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Figure 1 (A) Topology model of R.gelatinosus LH2 (strain S1; gene sequence accession No. AF312921). The  - (consisting of 71 amino acids) and the  -polypeptide (consisting of 51 amino acids) cross the membrane once each. The boxed regions in the sequence correspond to -helical stretches in the R.acidophila LH2 structure, after sequence alignment [using Clustal_W (http://www.ch.embnet.org/software/ClustalW.html)]; amino acids surrounded by circles in dark gray are predicted to be transmembrane [using TMpred (http://www.ch.embnet.org/software/TMPRED_form.html)], those surrounded by circles in light gray are predicted to be -helical [using GOR4 (http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl/page=npsa_gor4.html)]. The triangle indicates the thermolysin cleavage site on the C-terminus of the -polypeptide. The arrow points towards the center of the nonamer in the membrane plane. (B) Silver-stained SDS–polyacrylamide 10% (w/v) gel. Columns from left to right: (1) markers at 97.4, 66.2, 42.7 and 31.0 kDa; (2) thermolysin (37 kDa); (3) crystals of native LH2, band at 115 kDa; (4) crystals of thermolysin-treated LH2, band at 82 kDa. (C) Absorption spectra of native and thermolysin-cleaved LH2 reconstituted into lipid bilayers. The bacteriochlorophyll and carotenoid absorption spectra do not change upon cleavage of the C-terminus of the -subunit (native LH2, black line; digested LH2, gray line). The absorption spectra document the native state of the protein: arrows 1–3, carotenoid peaks at 460, 488 and 517 nm, respectively; arrow 4, Qx peak at 595 nm; arrow 5, Qy peak at 802 nm; arrow 6, Qy peak at 859 nm.
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 | Figure 2 Height measurements of LH2 two-dimensional crystals adsorbed to mica in buffer (10 mM Tris–HCl pH 7.2, 150 mM KCl, 25 mM MgCl2) and imaged under physiological conditions (10 mM Tris–HCl pH 7.2, 150 mM KCl). (A) AFM topograph of double and multilayered areas which can be distinguished clearly from single layer crystals by their height (full image size, 4  m; full gray scale, 30 nm). (B) Section analysis along the white line in image (A). The two-dimensional crystals show a uniform height of 64.5  2.8 Å (n = 46) (vertical scale bar: 100 Å). (C) AFM topograph of an LH2 sheet containing particles in up-and-down crystalline packing in the center and crystalline areas exposing only the lower surface on the edges (full image size, 700 nm; full gray scale, 10 nm). (D) Section analysis along the white line in image (C). The two different surface types are clearly visible. While the central region shows a characteristic section analysis for up-and-down packing with strong surface corrugation, the edge areas appear smooth and show a height of only 57 Å above the mica support (vertical scale bar: 50 Å). (E) Medium magnification image of a crystalline sheet of LH2 rings. At this magnification, the ring structure of the complexes is already clearly visible. The crystals show coherence only over small regions, and lattice displacements of half a unit cell are frequent. While the ring structure of the high side is clearly visible in the crystalline areas, the lower circles can be seen better within the crystal defects (bottom right) (full image size, 400 nm; full gray scale, 4 nm). (F) Section analysis along the white line in image (E). The height of LH2 rings can be measured directly from such section analyses of raw data (vertical scale bar: 20 Å).
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Figure 3 High-resolution raw data AFM topographs and corresponding averages (all in 15° tilted representation and corresponding heights). Averages were calculated after a single particle alignment and 9-fold symmetrized. (A) Raw data topography of the strongly ( 14 Å) protruding surface of the native LH2 complex. The 9-fold symmetry is visible in the raw data. (B) Average of image (A) (full gray scale: 14 Å). (C) Raw data topography of the weakly (5.6 Å) protruding surface of the native LH2 complex. (D) Average of image (C) (full gray scale: 6 Å). (E) Raw data topography of the strongly (9 Å) protruding surface of the digested LH2 complex. (F) Average of image (E). The loss of protruding structure compared with (B) localizes the C-terminal position of the -subunit (full gray scale: 9 Å). (G) Raw data topography of the weakly (5.4 Å) protruding surface of the digested LH2 complex. (H) Average of image (G). The proteolysis had no influence on the topography of the weakly protruding surface (full gray scale: 6 Å). Raw data are displayed with a full gray scale corresponding to 20 Å. Scale bars represent 100 Å in the raw data and 20 Å in the averages.
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 | Figure 4 (A and B) Raw data AFM topographs showing an 120 Å ring surrounded by LH2 nonamers revealing top ring distances between the complexes of 35 Å (see Discussion; scale bar, 100 Å; full gray scale, 20 Å).
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