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Liu LN, Bracun L, Li M. Structural diversity and modularity of photosynthetic RC-LH1 complexes. Trends Microbiol 2024; 32:38-52. [PMID: 37380557 DOI: 10.1016/j.tim.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
Bacterial photosynthesis is essential for sustaining life on Earth as it aids in carbon assimilation, atmospheric composition, and ecosystem maintenance. Many bacteria utilize anoxygenic photosynthesis to convert sunlight into chemical energy while producing organic matter. The core machinery of anoxygenic photosynthesis performed by purple photosynthetic bacteria and Chloroflexales is the reaction center-light-harvesting 1 (RC-LH1) pigment-protein supercomplex. In this review, we discuss recent structural studies of RC-LH1 core complexes based on the advancement in structural biology techniques. These studies have provided fundamental insights into the assembly mechanisms, structural variations, and modularity of RC-LH1 complexes across different bacterial species, highlighting their functional adaptability. Understanding the natural architectures of RC-LH1 complexes will facilitate the design and engineering of artificial photosynthetic systems, which can enhance photosynthetic efficiency and potentially find applications in sustainable energy production and carbon capture.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China.
| | - Laura Bracun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Tani K, Kanno R, Ji XC, Satoh I, Kobayashi Y, Hall M, Yu LJ, Kimura Y, Mizoguchi A, Humbel BM, Madigan MT, Wang-Otomo ZY. Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex. Nat Commun 2023; 14:846. [PMID: 36792596 PMCID: PMC9932092 DOI: 10.1038/s41467-023-36460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the light-harvesting 1-reaction center (LH1-RC) complex, but lacks protein-U, a U-shaped polypeptide in the LH1-RC of its close relative Rba. sphaeroides. Here we present a cryo-EM structure of the Rba. capsulatus LH1-RC purified by DEAE chromatography. The crescent-shaped LH1-RC exhibits a compact structure containing only 10 LH1 αβ-subunits. Four αβ-subunits corresponding to those adjacent to protein-U in Rba. sphaeroides were absent. PufX in Rba. capsulatus exhibits a unique conformation in its N-terminus that self-associates with amino acids in its own transmembrane domain and interacts with nearby polypeptides, preventing it from interacting with proteins in other complexes and forming dimeric structures. These features are discussed in relation to the minimal requirements for the formation of LH1-RC monomers and dimers, the spectroscopic behavior of both the LH1 and RC, and the bioenergetics of energy transfer from LH1 to the RC.
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Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, Japan.
| | - Ryo Kanno
- Scientific Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-Son, Kunigami-Gun, Okinawa, Japan.,Quantum wave microscopy unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-Son, Kunigami-Gun, Okinawa, Japan
| | | | | | | | - Malgorzata Hall
- Scientific Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-Son, Kunigami-Gun, Okinawa, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Japan
| | | | - Bruno M Humbel
- Scientific Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-Son, Kunigami-Gun, Okinawa, Japan.,Department of Cell Biology and Neuroscience, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, USA
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Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex. Nat Commun 2022; 13:1977. [PMID: 35418573 PMCID: PMC9007983 DOI: 10.1038/s41467-022-29563-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.
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A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex. Nat Commun 2021; 12:6300. [PMID: 34728609 PMCID: PMC8564508 DOI: 10.1038/s41467-021-26561-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/01/2021] [Indexed: 11/27/2022] Open
Abstract
Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general. Rhodobacter (Rba.) sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present the 2.9 Å cryo-EM structure of the monomeric light-harvesting-reaction center core complex from Rba. sphaeroides strain IL106, which revealed the position and conformation of PufX and the presence of an additional component protein-U, an integral membrane protein.
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Bracun L, Yamagata A, Christianson BM, Terada T, Canniffe DP, Shirouzu M, Liu LN. Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution. SCIENCE ADVANCES 2021; 7:7/25/eabf8864. [PMID: 34134992 PMCID: PMC8208714 DOI: 10.1126/sciadv.abf8864] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/04/2021] [Indexed: 05/07/2023]
Abstract
The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo-electron microscopy structure of the RC-LH1-PufX supercomplex from Rhodobacter veldkampii at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular "cross brace" to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation.
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Affiliation(s)
- Laura Bracun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Bern M Christianson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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6
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Abstract
Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two types of intensively studied bacterial photosynthetic membranes: the chromatophore membranes of purple bacteria and the thylakoid membranes of cyanobacteria. Both systems are distinct from the plasma membrane, and both have a distinctive protein composition that reflects their specialized roles. Chromatophores are formed from plasma membrane invaginations, while thylakoid membranes appear to be an independent intracellular membrane system. We discuss the techniques that can be applied to study the organization and dynamics of these membrane systems, including electron microscopy techniques, atomic force microscopy, and many variants of fluorescence microscopy. We go on to discuss the insights that havebeen acquired from these techniques, and the role of membrane dynamics in the physiology of photosynthetic membranes. Membrane dynamics on multiple timescales are crucial for membrane function, from electron transport on timescales of microseconds to milliseconds to regulation and biogenesis on timescales of minutes to hours. We emphasize the open questions that remain in the field.
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Affiliation(s)
- Conrad W. Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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Nagatsuma S, Gotou K, Yamashita T, Yu LJ, Shen JR, Madigan M, Kimura Y, Wang-Otomo ZY. Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:461-468. [DOI: 10.1016/j.bbabio.2019.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/06/2019] [Accepted: 04/07/2019] [Indexed: 02/06/2023]
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Ting JJL. Proposal for verifying dipole properties of light-harvesting antennas. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 179:134-138. [PMID: 29367148 DOI: 10.1016/j.jphotobiol.2018.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 11/26/2022]
Abstract
For light harvesters with a reaction center complex (LH1-RC complex) of three types, we propose an experiment to verify our analysis based upon antenna theories that automatically include the required structural information. Our analysis conforms to the current understanding of light-harvesting antennas in that we can explain known properties of these complexes. We provide an explanation for the functional roles of the notch at the light harvester, a functional role of the polypeptide called PufX or W at the opening, a functional role of the special pair, a reason that the cross section of the light harvester must not be circular, a reason that the light harvester must not be spherical, reasons for the use of dielectric bacteriochlorophylls instead of conductors to make the light harvester, a mechanism to prevent damage from excess sunlight, an advantage of the dimeric form, and reasons for the modular design of nature. Based upon our analysis we provide a mechanism for dimerization. We predict that the dimeric form of light-harvesting complexes is favored under intense sunlight. We further comment upon the classification of the dimeric or S-shape complexes. The S-shape complexes should not be considered as the third type of light harvester but simply as a composite form.
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Sznee K, Crouch LI, Jones MR, Dekker JP, Frese RN. Variation in supramolecular organisation of the photosynthetic membrane of Rhodobacter sphaeroides induced by alteration of PufX. PHOTOSYNTHESIS RESEARCH 2014; 119:243-256. [PMID: 24197265 DOI: 10.1007/s11120-013-9949-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/24/2013] [Indexed: 06/02/2023]
Abstract
In purple bacteria of the genus Rhodobacter (Rba.), an LH1 antenna complex surrounds the photochemical reaction centre (RC) with a PufX protein preventing the LH1 complex from completely encircling the RC. In membranes of Rba. sphaeroides, RC-LH1 complexes associate as dimers which in turn assemble into longer range ordered arrays. The present work uses linear dichroism (LD) and dark-minus-light difference LD (ΔLD) to probe the organisation of genetically altered RC-LH1 complexes in intact membranes. The data support previous proposals that Rba. capsulatus, and Rba. sphaeroides heterologously expressing the PufX protein from Rba. capsulatus, produce monomeric core complexes in membranes that lack long-range order. Similarly, Rba. sphaeroides with a point mutation in the Gly 51 residue of PufX, which is located on the membrane-periplasm interface, assembles mainly non-ordered RC-LH1 complexes that are most likely monomeric. All the Rba. sphaeroides membranes in their ΔLD spectra exhibited a spectral fingerprint of small degree of organisation implying the possibility of ordering influence of LH1, and leading to an important conclusion that PufX itself has no influence on ordering RC-LH1 complexes, as long-range order appears to be induced only through its role of configuring RC-LH1 complexes into dimers.
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Affiliation(s)
- Kinga Sznee
- Division of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands,
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Semchonok DA, Chauvin JP, Frese RN, Jungas C, Boekema EJ. Structure of the dimeric RC-LH1-PufX complex from Rhodobaca bogoriensis investigated by electron microscopy. Philos Trans R Soc Lond B Biol Sci 2013; 367:3412-9. [PMID: 23148268 DOI: 10.1098/rstb.2012.0063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Electron microscopy and single-particle averaging were performed on isolated reaction centre (RC)-antenna complexes (RC-LH1-PufX complexes) of Rhodobaca bogoriensis strain LBB1, with the aim of establishing the LH1 antenna conformation, and, in particular, the structural role of the PufX protein. Projection maps of dimeric complexes were obtained at 13 Å resolution and show the positions of the 2 × 14 LH1 α- and β-subunits. This new dimeric complex displays two open, C-shaped LH1 aggregates of 13 αβ polypeptides partially surrounding the RCs plus two LH1 units forming the dimer interface in the centre. Between the interface and the two half rings are two openings on each side. Next to the openings, there are four additional densities present per dimer, considered to be occupied by four copies of PufX. The position of the RC in our model was verified by comparison with RC-LH1-PufX complexes in membranes. Our model differs from previously proposed configurations for Rhodobacter species in which the LH1 ribbon is continuous in the shape of an S, and the stoichiometry is of one PufX per RC.
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Affiliation(s)
- Dmitry A Semchonok
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen, The Netherlands
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Crouch LI, Jones MR. Cross-species investigation of the functions of the Rhodobacter PufX polypeptide and the composition of the RC-LH1 core complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:336-52. [PMID: 22079525 DOI: 10.1016/j.bbabio.2011.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/24/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
Abstract
In well-characterised species of the Rhodobacter (Rba.) genus of purple photosynthetic bacteria it is known that the photochemical reaction centre (RC) is intimately-associated with an encircling LH1 antenna pigment protein, and this LH1 antenna is prevented from completely surrounding the RC by a single copy of the PufX protein. In Rba. veldkampii only monomeric RC-LH1 complexes are assembled in the photosynthetic membrane, whereas in Rba. sphaeroides and Rba. blasticus a dimeric form is also assembled in which two RCs are surrounded by an S-shaped LH1 antenna. The present work established that dimeric RC-LH1 complexes can also be isolated from Rba. azotoformans and Rba. changlensis, but not from Rba. capsulatus or Rba. vinaykumarii. The compositions of the monomers and dimers isolated from these four species of Rhodobacter were similar to those of the well-characterised RC-LH1 complexes present in Rba. sphaeroides. Pigment proteins were also isolated from strains of Rba. sphaeroides expressing chimeric RC-LH1 complexes. Replacement of either the Rba. sphaeroides LH1 antenna or PufX with its counterpart from Rba. capsulatus led to a loss of the dimeric form of the RC-LH1 complex, but the monomeric form had a largely unaltered composition, even in strains in which the expression level of LH1 relative to the RC was reduced. The chimeric RC-LH1 complexes were also functional, supporting bacterial growth under photosynthetic conditions. The findings help to tease apart the different functions of PufX in different species of Rhodobacter, and a specific protein structural arrangement that allows PufX to fulfil these three functions is proposed.
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Hsin J, LaPointe LM, Kazy A, Chipot C, Senes A, Schulten K. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix. J Am Chem Soc 2011; 133:14071-81. [PMID: 21790140 PMCID: PMC3168531 DOI: 10.1021/ja204869h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the Rhodobacter (Rba.) species of photosynthetic purple bacteria, a single transmembrane α-helix, PufX, is found within the core complex, an essential photosynthetic macromolecular assembly that performs the absorption and the initial processing of light energy. Despite its structural simplicity, many unresolved questions surround PufX, the most important of which is its location within the photosynthetic core complex. One proposed placement of PufX is at the center of a core complex dimer, where two PufX helices associate in the membrane and form a homodimer. Inability for PufX of certain Rba. species to form a homodimer is thought to lead to monomeric core complexes. In the present study, we employ a combination of computational and experimental techniques to test the hypothesized homodimerization of PufX. We carry out a systematic investigation to measure the dimerization affinity of PufX from four Rba. species, Rba. blasticus , Rba. capsulatus , Rba. sphaeroides , and Rba. veldkampii , using a molecular dynamics-based free-energy method, as well as experimental TOXCAT assays. We found that the four PufX helices have substantially different dimerization affinities. Both computational and experimental techniques demonstrate that species with dimeric core complexes have PufX that can potentially form a homodimer, whereas the one species with monomeric core complexes has a PufX with little to no dimerization propensity. Our analysis of the helix-helix interface revealed a number of positions that may be important for PufX dimerization and the formation of a hydrogen-bond network between these GxxxG-containing helices. Our results suggest that the different oligomerization states of core complexes in various Rba. species can be attributed, among other factors, to the different propensity of its PufX helix to homodimerize.
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13
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Ratcliffe EC, Tunnicliffe RB, Ng IW, Adams PG, Qian P, Holden-Dye K, Jones MR, Williamson MP, Hunter CN. Experimental evidence that the membrane-spanning helix of PufX adopts a bent conformation that facilitates dimerisation of the Rhodobacter sphaeroides RC-LH1 complex through N-terminal interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:95-107. [PMID: 20937243 DOI: 10.1016/j.bbabio.2010.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 10/19/2022]
Abstract
The PufX polypeptide is an integral component of some photosynthetic bacterial reaction center-light harvesting 1 (RC-LH1) core complexes. Many aspects of the structure of PufX are unresolved, including the conformation of its long membrane-spanning helix and whether C-terminal processing occurs. In the present report, NMR data recorded on the Rhodobacter sphaeroides PufX in a detergent micelle confirmed previous conclusions derived from equivalent data obtained in organic solvent, that the α-helix of PufX adopts a bent conformation that would allow the entire helix to reside in the membrane interior or at its surface. In support of this, it was found through the use of site-directed mutagenesis that increasing the size of a conserved glycine on the inside of the bend in the helix was not tolerated. Possible consequences of this bent helical structure were explored using a series of N-terminal deletions. The N-terminal sequence ADKTIFNDHLN on the cytoplasmic face of the membrane was found to be critical for the formation of dimers of the RC-LH1 complex. It was further shown that the C-terminus of PufX is processed at an early stage in the development of the photosynthetic membrane. A model in which two bent PufX polypeptides stabilise a dimeric RC-LH1 complex is presented, and it is proposed that the N-terminus of PufX from one half of the dimer engages in electrostatic interactions with charged residues on the cytoplasmic surface of the LH1α and β polypeptides on the other half of the dimer.
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Affiliation(s)
- Emma C Ratcliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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14
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Liu LN, Sturgis JN, Scheuring S. Native architecture of the photosynthetic membrane from Rhodobacter veldkampii. J Struct Biol 2010; 173:138-45. [PMID: 20797440 DOI: 10.1016/j.jsb.2010.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/18/2010] [Accepted: 08/19/2010] [Indexed: 11/27/2022]
Abstract
The photosynthetic membrane in purple bacteria contains several pigment-protein complexes that assure light capture and establishment of the chemiosmotic gradient. The bioenergetic tasks of the photosynthetic membrane require the strong interaction between these various complexes. In the present work, we acquired the first images of the native outer membrane architecture and the supramolecular organization of the photosynthetic apparatus in vesicular chromatophores of Rhodobacter (Rb.) veldkampii. Mixed with LH2 (light-harvesting complex 2) rings, the PufX-containing LH1-RC (light-harvesting complex 1--reaction center) core complexes appear as C-shaped monomers, with random orientations in the photosynthetic membrane. Within the LH1 fence surrounding the RC, a remarkable gap that is probably occupied (or partially occupied) by PufX is visualized. Sequence alignment revealed that one specific region in PufX may be essential for PufX-induced core dimerization. In this region of ten amino acids in length all Rhodobacter species had five conserved amino acids, with the exception of Rb. veldkampii. Our findings provide direct evidence that the presence of PufX in Rb. veldkampii does not directly govern the dimerization of LH1-RC core complexes in the native membrane. It is indicated, furthermore, that the high membrane curvature of Rb. veldkampii chromatophores (Rb. veldkampii features equally small vesicular chromatophores alike Rb. sphaeroides) is not due to membrane bending induced by dimeric RC-LH1-PufX cores, as it has been proposed in Rb. sphaeroides.
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Affiliation(s)
- Lu-Ning Liu
- Institut Curie, U1006 INSERM, UMR168 CNRS, 26 Rue d'Ulm, 75248 Paris, France
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15
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Dezi M, Fribourg PF, Di Cicco A, Arnaud O, Marco S, Falson P, Di Pietro A, Lévy D. The multidrug resistance half-transporter ABCG2 is purified as a tetramer upon selective extraction from membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:2094-101. [PMID: 20691149 DOI: 10.1016/j.bbamem.2010.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 07/27/2010] [Accepted: 07/27/2010] [Indexed: 01/07/2023]
Abstract
ABCG2 is a human membrane ATP-binding cassette half-transporter that hydrolyzes ATP to efflux a large number of chemotherapeutic agents. Several oligomeric states of ABCG2 from homodimers to dodecamers have been reported depending on the overexpression systems and/or the protocols used for purification. Here, we compared the oligomeric state of His(6)-ABCG2 expressed in Sf9 insect cells and in human Flp-In-293/ABCG2 cells after solubilization in mild detergents. His(6)-ABCG2 was purified through a new approach involving its specific recognition onto a functionalized lipid layer containing a Ni-NTA lipid. This approach allowed the purification of His-ABCG2 in presence of all solubilized membrane components that might be involved in the stabilisation of native oligomers and without requiring any additional washing or concentration passages. ABCG2 purified onto the NiNTA lipid surfaces were directly analyzed by electron microscopy and by biochemical assays. Altogether, our data are consistent with a tetrameric organization of ABCG2 when expressed in either heterologous Sf9 insect cells or in human homologous cells.
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Affiliation(s)
- Manuela Dezi
- Institut Curie, Centre de Recherche, Paris, F-75231, France
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16
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Hsin J, Strümpfer J, Sener M, Qian P, Hunter CN, Schulten K. Energy Transfer Dynamics in an RC-LH1-PufX Tubular Photosynthetic Membrane. NEW JOURNAL OF PHYSICS 2010; 12:085005. [PMID: 21152381 PMCID: PMC2997751 DOI: 10.1088/1367-2630/12/8/085005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Light absorption and the subsequent transfer of excitation energy are the first two steps of the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of light-harvesting complexes II, the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet computationally costly, treat the coupling between BChls and their protein environment. A widely employed description, generalized Förster theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rhodobacter sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced in the BChl organization. It is shown that the energy transfer dynamics is not affected by the considered changes in the BChl organization, and that generalized Förster theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.
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Affiliation(s)
- Jen Hsin
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strümpfer
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Melih Sener
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
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17
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Crouch LI, Holden-Dye K, Jones MR. Dimerisation of the Rhodobacter sphaeroides RC-LH1 photosynthetic complex is not facilitated by a GxxxG motif in the PufX polypeptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1812-9. [PMID: 20646993 DOI: 10.1016/j.bbabio.2010.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/09/2010] [Accepted: 07/13/2010] [Indexed: 11/24/2022]
Abstract
In purple photosynthetic bacteria the initial steps of light energy transduction take place in an RC-LH1 complex formed by the photochemical reaction centre (RC) and the LH1 light harvesting pigment-protein. In Rhodobacter sphaeroides, the RC-LH1 complex assembles in a dimeric form in which two RCs are surrounded by an S-shaped LH1 antenna. There is currently debate over the detailed architecture of this dimeric RC-LH1 complex, with particular emphasis on the location and precise function of a minor polypeptide component termed PufX. It has been hypothesised that the membrane-spanning helical region of PufX contains a GxxxG dimerisation motif that facilitates the formation of a dimer of PufX at the interface of the RC-LH1 dimer, and more specifically that the formation of this PufX dimer seeds assembly of the remaining RC-LH1 dimer (J. Busselez et al., 2007). In the present work this hypothesis was tested by site directed mutagenesis of the glycine residues proposed to form the GxxxG motif. Mutation of these glycines to leucine did not decrease the propensity of the RC-LH1 complex to assemble in a dimeric form, as would be expected from experimental studies of the effect of mutation on GxxxG motifs in other membrane proteins. Indeed increased yields of dimer were seen in two of the glycine-to-leucine mutants constructed. It is concluded that the PufX from Rhodobacter sphaeroides does not contain a genuine GxxxG helix dimerisation motif.
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Affiliation(s)
- Lucy I Crouch
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol, UK
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18
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Hsin J, Chandler DE, Gumbart J, Harrison CB, Şener M, Strumpfer J, Schulten K. Self-assembly of photosynthetic membranes. Chemphyschem 2010; 11:1154-9. [PMID: 20183845 PMCID: PMC3086839 DOI: 10.1002/cphc.200900911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Indexed: 11/08/2022]
Abstract
Bacterial photosynthetic membranes, also known as chromatophores, are tightly packed with integral membrane proteins that work together to carry out photosynthesis. Chromatophores display a wide range of cellular morphologies; spherical, tubular, and lamellar chromatophores have all been observed in different bacterial species, or with different protein constituents. Through recent computational modeling and simulation, it has been demonstrated that the light-harvesting complexes abundant in chromatophores induce local membrane curvature via multiple mechanisms. These protein complexes assemble to generate a global curvature and sculpt the chromatophores into various cellular-scale architectures.
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Affiliation(s)
- Jen Hsin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Danielle E. Chandler
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - James Gumbart
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | | | - Melih Şener
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strumpfer
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
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19
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Hsin J, Chipot C, Schulten K. A glycophorin A-like framework for the dimerization of photosynthetic core complexes. J Am Chem Soc 2010; 131:17096-8. [PMID: 19891482 DOI: 10.1021/ja905903n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The core complex in photosynthetic bacteria plays a central role in photosynthesis. This molecular assembly is composed of two protein complexes, viz., the light-harvesting complex I (LH1), which absorbs sunlight by means of the protein-bound bacteriochlorophylls, and the reaction center (RC), which uses the light-excitation energy absorbed by the LH complexes to produce a transmembrane (TM) charge gradient, subsequently employed for energy conversion. In Rhodobacter (Rba.) sphaeroides, the core complex contains, in addition, two copies of the single TM alpha-helix protein, PufX, and forms a (RC-LH1-PufX)(2) dimer. To this date, no high-resolution structure has been reported for the entire core complex. In particular, the location of PufX within the (RC-LH1-PufX)(2) dimer is still the subject of much debate. Here, one of the proposed locations for PufX, requiring its dimerization, is examined. The PufX-dimer model on the basis of the glycophorin A (GpA) dimer was constructed, and its robustness was probed through a series of molecular dynamics (MD) simulations. The free-energy change due to the replacement of Gly35 by valine was also determined to assess whether this mutation is responsible for distinct PufX oligomerization states in different Rba. species. The present study shows that PufX helices form a stable GpA-like dimer with a helix-helix crossing angle that could constitute the molecular basis of the reported highly bent and V-shaped structure of the Rba. sphaeroides core complex dimer.
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Affiliation(s)
- Jen Hsin
- Department of Physics and Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, Urbana 61801, USA
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20
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Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophys J 2009; 97:321-9. [PMID: 19580770 PMCID: PMC2711417 DOI: 10.1016/j.bpj.2009.04.031] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 04/04/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022] Open
Abstract
In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-LH1-PufX dimers aggregate into tubular vesicles with a radius of approximately 250-550 A, making RC-LH1-PufX one of the few integral membrane proteins known to actively induce membrane curvature. Recently, a three-dimensional electron microscopy density map showed that the Rba. sphaeroides RC-LH1-PufX dimer exhibits a prominent bend at its dimerizing interface. To investigate the curvature properties of this highly bent protein, we employed molecular dynamics simulations to fit an all-atom structural model of the RC-LH1-PufX dimer within the electron microscopy density map. The simulations reveal how the dimer produces a membrane with high local curvature, even though the location of PufX cannot yet be determined uniquely. The resulting membrane curvature agrees well with the size of RC-LH1-PufX tubular vesicles, and demonstrates how the local curvature properties of the RC-LH1-PufX dimer propagate to form the observed long-range organization of the Rba. sphaeroides tubular vesicles.
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Affiliation(s)
- Jen Hsin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - James Gumbart
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Leonardo G. Trabuco
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Elizabeth Villa
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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22
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Scheres SHW, Núñez-Ramírez R, Sorzano COS, Carazo JM, Marabini R. Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 2008; 3:977-90. [PMID: 18536645 DOI: 10.1038/nprot.2008.62] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.
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Affiliation(s)
- Sjors H W Scheres
- Centro Nacional de Biotecnología CSIC, Unidad de Biocomputación, Cantoblanco, 28049 Madrid, Spain
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23
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Holden-Dye K, Crouch LI, Jones MR. Structure, function and interactions of the PufX protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:613-30. [DOI: 10.1016/j.bbabio.2008.04.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 04/06/2008] [Accepted: 04/10/2008] [Indexed: 11/26/2022]
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Qian P, Bullough PA, Hunter CN. Three-dimensional reconstruction of a membrane-bending complex: the RC-LH1-PufX core dimer of Rhodobacter sphaeroides. J Biol Chem 2008; 283:14002-11. [PMID: 18326046 DOI: 10.1074/jbc.m800625200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A three-dimensional model of the dimeric reaction center-light harvesting I-PufX (RC-LH1-PufX) complex from Rhodobacter sphaeroides, calculated from electron microscope single particle analysis of negatively stained complexes, shows that the two halves of the dimer molecule incline toward each other on the periplasmic side, creating a remarkable V-shaped structure. The distribution of negative stain is consistent with loose packing of the LH1 ring near the 14th LH1 alpha/beta pair, which could facilitate the migration of quinone and quinol molecules across the LH1 boundary. The three-dimensional model encloses a space near the reaction center Q(B) site and the 14th LH1 alpha/beta pair, which is approximately 20 angstroms in diameter, sufficient to sequester a quinone pool. Helical arrays of dimers were used to construct a three-dimensional membrane model, which matches the packing lattice deduced from electron microscope analysis of the tubular dimer-only membranes found in mutants of Rba. sphaeroides lacking the LH2 complex. The intrinsic curvature of the dimer explains the shape and approximately 70-nm diameter of these membrane tubules, and at least partially accounts for the spherical membrane invaginations found in wild-type Rba. sphaeroides. A model of dimer aggregation and membrane curvature in these spherical membrane invaginations is presented.
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Affiliation(s)
- Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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