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

Lomize, Andrei L; Pogozheva, Irina D; Lomize, Mikhail A; Mosberg, Henry I

doi:10.1186/1472-6807-7-44

BMC Structural Biology

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

		Experiment^a			Calculation^b
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, W181^c, 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

^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.
^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).
^cW181 is missing in the crystal structure.
^dData for a homologous protein

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ISSN: 1472-6807

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