Cδ 1ptr W252, L254, V255 Bn [89] -5.7 6.8 M239, P241, L250, W252, G253, L254, V255
Epsin ENTH domain 1h0a L6, M10 Bn [77] -5.2 2.9 L6, M10, I13, V14
Discoidin domain of factor V 1czs W26, W27 Bn [90] -3.0 4.2 W26, W27, L79, and S80
Discoidin domain of factor Va 1sdd Y1956, L1957, W2063, W2064 Bn [91] -5.6 3.3 Y1956, L1957, W2063, W2064
Discoidin domain of factor VIII 1d7p M2199, F2200, L2251, L2252 Bn [92] -8.1 3.9 M2199, F2200, L2251, L2252
Annexin V 1a8a T72, S144 , W185, S228, S303 SL [93] -6.3 2.5 L29, T72, A101, W185, A260
Annexin XII 1dm5 E142, S144, G145 SL [94] -8.3 3.1 I29, L101, I185
Equinatoxin II 1iaz W112 NMR [95] -2.2 3.1 P81, V82, W112
Other proteins
Prostaglandin H2 synthase 1 1q4g I74, W75, W77, L78, F88, F91, L92, W98, L99, F102 Bn, Fn [96] -37.8 7.2 I74, W75, W77, L78, T81, L82, F88, F91, L92, W98, L99, F102, V103, T106, F107, I108
Antimicrobial peptide kalata B1 1nb1 W19-V21, L27-V29 NMR [97] -5.4 5.2 W19-V21, L27-V29
Pancreatic phospholipase A2, group IB 4p2p W3 Flq [11] -8.7 3.5 W3, H17, L19, M20, L64, V65
Bee venom phospholipase A2 1poc I2, K14, I78 SL* [42] -10.3 5.7 I1, I2, Y3, P4, G5,I78, F82, M86, L90
Human secretory phospholipase A2, group IIa 1n28 V3, K10, L19, F23, F63 SL* [43] -6.6 4.8 V3, L19, F23, F63
Snake venom phospholipase A2, group I 1poa W61, F64, Y110 Bn [98] -5.4 4.5 Y3, W18, W19, W61, F64
Snake venom phospholipase A2, group II 1vap W20, W30, W109 FL [99] -10.2 4.3 F3, M13, L19, W30, M61, W109
Snake venom phospholipase A2, group IIB 1jia Y120, P121, I124, L125 Bn [100]d -8.7 3.1 V20, F24, A119, P121, I124
Phospholipase C 2ptd I43, W47, W242 Bn [101] -6.0 3.9 P42, I43, W47, T240, A241, W242
α-toxin (bacterial phospholipase C) 1ca1 Y331, F334 Fn [102] -4.5 2.2 V143, A146, M210, W214, Y331, F334
15-lipoxygenase 1lox Y15, F70, L71, W181c, L195 Bn [103] -7.4 6.3 L71, I194, L195, L291, Y292, F412
8R-lipoxygenase 1zq4 W413, W449 FL, Fn [104] -5.0 5.9 W413, F414, Y448, W449, V560, M570
Cholesterol oxidase 1coy M81 FLq [105] -4.1 5.3 M81, M332, W333, L369, Y372
Signal peptidase 1kn9 W300 Fn [106] -4.5 4.5 W300, M301, F303, L314, L316
Synapsin I 1auv Regions 166–192, 233–258, 278–327 CL [107] -4.4 2.5 L168, V172, L297
α-synuclein 1xq8 T59, V63, G67, V70, V74, V77, T81, A85, A89 SL [108] -22.8 17.9 T59, V63, V66, G67, V70, V74, V77, A78, T81, A85, I88, A89
Perfringolysin 1pfo W466 Bn [109] -5.5 3.4 L462, W466, L491, Y492
Daptomycin 1t5n Kyn14 FL [110] -9.8 4.9 Dka1, W2, Kyn14
Lactoferricin B 1lfc W6, W8 FL [111] -4.6 5.3 W6, W8, L13-P16, I18
Hanatoxin 1d1h W30 FLq [112] -2.5 3.9 Y4, L5, F6, W30
Subtilosin 1pxq W34 FL [113] -6.7 5.1 F22, F31, W34
  1. aBn – based on membrane binding affinities of mutants; SL – spin-labeling data based on depth parameters Φ (SL* – based only on exposure of labels to polar probes); FL – fluorescence; FLq – fluorescence quenching; Fn – functional studies of mutants; CL – chemical labeling. Underlined residues are located in the lipid headgroup region, close to the hydrophobic boundaries. Coinciding residues in two sets are shown as bold.
  2. bΔG calc , calculated binding energies (kcal/mol); D (Å) maximal penetration depths of atoms into the hydrocarbon core. Residues penetrating into lipid acyl chain region are identified based on locations of side-chain atoms or NH hydrogens (when compared with NMR data).
  3. cW181 is missing in the crystal structure.
  4. dData for a homologous protein
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