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.1998 Sep 29;95(20):11673-8.
doi: 10.1073/pnas.95.20.11673.

Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex

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Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex

L Essen et al. Proc Natl Acad Sci U S A..

Abstract

Heterogenous nucleation on small molecule crystals causes a monoclinic crystal form of bacteriorhodopsin (BR) in which trimers of this membrane protein pack differently than in native purple membranes. Analysis of single crystals by nano-electrospray ionization-mass spectrometry demonstrated a preservation of the purple membrane lipid composition in these BR crystals. The 2.9-A x-ray structure shows a lipid-mediated stabilization of BR trimers where the glycolipid S-TGA-1 binds into the central compartment of BR trimers. The BR trimer/lipid complex provides an example of local membrane thinning as the lipid head-group boundary of the central lipid patch is shifted by 5 A toward the membrane center. Nonbiased electron density maps reveal structural differences to previously reported BR structures, especially for the cytosolic EF loop and the proton exit pathway. The terminal proton release complex now comprises an E194-E204 dyad as a diffuse proton buffer.

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Figures

Figure 1
Figure 1
(A) Negative-ion nanoESI-MS of lipidextracts from PM. The phospholipids PGS and PGP-Me show signals atm/z 442.5, 449.5 (z= 2), and 885.6. The signal atm/z899.5 is absent because of the double-negative state of detectedPGP-Me. PG, the major hydrolysis product of PGS and PGP-Me, wasdetected atm/z 805.6; phosphatidicacid (PA,m/z 731.5) is absent. Thesulfated glycolipids S-TGA-1 and S-TeGA (sulfatedtetraglycosyldiphytanylglycerol, a minor species in PM) show signals atm/z 1217.6 and 1379.8. The phospho- andglycolipids were identified by class-specific fragmentations in tandemMS (MS/MS) analyses at their optimized collision energies.(B) NanoESI-MS of the lipid extract of the BR crystal usedfor crystallographic data collection (shown inC).Pictograms summarize the experimental setup according to ref. .
Figure 2
Figure 2
Comparison between monomer B of the BR trimer(yellow) and recent BR structures (green, ref. ; cyan, ref. ;orange, ref. 23). The stereodiagrams show the cytosolic (A)and extracellular (B) surface loops. (C)Conformation of the EF loop and the cytosolic ends of helices E and F.Thesigmaa-weighted 2Fobs-Fcalcelectron density (14) is contoured at 0.175 e/Å3. Figs.2–4 were made withmolscript (42) andraster3d(43).
Figure 3
Figure 3
Lipid binding and layer packing of BR trimers inPM and monoclinic BR crystals. (A) Top view on the BRtrimer/lipid complex from the extracellular side. Lipids are shown asspace-filling models. Single phytanols (gray) are located on thecytosolic side of the BR trimer. (B) View along thea*-axis of the monoclinic BR crystal (monomer A, yellow;B, green; C, red). (C) Binding site of the glycolipidS-TGA-1 as viewed from the trimer axis. (D) Cross section ofthe PM model. Monomer B and an associated S-TGA-1 lipid replaced BR andthe lipids 261, 266 of the previous PM model of Grigorieffetal. (11). The white lines show the head group/lipidboundaries.
Figure 4
Figure 4
Proton conductance in the BR trimer.(A) Proton collection surface of the cytosolic side.(B) Proton exit surface of the extracellular side.Electrostatic surface potentials were calculated withgrasp(44) and shown from −20 kcal/mol (red) to +20 kcal/mol (blue). Theinternal residues D96, D115, and E204 were assumed to be protonated.(C) Internal cavities of BR. Twelve cavities were found byvoidoo (45) using a probe radius of 1 Å and a primary gridspacing of 0.25 Å for enhanced sensitivity. Eight cavities (blue)fulfilled the criteria to be discontinuous from the molecular surfaceand capable of accommodating at least one water. White numbers indicatethe maximal number of waters per cavity. (D) Proton exitpathway with the E194/E204 dyad (white). Cavities are shown in blue,H bonds within a 3.5-Å cutoff in white.
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References

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