Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle

Abstract

The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

Fig. 1.

Architecture and constituents of a spherical chromatophore vesicle from R. sphaeroides constructed from AFM/LD data (37, 39). (a) Light-harvesting complexes, LH2 (green) and LH1 (red), absorb light and transfer the resulting excitation to the RC (blue), which subsequently initiates electron transfers reducing quinone to hydroquinone (not shown); the bc₁ complex (yellow) oxidizes hydroquinone to create a proton gradient across the membrane, which in turn is used by ATP synthase (orange) for ATP production. Electrons are shuttled back to the RC by cytochrome c₂ (not shown). The current study focuses solely on the light-harvesting process within the vesicle, and accordingly, bc₁ complexes and ATP synthase are not considered, being depicted schematically peripheral to the chromatophore, although other bc₁ complexes may be located within the vesicle closer to the RC–LH1–PufX complexes. The ratio of surface area covered by RC-LH1 versus LH2 complexes is 1:1.31 for the first vesicle (shown) and 1:3.23 for the second vesicle (Fig. 2 d and f). (b) BChls (represented by their porphyrin rings) of the atomic model for the RC-LH1 complex constructed for this study based on cryo-EM data (24). The PufX polypeptide is not included. (c) BChls of the LH2 complex based on R. acidophila (23). AFM images (d) (37) are used to identify the arrangement of pigment–protein complexes within planar patches (e). An area-preserving map from the plane on to the sphere, the inverse-Mollweide projection (89) (Eq. 1), is then used to position pigment–protein complexes on the vesicle surface (f). To minimize distortions, multiple planar patches were used, whose sizes are small compared with the inner diameter of the reconstructed vesicle (60 nm). [a–c were made with the program VMD (Visual Molecular Dynamics) (90).]

Fig. 2.

Electronic interactions and excitation energy transfer across a chromatophore vesicle. BChls are represented by their porphyrin rings and colored as follows: blue, LH2 B800; green, B850; red, LH1 B875; purple, RC/accessory; orange, RC/special pair. (a) Electronic couplings (see text) between BChls of the reconstructed chromatophore vesicle. For the sake of clarity, only couplings >3 cm⁻¹ are shown on a logarithmic scale. (b) The rate of excitation transfer (Eq. 2) between the BChl groups of the LH2 B850 ring (green) and the S-shaped LH1 assembly (red), represented as bonds connecting the respective center of mass of each BChl group. For clarity, only strong connections are displayed on a logarithmic scale and the transfers involving other BChl groups, such as LH2 B800 BChls or the RC BChls, are not shown. (c) Excitation lifetime as a function of the initially excited BChl for the first vesicle (compare with a and b). (d) Excitation lifetime as a function of the initially excited BChl for the second, LH2-rich, vesicle. The cross-transfer probability between RCs, i.e., the probability that an excitation which has just been detrapped from a RC will be trapped at a given RC, is displayed in e and f for the first and second vesicles, respectively, for a detrapping event at the RC pair shown at the center. The probability is color-coded according to the color bar shown. Notably, excitation sharing between RCs arises mainly between adjacent RCs. The distribution of excitation lifetimes (compare with c and d) are shown in g and h for the two vesicles as a function of distance to the nearest RC (filled, B850 BChls; open, B800 BChls). The continuity of the distributions in g and h indicates that all BChl clusters are functionally connected. The distribution of lifetimes is reminiscent of random walks on graphs. [a and b were made with the program VMD (Visual Molecular Dynamics) (90).]