1
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Martin EC, Bowie AGM, Wellfare Reid T, Neil Hunter C, Hitchcock A, Swainsbury DJK. Sulfoquinovosyl diacylglycerol is required for dimerisation of the Rhodobacter sphaeroides reaction centre-light harvesting 1 core complex. Biochem J 2024; 481:823-838. [PMID: 38780411 DOI: 10.1042/bcj20240125] [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: 03/24/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
The reaction centre-light harvesting 1 (RC-LH1) core complex is indispensable for anoxygenic photosynthesis. In the purple bacterium Rhodobacter (Rba.) sphaeroides RC-LH1 is produced both as a monomer, in which 14 LH1 subunits form a C-shaped antenna around 1 RC, and as a dimer, where 28 LH1 subunits form an S-shaped antenna surrounding 2 RCs. Alongside the five RC and LH1 subunits, an additional polypeptide known as PufX provides an interface for dimerisation and also prevents LH1 ring closure, introducing a channel for quinone exchange that is essential for photoheterotrophic growth. Structures of Rba. sphaeroides RC-LH1 complexes revealed several new components; protein-Y, which helps to form the quinone channel; protein-Z, of unknown function and seemingly unique to dimers; and a tightly bound sulfoquinovosyl diacylglycerol (SQDG) lipid that interacts with two PufX arginine residues. This lipid lies at the dimer interface alongside weak density for a second molecule, previously proposed to be an ornithine lipid. In this work we have generated strains of Rba. sphaeroides lacking protein-Y, protein-Z, SQDG or ornithine lipids to assess the roles of these previously unknown components in the assembly and activity of RC-LH1. We show that whilst the removal of either protein-Y, protein-Z or ornithine lipids has only subtle effects, SQDG is essential for the formation of RC-LH1 dimers but its absence has no functional effect on the monomeric complex.
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Affiliation(s)
- Elizabeth C Martin
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, U.K
| | - Adam G M Bowie
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, U.K
| | - Taylor Wellfare Reid
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, U.K
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, U.K
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, U.K
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2
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Kis M, Smart JL, Maróti P. Probing ligands to reaction centers to limit the photocycle in photosynthetic bacterium Rubrivivax gelatinosus. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 257:112969. [PMID: 38959527 DOI: 10.1016/j.jphotobiol.2024.112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Light-induced electron flow between reaction center and cytochrome bc1 complexes is mediated by quinones and electron donors in purple photosynthetic bacteria. Upon high-intensity excitation, the contribution of the cytochrome bc1 complex is limited kinetically and the electron supply should be provided by the pool of reduced electron donors. The kinetic limitation of electron shuttle between reaction center and cytochrome bc1 complex and its consequences on the photocycle were studied by tracking the redox changes of the primary electron donor (BChl dimer) via absorption change and the opening of the closed reaction center via relaxation of the bacteriochlorophyll fluorescence in intact cells of wild type and pufC mutant strains of Rubrivivax gelatinosus. The results were simulated by a minimum model of reversible binding of different ligands (internal and external electron donors and inhibitors) to donor and acceptor sides of the reaction center. The calculated binding and kinetic parameters revealed that control of the rate of the photocycle is primarily due to 1) the light intensity, 2) the size and redox state of the donor pool, and 3) the unbinding rates of the oxidized donor and inhibitor from the reaction center. The similar kinetics of strains WT and pufC lacking the tetraheme cytochrome subunit attached to the reaction center raise the issue of the physiological importance of this subunit discussed from different points of view. SIGNIFICANCE: A crucial factor for the efficacy of electron donors in photosynthetic photocycle is not just the substantial size of the pool and large binding affinity (small dissociation constant KD = koff/kon) to the RC, but also the mean residence time (koff)-1 in the binding pocket. This is an important parameter that regulates the time of re-activation of the RC during multiple turnovers. The determination of koff has proven challenging and was performed by simulation of widespread experimental data on the kinetics of P+ and relaxation of fluorescence. This work is a step towards better understanding the complex pathways of electron transfer in proteins and simulation-based design of more effective electron transfer components in natural and artificial systems.
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Affiliation(s)
- M Kis
- Institute of Medical Physics, University of Szeged, Korányi Fasor 9, Szeged 6720, Hungary; HUN-REN Balaton Limnological Research Institute, Klebelsberg K. utca 3, Tihany 8237, Hungary
| | - J L Smart
- Department of Biological Sciences, University of Tennessee at Martin, Martin, TN 38238, USA
| | - P Maróti
- Institute of Medical Physics, University of Szeged, Korányi Fasor 9, Szeged 6720, Hungary.
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3
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Pirnia A, Maqdisi R, Mittal S, Sener M, Singharoy A. Perspective on Integrative Simulations of Bioenergetic Domains. J Phys Chem B 2024; 128:3302-3319. [PMID: 38562105 DOI: 10.1021/acs.jpcb.3c07335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.
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Affiliation(s)
- Adam Pirnia
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Ranel Maqdisi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Sumit Mittal
- VIT Bhopal University, Sehore 466114, Madhya Pradesh, India
| | - Melih Sener
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
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4
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Huang X, Vasilev C, Swainsbury D, Hunter C. Excitation energy transfer in proteoliposomes reconstituted with LH2 and RC-LH1 complexes from Rhodobacter sphaeroides. Biosci Rep 2024; 44:BSR20231302. [PMID: 38227291 PMCID: PMC10876425 DOI: 10.1042/bsr20231302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/30/2023] [Accepted: 01/16/2024] [Indexed: 01/17/2024] Open
Abstract
Light-harvesting 2 (LH2) and reaction-centre light-harvesting 1 (RC-LH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were reconstituted into proteoliposomes either separately, or together at three different LH2:RC-LH1 ratios, for excitation energy transfer studies. Atomic force microscopy (AFM) was used to investigate the distribution and association of the complexes within the proteoliposome membranes. Absorption and fluorescence emission spectra were similar for LH2 complexes in detergent and liposomes, indicating that reconstitution retains the structural and optical properties of the LH2 complexes. Analysis of fluorescence emission shows that when LH2 forms an extensive series of contacts with other such complexes, fluorescence is quenched by 52.6 ± 1.4%. In mixed proteoliposomes, specific excitation of carotenoids in LH2 donor complexes resulted in emission of fluorescence from acceptor RC-LH1 complexes engineered to assemble with no carotenoids. Extents of energy transfer were measured by fluorescence lifetime microscopy; the 0.72 ± 0.08 ns lifetime in LH2-only membranes decreases to 0.43 ± 0.04 ns with a ratio of 2:1 LH2 to RC-LH1, and to 0.35 ± 0.05 ns for a 1:1 ratio, corresponding to energy transfer efficiencies of 40 ± 14% and 51 ± 18%, respectively. No further improvement is seen with a 0.5:1 LH2 to RC-LH1 ratio. Thus, LH2 and RC-LH1 complexes perform their light harvesting and energy transfer roles when reconstituted into proteoliposomes, providing a way to integrate native, non-native, engineered and de novo designed light-harvesting complexes into functional photosynthetic systems.
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Affiliation(s)
- Xia Huang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Jinan Guoke Medical Technology Development Co., Ltd, Jinan, Shandong 250101, China
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - Cvetelin Vasilev
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - David J.K. Swainsbury
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
| | - C. Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
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5
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Fufina TY, Vasilieva LG. Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. Biophys Rev 2023; 15:921-937. [PMID: 37974998 PMCID: PMC10643783 DOI: 10.1007/s12551-023-01109-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/01/2023] [Indexed: 11/19/2023] Open
Abstract
For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.
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Affiliation(s)
- T. Yu. Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
| | - L. G. Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
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6
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Hsieh YC, Delarue M, Orland H, Koehl P. Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories. Viruses 2023; 15:1366. [PMID: 37376665 DOI: 10.3390/v15061366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and on their gene products. It is important to have methods that enable the analyses of structural information on such large macromolecular systems. We review some of those methods in this paper. We focus on understanding the geometry of virions and viral structural proteins, their dynamics, and their energetics, with the ambition that this understanding can help design antiviral agents. We discuss those methods in light of the specificities of those structures, mainly that they are huge. We focus on three of our own methods based on the alpha shape theory for computing geometry, normal mode analyses to study dynamics, and modified Poisson-Boltzmann theories to study the organization of ions and co-solvent and solvent molecules around biomacromolecules. The corresponding software has computing times that are compatible with the use of regular desktop computers. We show examples of their applications on some outer shells and structural proteins of the West Nile Virus.
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Affiliation(s)
- Yin-Chen Hsieh
- Institute for Arctic and Marine Biology, Department of Biosciences, Fisheries, and Economics, UiT The Arctic University of Norway, 9037 Tromso, Norway
| | - Marc Delarue
- Institut Pasteur, Université Paris-Cité and CNRS, UMR 3528, Unité Architecture et Dynamique des Macromolécules Biologiques, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Patrice Koehl
- Department of Computer Science, University of California, Davis, CA 95616, USA
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7
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Albanese P, Mavelli F, Altamura E. Light energy transduction in liposome-based artificial cells. Front Bioeng Biotechnol 2023; 11:1161730. [PMID: 37064236 PMCID: PMC10091278 DOI: 10.3389/fbioe.2023.1161730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
In this work we review the latest strategies for the bottom-up assembly of energetically autonomous artificial cells capable of transducing light energy into chemical energy and support internalized metabolic pathways. Such entities are built by taking inspiration from the photosynthetic machineries found in nature which are purified and reconstituted directly in the membrane of artificial compartments or encapsulated in form of organelle-like structures. Specifically, we report and discuss recent examples based on liposome-technology and multi-compartment (nested) architectures pointing out the importance of this matter for the artificial cell synthesis research field and some limitations and perspectives of the bottom-up approach.
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Affiliation(s)
- Paola Albanese
- Department of Earth, Environmental and Physical Sciences, University of Siena, Siena, Italy
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences, University of Siena, Siena, Italy
| | - Fabio Mavelli
- Department of Chemistry, University of Bari, Bari, Italy
- *Correspondence: Fabio Mavelli, ; Emiliano Altamura,
| | - Emiliano Altamura
- Department of Chemistry, University of Bari, Bari, Italy
- *Correspondence: Fabio Mavelli, ; Emiliano Altamura,
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8
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Muñoz-Gómez SA, Cadena LR, Gardiner AT, Leger MM, Sheikh S, Connell LB, Bilý T, Kopejtka K, Beatty JT, Koblížek M, Roger AJ, Slamovits CH, Lukeš J, Hashimi H. Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr Biol 2023; 33:1099-1111.e6. [PMID: 36921606 DOI: 10.1016/j.cub.2023.02.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Abstract
Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| | - Lawrence Rudy Cadena
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Alastair T Gardiner
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003 Catalonia, Spain
| | - Shaghayegh Sheikh
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Louise B Connell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomáš Bilý
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic.
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9
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Hu YY, Liu XL, Yao HD, Jiang YL, Li K, Chen MQ, Wang P, Zhang JP. PEG effects on excitonic properties of LH2 from Rhodobacter sphaeroides 2.4.1 in different environments. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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10
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Koehl P, Akopyan A, Edelsbrunner H. Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives. J Chem Inf Model 2023; 63:973-985. [PMID: 36638318 PMCID: PMC9930125 DOI: 10.1021/acs.jcim.2c01346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software.
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Affiliation(s)
- Patrice Koehl
- Department
of Computer Science, University of California, Davis, California95616, United States,
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11
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Allen JP, Chamberlain KD, Williams JC. Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides. PHOTOSYNTHESIS RESEARCH 2023; 155:23-34. [PMID: 36197600 DOI: 10.1007/s11120-022-00968-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.
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Affiliation(s)
- J P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
| | - K D Chamberlain
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - J C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
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12
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Elvers I, Nguyen-Phan TC, Gardiner AT, Hunter CN, Cogdell RJ, Köhler J. Phasor Analysis Reveals Multicomponent Fluorescence Kinetics in the LH2 Complex from Marichromatium purpuratum. J Phys Chem B 2022; 126:10335-10346. [PMID: 36449272 DOI: 10.1021/acs.jpcb.2c04983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We investigated the fluorescence kinetics of LH2 complexes from Marichromatium purpuratum, the cryo-EM structure of which has been recently elucidated with 2.4 Å resolution. The experiments have been carried out as a function of the excitation density by varying both the excitation fluence and the repetition rate of the laser excitation. Instead of the usual multiexponential fitting procedure, we applied the less common phasor formalism for evaluating the transients because this allows for a model-free analysis of the data without a priori knowledge about the number of processes that contribute to a particular decay. For the various excitation conditions, this analysis reproduces consistently three lifetime components with decay times below 100 ps, 500 ps, and 730 ps, which were associated with the quenched state, singlet-triplet annihilation, and fluorescence decay, respectively. Moreover, it reveals that the number of decay components that contribute to the transients depends on whether the excitation wavelength is in resonance with the B800 BChl a molecules or with the carotenoids. Based on the mutual arrangement of the chromophores in their binding pockets, this leads us to conclude that the energy transfer pathways within the LH2 complex of this species differ significantly from each other for exciting either the B800 BChl molecules or the carotenoids. Finally, we speculate whether the illumination with strong laser light converts the LH2 complexes studied here into a quenched conformation that might be related to the development of the non-photochemical quenching mechanism that occurs in higher plants.
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Affiliation(s)
- Inga Elvers
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany
| | - Tu C Nguyen-Phan
- School of Infection and Immunity, Glasgow University, Glasgow G12 8TA, U.K
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81 Třeboň, Czech Republic
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - Richard J Cogdell
- School of Molecular Biosciences, Glasgow University, Glasgow G12 8QQ, U.K
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany.,Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany.,Bavarian Polymer Institute, University of Bayreuth, Universitätsstr. 30, D-95440 Bayreuth, Germany
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13
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Cryo-EM structures of light-harvesting 2 complexes from Rhodopseudomonas palustris reveal the molecular origin of absorption tuning. Proc Natl Acad Sci U S A 2022; 119:e2210109119. [PMID: 36251992 PMCID: PMC9618040 DOI: 10.1073/pnas.2210109119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The light-harvesting (LH) complexes of phototrophic bacteria absorb solar energy for photosynthesis, and it is important to understand how the protein components influence the way bound pigments absorb light. We studied the LH2 complexes of Rhodopseudomonas palustris, which are encoded by a multigene family. Various combinations of LH2 genes were deleted, yielding strains that assemble only one of the four types of LH2. Following purification, the structures of four LH2 complexes were determined by cryogenic electron microscopy, revealing a basic nonameric ring structure comprising nine αβ-polypeptide pairs. An additional hitherto unknown polypeptide, γ, was found in each structure that binds six further bacteriochlorophylls. Comparison of these different structures shows how nature tunes their ability to absorb different wavelengths of light. The genomes of some purple photosynthetic bacteria contain a multigene puc family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of puc deletion mutants in Rhodopseudomonas palustris, each encoding a single type of pucBA gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.
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Anionic Lipids Confine Cytochrome c2 to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners. Biochemistry 2022; 61:385-397. [PMID: 35025510 PMCID: PMC8909606 DOI: 10.1021/acs.biochem.1c00696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cytochrome c2 (cyt. c2) is a major element in electron transfer between redox proteins in bioenergetic membranes. While the interaction between cyt. c2 and anionic lipids abundant in bioenergetic membranes has been reported, their effect on the shuttling activity of cyt. c2 remains elusive. Here, the effect of anionic lipids on the interaction and binding of cyt. c2 to the cytochrome bc1 complex (bc1) is investigated using a combination of molecular dynamics (MD) and Brownian dynamics (BD) simulations. MD is used to generate thermally accessible conformations of cyt. c2 and membrane-embedded bc1, which were subsequently used in multireplica BD simulations of diffusion of cyt. c2 from solution to bc1, in the presence of various lipids. We show that, counterintuitively, anionic lipids facilitate association of cyt. c2 with bc1 by localizing its diffusion to the membrane surface. The observed lipid-mediated bc1 association is further enhanced by the oxidized state of cyt. c2, in line with its physiological function. This lipid-mediated enhancement is salinity-dependent, and anionic lipids can disrupt cyt. c2-bc1 interaction at nonphysiological salt levels. Our data highlight the importance of the redox state of cyt. c2, the lipid composition of the chromatophore membrane, and the salinity of the chromatophore in regulating the efficiency of the electron shuttling process mediated by cyt. c2. The conclusions can be extrapolated to mitochondrial systems and processes, or any bioenergetic membrane, given the structural similarity between cyt. c2 and bc1 and their mitochondrial counterparts.
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15
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Qian P, Gardiner AT, Šímová I, Naydenova K, Croll TI, Jackson PJ, Nupur, Kloz M, Čubáková P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hájek J, Agirre J, Siebert CA, Bína D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polívka T, Hunter CN, Koblížek M. 2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem. SCIENCE ADVANCES 2022; 8:eabk3139. [PMID: 35171663 PMCID: PMC8849296 DOI: 10.1126/sciadv.abk3139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/22/2021] [Indexed: 07/21/2023]
Abstract
Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.
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Affiliation(s)
- Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alastair T. Gardiner
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
| | - Ivana Šímová
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tristan I. Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Philip J. Jackson
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Nupur
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
| | - Miroslav Kloz
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague, Czechia
| | - Petra Čubáková
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague, Czechia
| | - Marek Kuzma
- Lab of Molecular Structure, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Yonghui Zeng
- Department of Plant and Environmental Sciences, University of Copenhagen, Nørregade 10, DK-1165 Copenhagen, Denmark
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Bart van Knippenberg
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Kenneth N. Goldie
- BioEM lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - David Kaftan
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
| | - Pavel Hrouzek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
| | - Jan Hájek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
| | - Jon Agirre
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - David Bína
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, SB, EPFL, and Faculty of Biology and Medicine, Uni Lausanne, CH-1015 Lausanne, Switzerland
| | - Roman Sobotka
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia
| | - Christopher J. Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tomáš Polívka
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czechia
| | - C. Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37981 Třeboň, Czechia
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Hitchcock A, Hunter CN, Sobotka R, Komenda J, Dann M, Leister D. Redesigning the photosynthetic light reactions to enhance photosynthesis - the PhotoRedesign consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:23-34. [PMID: 34709696 DOI: 10.1111/tpj.15552] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
In this Perspective article, we describe the visions of the PhotoRedesign consortium funded by the European Research Council of how to enhance photosynthesis. The light reactions of photosynthesis in individual phototrophic species use only a fraction of the solar spectrum, and high light intensities can impair and even damage the process. In consequence, expanding the solar spectrum and enhancing the overall energy capacity of the process, while developing resilience to stresses imposed by high light intensities, could have a strong positive impact on food and energy production. So far, the complexity of the photosynthetic machinery has largely prevented improvements by conventional approaches. Therefore, there is an urgent need to develop concepts to redesign the light-harvesting and photochemical capacity of photosynthesis, as well as to establish new model systems and toolkits for the next generation of photosynthesis researchers. The overall objective of PhotoRedesign is to reconfigure the photosynthetic light reactions so they can harvest and safely convert energy from an expanded solar spectrum. To this end, a variety of synthetic biology approaches, including de novo design, will combine the attributes of photosystems from different photoautotrophic model organisms, namely the purple bacterium Rhodobacter sphaeroides, the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana. In parallel, adaptive laboratory evolution will be applied to improve the capacity of reimagined organisms to cope with enhanced input of solar energy, particularly in high and fluctuating light.
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Affiliation(s)
- Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Christopher Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Roman Sobotka
- Laboratory of Photosynthesis, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, 37901, Czech Republic
| | - Josef Komenda
- Laboratory of Photosynthesis, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, 37901, Czech Republic
| | - Marcel Dann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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Sutherland GA, Qian P, Hunter CN, Swainsbury DJ, Hitchcock A. Engineering purple bacterial carotenoid biosynthesis to study the roles of carotenoids in light-harvesting complexes. Methods Enzymol 2022; 674:137-184. [DOI: 10.1016/bs.mie.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Vasilev C, Swainsbury DJK, Cartron ML, Martin EC, Kumar S, Hobbs JK, Johnson MP, Hitchcock A, Hunter CN. FRET measurement of cytochrome bc 1 and reaction centre complex proximity in live Rhodobacter sphaeroides cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1863:148508. [PMID: 34793767 DOI: 10.1016/j.bbabio.2021.148508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022]
Abstract
In the model purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides, solar energy is converted via coupled electron and proton transfer reactions within the intracytoplasmic membranes (ICMs), infoldings of the cytoplasmic membrane that form spherical 'chromatophore' vesicles. These bacterial 'organelles' are ideal model systems for studying how the organisation of the photosynthetic complexes therein shape membrane architecture. In Rba. sphaeroides, light-harvesting 2 (LH2) complexes transfer absorbed excitation energy to dimeric reaction centre (RC)-LH1-PufX complexes. The PufX polypeptide creates a channel that allows the lipid soluble electron carrier quinol, produced by RC photochemistry, to diffuse to the cytochrome bc1 complex, where quinols are oxidised to quinones, with the liberated protons used to generate a transmembrane proton gradient and the electrons returned to the RC via cytochrome c2. Proximity between cytochrome bc1 and RC-LH1-PufX minimises quinone/quinol/cytochrome c2 diffusion distances within this protein-crowded membrane, however this distance has not yet been measured. Here, we tag the RC and cytochrome bc1 with yellow or cyan fluorescent proteins (YFP/CFP) and record the lifetimes of YFP/CFP Förster resonance energy transfer (FRET) pairs in whole cells. FRET analysis shows that that these complexes lie on average within 6 nm of each other. Complementary high-resolution atomic force microscopy (AFM) of intact, purified chromatophores verifies the close association of cytochrome bc1 complexes with RC-LH1-PufX dimers. Our results provide a structural basis for the close kinetic coupling between RC-LH1-PufX and cytochrome bc1 observed by spectroscopy, and explain how quinols/quinones and cytochrome c2 shuttle on a millisecond timescale between these complexes, sustaining efficient photosynthetic electron flow.
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Affiliation(s)
- Cvetelin Vasilev
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.
| | - David J K Swainsbury
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Michael L Cartron
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Elizabeth C Martin
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Sandip Kumar
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7HR, United Kingdom; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jamie K Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7HR, United Kingdom
| | - Matthew P Johnson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation. Biochem J 2021; 478:3923-3937. [PMID: 34622934 PMCID: PMC8652583 DOI: 10.1042/bcj20210696] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022]
Abstract
The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the light-driven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 β polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 αβ subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half.
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20
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Qian P, Swainsbury DJK, Croll TI, Castro-Hartmann P, Divitini G, Sader K, Hunter CN. Cryo-EM Structure of the Rhodobacter sphaeroides Light-Harvesting 2 Complex at 2.1 Å. Biochemistry 2021; 60:3302-3314. [PMID: 34699186 PMCID: PMC8775250 DOI: 10.1021/acs.biochem.1c00576] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Light-harvesting 2 (LH2) antenna
complexes augment the collection
of solar energy in many phototrophic bacteria. Despite its frequent
role as a model for such complexes, there has been no three-dimensional
(3D) structure available for the LH2 from the purple phototroph Rhodobacter sphaeroides. We used cryo-electron microscopy
(cryo-EM) to determine the 2.1 Å resolution structure of this
LH2 antenna, which is a cylindrical assembly of nine αβ
heterodimer subunits, each of which binds three bacteriochlorophyll a (BChl) molecules and one carotenoid. The high resolution
of this structure reveals all of the interpigment and pigment–protein
interactions that promote the assembly and energy-transfer properties
of this complex. Near the cytoplasmic face of the complex there is
a ring of nine BChls, which absorb maximally at 800 nm and are designated
as B800; each B800 is coordinated by the N-terminal carboxymethionine
of LH2-α, part of a network of interactions with nearby residues
on both LH2-α and LH2-β and with the carotenoid. Nine
carotenoids, which are spheroidene in the strain we analyzed, snake
through the complex, traversing the membrane and interacting with
a ring of 18 BChls situated toward the periplasmic side of the complex.
Hydrogen bonds with C-terminal aromatic residues modify the absorption
of these pigments, which are red-shifted to 850 nm. Overlaps between
the macrocycles of the B850 BChls ensure rapid transfer of excitation
energy around this ring of pigments, which act as the donors of energy
to neighboring LH2 and reaction center light-harvesting 1 (RC–LH1)
complexes.
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Affiliation(s)
- Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, U.K
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Giorgio Divitini
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge CB3 0FS, U.K
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
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21
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Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 Å. Biochem J 2021; 478:3775-3790. [PMID: 34590677 PMCID: PMC8589327 DOI: 10.1042/bcj20210631] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 12/02/2022]
Abstract
Reaction centre light-harvesting 1 (RC–LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC–LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC–LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11–14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion.
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22
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Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 Å. Biochem J 2021; 478:3253-3263. [PMID: 34402504 PMCID: PMC8454704 DOI: 10.1042/bcj20210511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/03/2022]
Abstract
The reaction centre light-harvesting 1 (RC–LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC–LH1 complex from Rhodospirillum rubrum at 2.5 Å resolution, which reveals a unique monomeric bacteriochlorophyll with a phospholipid ligand in the gap between the RC and LH1 complexes. The LH1 complex comprises a circular array of 16 αβ-polypeptide subunits that completely surrounds the RC, with a preferential binding site for a quinone, designated QP, on the inner face of the encircling LH1 complex. Quinols, initially generated at the RC QB site, are proposed to transiently occupy the QP site prior to traversing the LH1 barrier and diffusing to the cytochrome bc1 complex. Thus, the QP site, which is analogous to other such sites in recent cryo-EM structures of RC–LH1 complexes, likely reflects a general mechanism for exporting quinols from the RC–LH1 complex.
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Chromatophores efficiently promote light-driven ATP synthesis and DNA transcription inside hybrid multicompartment artificial cells. Proc Natl Acad Sci U S A 2021; 118:2012170118. [PMID: 33526592 DOI: 10.1073/pnas.2012170118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The construction of energetically autonomous artificial protocells is one of the most ambitious goals in bottom-up synthetic biology. Here, we show an efficient manner to build adenosine 5'-triphosphate (ATP) synthesizing hybrid multicompartment protocells. Bacterial chromatophores from Rhodobacter sphaeroides accomplish the photophosphorylation of adenosine 5'-diphosphate (ADP) to ATP, functioning as nanosized photosynthetic organellae when encapsulated inside artificial giant phospholipid vesicles (ATP production rate up to ∼100 ATP∙s-1 per ATP synthase). The chromatophore morphology and the orientation of the photophosphorylation proteins were characterized by cryo-electron microscopy (cryo-EM) and time-resolved spectroscopy. The freshly synthesized ATP has been employed for sustaining the transcription of a DNA gene, following the RNA biosynthesis inside individual vesicles by confocal microscopy. The hybrid multicompartment approach here proposed is very promising for the construction of full-fledged artificial protocells because it relies on easy-to-obtain and ready-to-use chromatophores, paving the way for artificial simplified-autotroph protocells (ASAPs).
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Meredith SA, Yoneda T, Hancock AM, Connell SD, Evans SD, Morigaki K, Adams PG. Model Lipid Membranes Assembled from Natural Plant Thylakoids into 2D Microarray Patterns as a Platform to Assess the Organization and Photophysics of Light-Harvesting Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006608. [PMID: 33690933 DOI: 10.1002/smll.202006608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Natural photosynthetic "thylakoid" membranes found in green plants contain a large network of light-harvesting (LH) protein complexes. Rearrangement of this photosynthetic machinery, laterally within stacked membranes called "grana", alters protein-protein interactions leading to changes in the energy balance within the system. Preparation of an experimentally accessible model system that allows the detailed investigation of these complex interactions can be achieved by interfacing thylakoid membranes and synthetic lipids into a template comprised of polymerized lipids in a 2D microarray pattern on glass surfaces. This paper uses this system to interrogate the behavior of LH proteins at the micro- and nanoscale and assesses the efficacy of this model. A combination of fluorescence lifetime imaging and atomic force microscopy reveals the differences in photophysical state and lateral organization between native thylakoid and hybrid membranes, the mechanism of LH protein incorporation into the developing hybrid membranes, and the nanoscale structure of the system. The resulting model system within each corral is a high-quality supported lipid bilayer that incorporates laterally mobile LH proteins. Photosynthetic activity is assessed in the hybrid membranes versus proteoliposomes, revealing that commonly used photochemical assays to test the electron transfer activity of photosystem II may actually produce false-positive results.
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Affiliation(s)
- Sophie A Meredith
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Takuro Yoneda
- Graduate School of Agricultural Science and Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe, 657-8501, Japan
| | - Ashley M Hancock
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon D Connell
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stephen D Evans
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Kenichi Morigaki
- Graduate School of Agricultural Science and Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe, 657-8501, Japan
| | - Peter G Adams
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Swainsbury DJK, Qian P, Jackson PJ, Faries KM, Niedzwiedzki DM, Martin EC, Farmer DA, Malone LA, Thompson RF, Ranson NA, Canniffe DP, Dickman MJ, Holten D, Kirmaier C, Hitchcock A, Hunter CN. Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels. SCIENCE ADVANCES 2021; 7:7/3/eabe2631. [PMID: 33523887 PMCID: PMC7806223 DOI: 10.1126/sciadv.abe2631] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/18/2020] [Indexed: 05/23/2023]
Abstract
The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC QB site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.
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Affiliation(s)
- David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Kaitlyn M Faries
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - David A Farmer
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Lorna A Malone
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Canniffe
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Dewey Holten
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christine Kirmaier
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Andrew Hitchcock
- 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.
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26
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DiRisio RJ, Jones CM, Ma H, Rousseau BJG. Viewpoints on the 2020 Virtual Conference on Theoretical Chemistry. J Phys Chem A 2020; 124:8875-8883. [PMID: 33054223 DOI: 10.1021/acs.jpca.0c08955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ryan J DiRisio
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Chey M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - He Ma
- Institute for Molecular engineering, University of Chicago, 5640 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benjamin J G Rousseau
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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27
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Huang X, Vasilev C, Hunter CN. Excitation energy transfer between monomolecular layers of light harvesting LH2 and LH1-reaction centre complexes printed on a glass substrate. LAB ON A CHIP 2020; 20:2529-2538. [PMID: 32662473 DOI: 10.1039/d0lc00156b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Light-harvesting 2 (LH2) and light-harvesting 1 - reaction centre (RCLH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were cross-patterned on glass surfaces for energy transfer studies. Atomic force microscopy (AFM) images of the RCLH1 and LH2 patterns show the deposition of monomolecular layers of complexes on the glass substrate. Spectral imaging and fluorescence life-time imaging microscopy (FLIM) revealed that RCLH1 and LH2 complexes, sealed under physiological conditions, retained their native light-harvesting and energy transfer functions. Measurements of the amplitude and lifetime decay of fluorescence emission from LH2 complexes, the energy transfer donors, and gain of fluorescence emission from acceptor RCLH1 complexes, provide evidence for excitation energy transfer from LH2 to RCLH1. Directional energy transfer on the glass substrate was unequivocally established by using LH2-carotenoid complexes and RCLH1 complexes with genetically removed carotenoids. Specific excitation of carotenoids in donor LH2 complexes elicited fluorescence emission from RCLH1 acceptors. To explore the longevity of this novel nanoprinted photosynthetic unit, RCLH1 and LH2 complexes were cross-patterned on a glass surface and sealed under a protective argon atmosphere. The results show that both complexes retained their individual and collective functions and are capable of directional excitation energy transfer for at least 60 days.
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Affiliation(s)
- Xia Huang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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28
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Rochaix JD. Dynamic Modeling of a 100-Million-Atom Organelle at the Source of Life. Cell 2020; 179:1012-1014. [PMID: 31730846 DOI: 10.1016/j.cell.2019.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this issue of Cell, Singharoy et al. present a rate kinetic model for the chromatophore of photosynthetic purple bacteria generated from molecular dynamics simulations. It shows that the chromatophore's architecture is optimized for producing bioenergy under low light typical of the natural bacterial habitat while minimizing photodamage under stress conditions.
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Affiliation(s)
- Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland.
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29
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Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov L, Chipot C, Singharoy A. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. J Am Chem Soc 2020; 142:9220-9230. [PMID: 32347721 DOI: 10.1021/jacs.9b13450] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron-sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron-sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form-a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.
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Affiliation(s)
- Chitrak Gupta
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States.,Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, City University of New York, New York, New York 10017, United States
| | - Chun Kit Chan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Mrinal Shekhar
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - M R Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, City University of New York, New York, New York 10017, United States
| | - Leonid Sazanov
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,University of Lorraine, Nancy 54000, France
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States.,Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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30
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Sener M, Levy S, Stone JE, Christensen AJ, Isralewitz B, Patterson R, Borkiewicz K, Carpenter J, Hunter CN, Luthey-Schulten Z, Cox D. Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. PARALLEL COMPUTING 2020; 102:102698. [PMID: 34824485 PMCID: PMC8612599 DOI: 10.1016/j.parco.2020.102698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay audience, including children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. Software advancements necessitated by this project have led to significant performance and feature advances, including hardware-accelerated cinematic ray tracing and instanced visualizations for efficient cell-scale modeling. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories-the interplay between light and life.
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Affiliation(s)
- Melih Sener
- Beckman Institute, University of Illinois at Urbana-Champaign
| | - Stuart Levy
- Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign
| | - John E. Stone
- Beckman Institute, University of Illinois at Urbana-Champaign
| | - AJ Christensen
- Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign
| | | | - Robert Patterson
- Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign
| | - Kalina Borkiewicz
- Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign
| | - Jeffrey Carpenter
- Advanced Visualization Laboratory, NCSA, University of Illinois at Urbana-Champaign
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, U.K
| | | | - Donna Cox
- Beckman Institute, University of Illinois at Urbana-Champaign
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31
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Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, Mallus MI, Chipot C, Luthey-Schulten Z, Tieleman DP, Hunter CN, Tajkhorshid E, Aksimentiev A, Schulten K. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell 2019; 179:1098-1111.e23. [PMID: 31730852 PMCID: PMC7075482 DOI: 10.1016/j.cell.2019.10.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/04/2019] [Accepted: 10/21/2019] [Indexed: 01/01/2023]
Abstract
We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.
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Affiliation(s)
- Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA.
| | - Christopher Maffeo
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karelia H Delgado-Magnero
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - John W Vant
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ 85282, USA
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Barry Isralewitz
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ivan Teo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Danielle E Chandler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James C Phillips
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - M Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Christophe Chipot
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Laboratoire International Associé CNRS-UIUC, UMR 7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy, France
| | - Zaida Luthey-Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Biochemistry, Chemistry, Bioengineering, and Pharmacology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Aleksei Aksimentiev
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Klaus Schulten
- Department of Physics, NSF Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Boehm BJ, Nguyen HTL, Huang DM. The interplay of interfaces, supramolecular assembly, and electronics in organic semiconductors. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:423001. [PMID: 31212263 DOI: 10.1088/1361-648x/ab2ac2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Organic semiconductors, which include a diverse range of carbon-based small molecules and polymers with interesting optoelectronic properties, offer many advantages over conventional inorganic semiconductors such as silicon and are growing in importance in electronic applications. Although these materials are now the basis of a lucrative industry in electronic displays, many promising applications such as photovoltaics remain largely untapped. One major impediment to more rapid development and widespread adoption of organic semiconductor technologies is that device performance is not easily predicted from the chemical structure of the constituent molecules. Fundamentally, this is because organic semiconductor molecules, unlike inorganic materials, interact by weak non-covalent forces, resulting in significant structural disorder that can strongly impact electronic properties. Nevertheless, directional forces between generally anisotropic organic-semiconductor molecules, combined with translational symmetry breaking at interfaces, can be exploited to control supramolecular order and consequent electronic properties in these materials. This review surveys recent advances in understanding of supramolecular assembly at organic-semiconductor interfaces and its impact on device properties in a number of applications, including transistors, light-emitting diodes, and photovoltaics. Recent progress and challenges in computer simulations of supramolecular assembly and orientational anisotropy at these interfaces is also addressed.
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Affiliation(s)
- Belinda J Boehm
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, SA 5005, Australia
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33
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Dissecting the cytochrome c 2-reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy. Biochem J 2019; 476:2173-2190. [PMID: 31320503 PMCID: PMC6688529 DOI: 10.1042/bcj20170519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022]
Abstract
The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c 2 and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC-LH1-PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c 2 molecules. Microscale patterns of cytochrome c 2 and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c 2 Following the transient association of photo-oxidised RC and reduced cytochrome c 2 molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC-c 2 complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c 2 molecules decreased 5-fold. Thus, the redox states of the cytochrome c 2 haem cofactor and RC 'special pair' bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c 2[oxidised]-RC[reduced] 'product' state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.
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34
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Lishchuk A, Vasilev C, Johnson MP, Hunter CN, Törmä P, Leggett GJ. Turning the challenge of quantum biology on its head: biological control of quantum optical systems. Faraday Discuss 2019; 216:57-71. [PMID: 31016297 DOI: 10.1039/c8fd00241j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When light-harvesting complex II (LHCII), isolated from spinach, is adsorbed onto arrays of gold nanostructures formed by interferometric lithography, a pronounced splitting of the plasmon band is observed that is attributable to strong coupling of the localised surface plasmon resonance to excitons in the pigment-protein complex. The system is modelled as coupled harmonic oscillators, yielding an exciton energy of 2.24 ± 0.02 eV. Analysis of dispersion curves yields a Rabi energy of 0.25 eV. Extinction spectra of the strongly coupled system yield a resonance at 1.43 eV that varies as a function of the density of nanostructures in the array. The enhanced intensity of this feature is attributed to strong plasmon-exciton coupling. Comparison of data for a large number of light-harvesting complexes indicates that by control of the protein structure and/or pigment compliment it is possible to manipulate the strength of plasmon-exciton coupling. In strongly coupled systems, ultra-fast exchange of energy occurs between pigment molecules: coherent coupling between non-local excitons can be manipulated via selection of the protein structure enabling the observation of transitions that are not seen in the weak coupling regime. Synthetic biology thus provides a means to control quantum-optical interactions in the strong coupling regime.
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Affiliation(s)
- Anna Lishchuk
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK.
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Matthew P Johnson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Päivi Törmä
- Department of Applied Physics, Aalto University, School of Science, P.O. Box 15100, 00076 Aalto, Finland
| | - Graham J Leggett
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK.
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35
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Barriers to 3-Hydroxypropionate-Dependent Growth of Rhodobacter sphaeroides by Distinct Disruptions of the Ethylmalonyl Coenzyme A Pathway. J Bacteriol 2019; 201:JB.00556-18. [PMID: 30455284 DOI: 10.1128/jb.00556-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides is able to use 3-hydroxypropionate as the sole carbon source through the reductive conversion of 3-hydroxypropionate to propionyl coenzyme A (propionyl-CoA). The ethylmalonyl-CoA pathway is not required in this process because a crotonyl-CoA carboxylase/reductase (Ccr)-negative mutant still grew with 3-hydroxypropionate. Much to our surprise, a mutant defective for another specific enzyme of the ethylmalonyl-CoA pathway, mesaconyl-CoA hydratase (Mch), lost its ability for 3-hydroxypropionate-dependent growth. Interestingly, the Mch-deficient mutant was rescued either by introducing an additional ccr in-frame deletion that resulted in the blockage of an earlier step in the pathway or by heterologously expressing a gene encoding a thioesterase (YciA) that can act on several CoA intermediates of the ethylmalonyl-CoA pathway. The mch mutant expressing yciA metabolized only less than half of the 3-hydroxypropionate supplied, and over 50% of that carbon was recovered in the spent medium as free acids of the key intermediates mesaconyl-CoA and methylsuccinyl-CoA. A gradual increase in growth inhibition due to the blockage of consecutive steps of the ethylmalonyl-CoA pathway by gene deletions suggests that the growth defects were due to the titration of free CoA and depletion of the CoA pool in the cell rather than to detrimental effects arising from the accumulation of a specific metabolite. Recovery of carbon in mesaconate for the wild-type strain expressing yciA demonstrated that carbon flux through the ethylmalonyl-CoA pathway occurs during 3-hydroxypropionate-dependent growth. A possible role of the ethylmalonyl-CoA pathway is proposed that functions outside its known role in providing tricarboxylic acid intermediates during acetyl-CoA assimilation.IMPORTANCE Mutant analysis is an important tool utilized in metabolic studies to understand which role a particular pathway might have under certain growth conditions for a given organism. The importance of the enzyme and of the pathway in which it participates is discretely linked to the resulting phenotype observed after mutation of the corresponding gene. This work highlights the possibility of incorrectly interpreting mutant growth results that are based on studying a single unit (gene and encoded enzyme) of a metabolic pathway rather than the pathway in its entirety. This work also hints at the possibility of using an enzyme as a drug target although the enzyme may participate in a nonessential pathway and still be detrimental to the cell when inhibited.
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36
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Massey SC, Ting PC, Yeh SH, Dahlberg PD, Sohail SH, Allodi MA, Martin EC, Kais S, Hunter CN, Engel GS. Orientational Dynamics of Transition Dipoles and Exciton Relaxation in LH2 from Ultrafast Two-Dimensional Anisotropy. J Phys Chem Lett 2019; 10:270-277. [PMID: 30599133 DOI: 10.1021/acs.jpclett.8b03223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Light-harvesting complexes in photosynthetic organisms display fast and efficient energy transfer dynamics, which depend critically on the electronic structure of the coupled chromophores within the complexes and their interactions with their environment. We present ultrafast anisotropy dynamics, resolved in both time and frequency, of the transmembrane light-harvesting complex LH2 from Rhodobacter sphaeroides in its native membrane environment using polarization-controlled two-dimensional electronic spectroscopy. Time-dependent anisotropy obtained from both experiment and modified Redfield simulation reveals an orientational preference for excited state absorption and an ultrafast equilibration within the B850 band in LH2. This ultrafast equilibration is favorable for subsequent energy transfer toward the reaction center. Our results also show a dynamic difference in excited state absorption anisotropy between the directly excited B850 population and the population that is initially excited at 800 nm, suggesting absorption from B850 states to higher-lying excited states following energy transfer from B850*. These results give insight into the ultrafast dynamics of bacterial light harvesting and the excited state energy landscape of LH2 in the native membrane environment.
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Affiliation(s)
- Sara C Massey
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Po-Chieh Ting
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Shu-Hao Yeh
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
- Qatar Environment and Energy Research Institute , Hamad Bin Khalifa University , Qatar Foundation, Doha , Qatar
| | - Peter D Dahlberg
- Graduate Program in the Biophysical Sciences, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Sara H Sohail
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Marco A Allodi
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology , University of Sheffield , Firth Court, Western Bank, Sheffield S10 2TN , United Kingdom
| | - Sabre Kais
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology , University of Sheffield , Firth Court, Western Bank, Sheffield S10 2TN , United Kingdom
| | - Gregory S Engel
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute , The University of Chicago , Chicago , Illinois 60637 , United States
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37
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Engineering of B800 bacteriochlorophyll binding site specificity in the Rhodobacter sphaeroides LH2 antenna. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:209-223. [PMID: 30414933 PMCID: PMC6358721 DOI: 10.1016/j.bbabio.2018.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/19/2018] [Accepted: 11/07/2018] [Indexed: 11/22/2022]
Abstract
The light-harvesting 2 complex (LH2) of the purple phototrophic bacterium Rhodobacter sphaeroides is a highly efficient, light-harvesting antenna that allows growth under a wide-range of light intensities. In order to expand the spectral range of this antenna complex, we first used a series of competition assays to measure the capacity of the non-native pigments 3-acetyl chlorophyll (Chl) a, Chl d, Chl f or bacteriochlorophyll (BChl) b to replace native BChl a in the B800 binding site of LH2. We then adjusted the B800 site and systematically assessed the binding of non-native pigments. We find that Arg-10 of the LH2 β polypeptide plays a crucial role in binding specificity, by providing a hydrogen-bond to the 3-acetyl group of native and non-native pigments. Reconstituted LH2 complexes harbouring the series of (B)Chls were examined by transient absorption and steady-state fluorescence spectroscopies. Although slowed 10-fold to ~6 ps, energy transfer from Chl a to B850 BChl a remained highly efficient. We measured faster energy-transfer time constants for Chl d (3.5 ps) and Chl f (2.7 ps), which have red-shifted absorption maxima compared to Chl a. BChl b, red-shifted from the native BChl a, gave extremely rapid (≤0.1 ps) transfer. These results show that modified LH2 complexes, combined with engineered (B)Chl biosynthesis pathways in vivo, have potential for retaining high efficiency whilst acquiring increased spectral range.
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38
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Mallus MI, Shakya Y, Prajapati JD, Kleinekathöfer U. Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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39
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Irgen-Gioro S, Spencer AP, Hutson WO, Harel E. Coherences of Bacteriochlorophyll a Uncovered Using 3D-Electronic Spectroscopy. J Phys Chem Lett 2018; 9:6077-6081. [PMID: 30273488 DOI: 10.1021/acs.jpclett.8b02217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mapping the multidimensional energy landscape of photosynthetic systems is crucial for understanding their high efficiencies. Multidimensional coherent spectroscopy is well suited to this task but has difficulty distinguishing between vibrational and electronic degrees of freedom. In pigment-protein complexes, energy differences between vibrations within a single electronic manifold are similar to differences between electronic states, leading to ambiguous assignments of spectral features and diverging physical interpretations. An important control experiment is that of the pigment monomer, but previous attempts using multidimensional coherent spectroscopy lacked the sensitivity to capture the relevant spectroscopic signatures. Here we apply a variety of methods to rapidly acquire 3D electronic-vibrational spectra in seconds, leading to a mapping of the vibrational states of Bacteriochlorophyll a (BChl a) in solution. Using this information, we can distinguish features of proteins containing BChl a from the monomer subunit and show that many of the previously reported contentious spectral signatures are vibrations of individual pigments.
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Affiliation(s)
- Shawn Irgen-Gioro
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Austin P Spencer
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - William O Hutson
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Elad Harel
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
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40
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Noble JM, Lubieniecki J, Savitzky BH, Plitzko J, Engelhardt H, Baumeister W, Kourkoutis LF. Connectivity of centermost chromatophores in Rhodobacter sphaeroides bacteria. Mol Microbiol 2018; 109:812-825. [PMID: 29995992 DOI: 10.1111/mmi.14077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 01/20/2023]
Abstract
The size of whole Rhodobacter sphaeroides prevents 3D visualization of centermost chromatophores in their native environment. This study combines cryo-focused ion beam milling with cryo-electron tomography to probe vesicle architecture both in situ and in 3D. Developing chromatophores are membrane-bound buds that remain in topological continuity with the cytoplasmic membrane and detach into vesicles when mature. Mature chromatophores closest to the cell wall are typically isolated vesicles, whereas centermost chromatophores are either linked to neighboring chromatophores or contain smaller, budding structures. Isolated chromatophores comprised a minority of centermost chromatophores. Connections between vesicles in growing bacteria are through ~10 nm-long, ~5 nm-wide linkers, and are thus physical rather than functional in terms of converting photons to ATP. In cells in the stationary phase, chromatophores fuse with neighboring vesicles, lose their spherical structure, and greatly increase in volume. The fusion and morphological changes seen in older bacteria are likely a consequence of the aging process, and are not representative of connectivity in healthy R. sphaeroides. Our results suggest that chromatophores can adopt either isolated or connected morphologies within a single bacterium. Revealing the organization of chromatophore vesicles throughout the cell is an important step in understanding the photosynthetic mechanisms in R. sphaeroides.
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Affiliation(s)
- Jade M Noble
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Johann Lubieniecki
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lena F Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.,Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, USA
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41
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Koehl P. Large Eigenvalue Problems in Coarse-Grained Dynamic Analyses of Supramolecular Systems. J Chem Theory Comput 2018; 14:3903-3919. [DOI: 10.1021/acs.jctc.8b00338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrice Koehl
- Department of Computer Sciences and Genome Center, University of California, Davis, California 95616, United States
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42
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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43
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Swainsbury DJK, Proctor MS, Hitchcock A, Cartron ML, Qian P, Martin EC, Jackson PJ, Madsen J, Armes SP, Hunter CN. Probing the local lipid environment of the Rhodobacter sphaeroides cytochrome bc 1 and Synechocystis sp. PCC 6803 cytochrome b 6f complexes with styrene maleic acid. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:215-225. [PMID: 29291373 PMCID: PMC5805856 DOI: 10.1016/j.bbabio.2017.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/21/2017] [Accepted: 12/28/2017] [Indexed: 01/21/2023]
Abstract
Intracytoplasmic vesicles (chromatophores) in the photosynthetic bacterium Rhodobacter sphaeroides represent a minimal structural and functional unit for absorbing photons and utilising their energy for the generation of ATP. The cytochrome bc1 complex (cytbc1) is one of the four major components of the chromatophore alongside the reaction centre-light harvesting 1-PufX core complex (RC-LH1-PufX), the light-harvesting 2 complex (LH2), and ATP synthase. Although the membrane organisation of these complexes is known, their local lipid environments have not been investigated. Here we utilise poly(styrene-alt-maleic acid) (SMA) co-polymers as a tool to simultaneously determine the local lipid environments of the RC-LH1-PufX, LH2 and cytbc1 complexes. SMA has previously been reported to effectively solubilise complexes in lipid-rich membrane regions whilst leaving lipid-poor ordered protein arrays intact. Here we show that SMA solubilises cytbc1 complexes with an efficiency of nearly 70%, whereas solubilisation of RC-LH1-PufX and LH2 was only 10% and 22% respectively. This high susceptibility of cytbc1 to SMA solubilisation is consistent with this complex residing in a locally lipid-rich region. SMA solubilised cytbc1 complexes retain their native dimeric structure and co-purify with 56 ± 6 phospholipids from the chromatophore membrane. We extended this approach to the model cyanobacterium Synechocystis sp. PCC 6803, and show that the cytochrome b6f complex (cytb6f) and Photosystem II (PSII) complexes are susceptible to SMA solubilisation, suggesting they also reside in lipid-rich environments. Thus, lipid-rich membrane regions could be a general requirement for cytbc1/cytb6f complexes, providing a favourable local solvent to promote rapid quinol/quinone binding and release at the Q0 and Qi sites. SMA preferentially solubilises cytbc1 from chromatophore membranes. Solubilised cytbc1 SMALPs contain dimeric complexes co-purified with 56 lipids. SMA-resistant fractions contain RC-LH1-PufX and LH2 rich membrane patches. The Rba. sphaeroides cytbc1 complex is likely to reside in a lipid-rich environment. Similar results for Synechocystis suggest cytbc1/b6f may be universally lipid-rich.
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Affiliation(s)
- David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew S Proctor
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Michaël L Cartron
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom; ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Jeppe Madsen
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Steven P Armes
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.
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44
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Chidgey JW, Jackson PJ, Dickman MJ, Hunter CN. PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase. Mol Microbiol 2017; 106:961-975. [PMID: 29030914 PMCID: PMC5725709 DOI: 10.1111/mmi.13861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
Facultative phototrophs such as Rhodobacter sphaeroides can switch between heterotrophic and photosynthetic growth. This transition is governed by oxygen tension and involves the large-scale production of bacteriochlorophyll, which shares a biosynthetic pathway with haem up to protoporphyrin IX. Here, the pathways diverge with the insertion of Fe2+ or Mg2+ into protoporphyrin by ferrochelatase or magnesium chelatase, respectively. Tight regulation of this branchpoint is essential, but the mechanisms for switching between respiratory and photosynthetic growth are poorly understood. We show that PufQ governs the haem/bacteriochlorophyll switch; pufQ is found within the oxygen-regulated pufQBALMX operon encoding the reaction centre-light-harvesting photosystem complex. A pufQ deletion strain synthesises low levels of bacteriochlorophyll and accumulates the biosynthetic precursor coproporphyrinogen III; a suppressor mutant of this strain harbours a mutation in the hemH gene encoding ferrochelatase, substantially reducing ferrochelatase activity and increasing cellular bacteriochlorophyll levels. FLAG-immunoprecipitation experiments retrieve a ferrochelatase-PufQ-carotenoid complex, proposed to regulate the haem/bacteriochlorophyll branchpoint by directing porphyrin flux toward bacteriochlorophyll production under oxygen-limiting conditions. The co-location of pufQ and the photosystem genes in the same operon ensures that switching of tetrapyrrole metabolism toward bacteriochlorophyll is coordinated with the production of reaction centre and light-harvesting polypeptides.
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Affiliation(s)
- Jack W. Chidgey
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
| | - Philip J. Jackson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - Mark J. Dickman
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - C. Neil Hunter
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
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45
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Jackson PJ, Hitchcock A, Swainsbury DJK, Qian P, Martin EC, Farmer DA, Dickman MJ, Canniffe DP, Hunter CN. Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:119-128. [PMID: 29126780 PMCID: PMC5764122 DOI: 10.1016/j.bbabio.2017.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 02/08/2023]
Abstract
The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc1 complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13 years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes. Identification of the protein W subunit of the Rps. palustris RC-LH1 core complex. The rpa4402 locus encoding protein W is not in the PGC. Protein W is present in only a sub-population of core complexes. Protein W is dispensable for photosynthetic growth. Pure plus/minus protein W core complex preparations will aid structural studies.
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Affiliation(s)
- Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK; ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Elizabeth C Martin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - David A Farmer
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Daniel P Canniffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
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46
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Mapping the ultrafast flow of harvested solar energy in living photosynthetic cells. Nat Commun 2017; 8:988. [PMID: 29042567 PMCID: PMC5715167 DOI: 10.1038/s41467-017-01124-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 08/20/2017] [Indexed: 11/23/2022] Open
Abstract
Photosynthesis transfers energy efficiently through a series of antenna complexes to the reaction center where charge separation occurs. Energy transfer in vivo is primarily monitored by measuring fluorescence signals from the small fraction of excitations that fail to result in charge separation. Here, we use two-dimensional electronic spectroscopy to follow the entire energy transfer process in a thriving culture of the purple bacteria, Rhodobacter sphaeroides. By removing contributions from scattered light, we extract the dynamics of energy transfer through the dense network of antenna complexes and into the reaction center. Simulations demonstrate that these dynamics constrain the membrane organization into small pools of core antenna complexes that rapidly trap energy absorbed by surrounding peripheral antenna complexes. The rapid trapping and limited back transfer of these excitations lead to transfer efficiencies of 83% and a small functional light-harvesting unit. During photosynthesis, energy is transferred from photosynthetic antenna to reaction centers via ultrafast energy transfer. Here the authors track energy transfer in photosynthetic bacteria using two-dimensional electronic spectroscopy and show that these transfer dynamics constrain antenna complex organization.
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47
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El Zubir O, Xia S, Ducker RE, Wang L, Mullin N, Cartron ML, Cadby AJ, Hobbs JK, Hunter CN, Leggett GJ. From Monochrome to Technicolor: Simple Generic Approaches to Multicomponent Protein Nanopatterning Using Siloxanes with Photoremovable Protein-Resistant Protecting Groups. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8829-8837. [PMID: 28551995 PMCID: PMC5588097 DOI: 10.1021/acs.langmuir.7b01255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/25/2017] [Indexed: 06/07/2023]
Abstract
We show that sequential protein deposition is possible by photodeprotection of films formed from a tetraethylene-glycol functionalized nitrophenylethoxycarbonyl-protected aminopropyltriethoxysilane (NPEOC-APTES). Exposure to near-UV irradiation removes the protein-resistant protecting group, and allows protein adsorption onto the resulting aminated surface. The protein resistance was tested using proteins with fluorescent labels and microspectroscopy of two-component structures formed by micro- and nanopatterning and deposition of yellow and green fluorescent proteins (YFP/GFP). Nonspecific adsorption onto regions where the protecting group remained intact was negligible. Multiple component patterns were also formed by near-field methods. Because reading and writing can be decoupled in a near-field microscope, it is possible to carry out sequential patterning steps at a single location involving different proteins. Up to four different proteins were formed into geometric patterns using near-field lithography. Interferometric lithography facilitates the organization of proteins over square cm areas. Two-component patterns consisting of 150 nm streptavidin dots formed within an orthogonal grid of bars of GFP at a period of ca. 500 nm could just be resolved by fluorescence microscopy.
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Affiliation(s)
- Osama El Zubir
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United
Kingdom
| | - Sijing Xia
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United
Kingdom
| | - Robert E. Ducker
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United
Kingdom
| | - Lin Wang
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Nic Mullin
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Michaël L. Cartron
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Ashley J. Cadby
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - Jamie K. Hobbs
- Department
of Physics and Astronomy, University of
Sheffield, Sheffield S3 7RH, United Kingdom
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Graham J. Leggett
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United
Kingdom
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48
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Altamura E, Fiorentino R, Milano F, Trotta M, Palazzo G, Stano P, Mavelli F. First moves towards photoautotrophic synthetic cells: In vitro study of photosynthetic reaction centre and cytochrome bc1 complex interactions. Biophys Chem 2017; 229:46-56. [PMID: 28688734 DOI: 10.1016/j.bpc.2017.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/26/2022]
Abstract
Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly "synthetic cells") can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles. Next, the details of our ongoing research program are presented. It involves the use of the reaction centre, the coenzyme Q-cytochrome c oxidoreductase, and the ATP synthase for creating an autonomous synthetic cell. We show experimental results on the chemistry of the first two proteins showing that they can efficiently sustain light-driven chemical oscillations. Moreover, the cyclic pattern has been reproduced in silico by a minimal kinetic model.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy
| | - Rosa Fiorentino
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy
| | - Francesco Milano
- CNR-IPCF, Istituto per i Processi Chimico Fisici, Via Orabona 4, I-70126 Bari, Italy
| | - Massimo Trotta
- CNR-IPCF, Istituto per i Processi Chimico Fisici, Via Orabona 4, I-70126 Bari, Italy
| | - Gerardo Palazzo
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, I-73100 Lecce, Italy
| | - Fabio Mavelli
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy.
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49
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MacGregor-Chatwin C, Sener M, Barnett SFH, Hitchcock A, Barnhart-Dailey MC, Maghlaoui K, Barber J, Timlin JA, Schulten K, Hunter CN. Lateral Segregation of Photosystem I in Cyanobacterial Thylakoids. THE PLANT CELL 2017; 29:1119-1136. [PMID: 28364021 PMCID: PMC5466035 DOI: 10.1105/tpc.17.00071] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 05/21/2023]
Abstract
Photosystem I (PSI) is the dominant photosystem in cyanobacteria and it plays a pivotal role in cyanobacterial metabolism. Despite its biological importance, the native organization of PSI in cyanobacterial thylakoid membranes is poorly understood. Here, we use atomic force microscopy (AFM) to show that ordered, extensive macromolecular arrays of PSI complexes are present in thylakoids from Thermosynechococcus elongatus, Synechococcus sp PCC 7002, and Synechocystis sp PCC 6803. Hyperspectral confocal fluorescence microscopy and three-dimensional structured illumination microscopy of Synechocystis sp PCC 6803 cells visualize PSI domains within the context of the complete thylakoid system. Crystallographic and AFM data were used to build a structural model of a membrane landscape comprising 96 PSI trimers and 27,648 chlorophyll a molecules. Rather than facilitating intertrimer energy transfer, the close associations between PSI primarily maximize packing efficiency; short-range interactions with Complex I and cytochrome b6f are excluded from these regions of the membrane, so PSI turnover is sustained by long-distance diffusion of the electron donors at the membrane surface. Elsewhere, PSI-photosystem II contact zones provide sites for docking phycobilisomes and the formation of megacomplexes. PSI-enriched domains in cyanobacteria might foreshadow the partitioning of PSI into stromal lamellae in plants, similarly sustained by long-distance diffusion of electron carriers.
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Affiliation(s)
- Craig MacGregor-Chatwin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Samuel F H Barnett
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Meghan C Barnhart-Dailey
- Bioenergy and Defense Technologies Department, Sandia National Laboratories, Albuquerque, New Mexico 87185
| | - Karim Maghlaoui
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James Barber
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jerilyn A Timlin
- Bioenergy and Defense Technologies Department, Sandia National Laboratories, Albuquerque, New Mexico 87185
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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50
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Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z. Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. J Phys Chem B 2017; 121:3871-3881. [PMID: 28291359 DOI: 10.1021/acs.jpcb.7b00672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle time scales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network. Here we present two examples to illustrate the challenges and techniques involved in integrating structural data into stochastic simulations. First, a tomographic reconstruction of Saccharomyces cerevisiae is used to construct the geometry of an entire cell through which a simple stochastic model of an inducible genetic switch is studied. Second, a tomogram of the nuclear periphery in a HeLa cell is converted directly to the simulation geometry through which we study the effects of cellular substructure on the stochastic dynamics of gene repression. These simple chemical models allow us to illustrate how to build whole-cell simulations using cryo-ET derived geometry and the challenges involved in such a process.
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Affiliation(s)
- Tyler M Earnest
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Reika Watanabe
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Julia Mahamid
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Elizabeth Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
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