1
|
Martin EC, Bowie AG, Wellfare Reid T, Neil Hunter C, Hitchcock A, Swainsbury DJ. 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 PMCID: PMC11346425 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.
Collapse
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
| | | |
Collapse
|
2
|
Tani K, Kanno R, Kikuchi R, Kawamura S, Nagashima KVP, Hall M, Takahashi A, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY. Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex. Nat Commun 2022; 13:1904. [PMID: 35393413 PMCID: PMC8991256 DOI: 10.1038/s41467-022-29453-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/08/2022] [Indexed: 11/18/2022] Open
Abstract
Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex.
Collapse
Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan.
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Riku Kikuchi
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Saki Kawamura
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Kenji V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ai Takahashi
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan
| | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | | |
Collapse
|
3
|
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 2022; 1863:148508. [PMID: 34793767 DOI: 10.1016/j.bbabio.2021.148508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
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
| |
Collapse
|
4
|
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]
|
5
|
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: 19] [Impact Index Per Article: 6.3] [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.
Collapse
|
6
|
Urbančič I, Schiffelers L, Jenkins E, Gong W, Santos AM, Schneider F, O'Brien-Ball C, Vuong MT, Ashman N, Sezgin E, Eggeling C. Aggregation and mobility of membrane proteins interplay with local lipid order in the plasma membrane of T cells. FEBS Lett 2021; 595:2127-2146. [PMID: 34160065 DOI: 10.1002/1873-3468.14153] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/07/2021] [Accepted: 06/18/2021] [Indexed: 01/17/2023]
Abstract
To disentangle the elusive lipid-protein interactions in T-cell activation, we investigate how externally imposed variations in mobility of key membrane proteins (T-cell receptor [TCR], kinase Lck, and phosphatase CD45) affect the local lipid order and protein colocalisation. Using spectral imaging with polarity-sensitive membrane probes in model membranes and live Jurkat T cells, we find that partial immobilisation of proteins (including TCR) by aggregation or ligand binding changes their preference towards a more ordered lipid environment, which can recruit Lck. Our data suggest that the cellular membrane is poised to modulate the frequency of protein encounters upon alterations of their mobility, for example in ligand binding, which offers new mechanistic insight into the involvement of lipid-mediated interactions in membrane-hosted signalling events.
Collapse
Affiliation(s)
- Iztok Urbančič
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Jožef Stefan Institute, Ljubljana, Slovenia
| | - Lisa Schiffelers
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Edward Jenkins
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Weijian Gong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Ana Mafalda Santos
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Falk Schneider
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | | | - Mai Tuyet Vuong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Nicole Ashman
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Erdinc Sezgin
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Christian Eggeling
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
| |
Collapse
|
7
|
Nepal B, Sepehri A, Lazaridis T. Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7. Protein Sci 2020; 29:1473-1485. [PMID: 32142182 DOI: 10.1002/pro.3851] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022]
Abstract
Certain proteins have the propensity to bind to negatively curved membranes and generate negative membrane curvature. The mechanism of action of these proteins is much less studied and understood than those that sense and generate positive curvature. In this work, we use implicit membrane modeling to explore the mechanism of an important negative curvature sensing and generating protein: the main ESCRT III subunit Snf7. We find that Snf7 monomers alone can sense negative curvature and that curvature sensitivity increases for dimers and trimers. We have observed spontaneous bending of Snf7 oligomers into circular structures with preferred radius of ~20 nm. The preferred curvature of Snf7 filaments is further confirmed by the simulations of preformed spirals on a cylindrical membrane surface. Snf7 filaments cannot bind with the same interface to flat and curved membranes. We find that even when a filament has the preferred radius, it is always less stable on the flat membrane surface than on the interior cylindrical membrane surface. This provides an additional energy for membrane bending which has not been considered in the spiral spring model. Furthermore, the rings on the cylindrical spirals are bridged together by helix 4 and hence are extra stabilized compared to the spirals on the flat membrane surface.
Collapse
Affiliation(s)
- Binod Nepal
- Department of Chemistry, City College of New York, New York, New York, USA
| | - Aliasghar Sepehri
- Department of Chemistry, City College of New York, New York, New York, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York, USA.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York, USA
| |
Collapse
|
8
|
González García Á, Ianiro A, Beljon R, Leermakers FAM, Tuinier R. (Homo)polymer-mediated colloidal stability of micellar solutions. SOFT MATTER 2020; 16:1560-1571. [PMID: 31950966 DOI: 10.1039/c9sm01665a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite their wide range of applications, there is a remarkable lack of fundamental understanding about how micelles respond to other components in solution. The colloidal stability of micellar solutions in presence of (homo)polymers is investigated here following a theoretical bottom-up approach. A polymer-mediated micelle-micelle interaction is extracted from changes in the micelle-unimer equilibrium as a function of the inter-micelle distance. The homopolymer-mediated diblock copolymer micelle-micelle interaction is studied both for depletion and adsorption of the homopolymer. The fluffy nature of the solvophilic domain (corona) of the micelle weakens the depletion-induced destabilization. Accumulation of polymers into the corona induces bridging attraction between micelles. In fact, both depletion and adsorption phenomena are regulated by the coronal thickness relative to the size of the added polymer. Penetration of guest compounds into the coronal domain of crew-cut micelles, with a narrower yet denser corona, is less pronounced as for starlike micelles (with a more diffuse corona). Therefore, crew-cut micelles are less sensitive to the effect of added compounds, and hence more suitable for applications in multicomponent systems, such as industrial formulations or biological fluids. The trends observed for the colloidal stability of crew-cut micelles qualitatively match with our experimental observations on aqueous dispersions of polycaprolactone-polyethylene glycol (PCL-PEO) micellar suspensions with added PEO chains.
Collapse
Affiliation(s)
- Álvaro González García
- Van't Hoff Laboratory for Physical and Colloid Chemistry, Department of Chemistry & Debye Institute, Utrecht University, Padualaan 8, 3584 CH, The Netherlands.
| | | | | | | | | |
Collapse
|
9
|
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: 105] [Impact Index Per Article: 21.0] [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.
Collapse
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
| |
Collapse
|
10
|
Kahraman O, Haselwandter CA. Supramolecular organization of membrane proteins with anisotropic hydrophobic thickness. SOFT MATTER 2019; 15:4301-4310. [PMID: 31070658 DOI: 10.1039/c9sm00358d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experiments have revealed that membrane proteins often self-assemble into locally ordered clusters. Such membrane protein lattices can play key roles in the functional organization of cell membranes. Membrane protein organization can be driven, at least in part, by bilayer-mediated elastic interactions between membrane proteins. For membrane proteins with anisotropic hydrophobic thickness, bilayer-mediated protein interactions are inherently directional. Here we establish general relations between anisotropy in membrane protein hydrophobic thickness and supramolecular membrane protein organization. We show that protein symmetry is distinctively reflected in the energy landscape of bilayer-mediated protein interactions, favoring characteristic lattice architectures of membrane protein clusters. We find that, in the presence of thermal fluctuations, anisotropy in protein hydrophobic thickness can induce membrane proteins to form mesh-like structures dividing the membrane into compartments. Our results help to elucidate the physical principles and mechanisms underlying the functional organization of cell membranes.
Collapse
Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | |
Collapse
|
11
|
Evans R, Galindo A, Jackson G, Lynden-Bell R, Rotenberg B. Daan Frenkel — An entropic career. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1514685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Robert Evans
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK
| | - Amparo Galindo
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - George Jackson
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ruth Lynden-Bell
- University Chemical Laboratory, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK
| | - Benjamin Rotenberg
- Physicochimie des Electrolytes et Nanosystèmes Interfaciaux, Sorbonne Université, CNRS, PHENIX, Paris F-75005, France
| |
Collapse
|
12
|
Swainsbury DJK, Martin EC, Vasilev C, Parkes-Loach PS, Loach PA, Neil Hunter C. Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:927-938. [PMID: 28826909 PMCID: PMC5604489 DOI: 10.1016/j.bbabio.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/02/2017] [Accepted: 08/17/2017] [Indexed: 01/01/2023]
Abstract
The reaction centre-light harvesting 1 (RC-LH1) complex of Thermochromatium (Tch.) tepidum has a unique calcium-ion binding site that enhances thermal stability and red-shifts the absorption of LH1 from 880nm to 915nm in the presence of calcium-ions. The LH1 antenna of mesophilic species of phototrophic bacteria such as Rhodobacter (Rba.) sphaeroides does not possess such properties. We have engineered calcium-ion binding into the LH1 antenna of Rba. sphaeroides by progressively modifying the native LH1 polypeptides with sequences from Tch. tepidum. We show that acquisition of the C-terminal domains from LH1 α and β of Tch. tepidum is sufficient to activate calcium-ion binding and the extent of red-shifting increases with the proportion of Tch. tepidum sequence incorporated. However, full exchange of the LH1 polypeptides with those of Tch. tepidum results in misassembled core complexes. Isolated α and β polypeptides from our most successful mutant were reconstituted in vitro with BChl a to form an LH1-type complex, which was stabilised 3-fold by calcium-ions. Additionally, carotenoid specificity was changed from spheroidene found in Rba. sphaeroides to spirilloxanthin found in Tch. tepidum, with the latter enhancing in vitro formation of LH1. These data show that the C-terminal LH1 α/β domains of Tch. tepidum behave autonomously, and are able to transmit calcium-ion induced conformational changes to BChls bound to the rest of a foreign antenna complex. Thus, elements of foreign antenna complexes, such as calcium-ion binding and blue/red switching of absorption, can be ported into Rhodobacter sphaeroides using careful design processes.
Collapse
Affiliation(s)
- David J K Swainsbury
- 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
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Pamela S Parkes-Loach
- Department of Molecular Biosciences, Northwestern University, Hogan 2100, 2205 Tech Drive, Evanston, IL 60208, United States
| | - Paul A Loach
- Department of Molecular Biosciences, Northwestern University, Hogan 2100, 2205 Tech Drive, Evanston, IL 60208, United States
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| |
Collapse
|
13
|
The C-terminus of PufX plays a key role in dimerisation and assembly of the reaction center light-harvesting 1 complex from Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:795-803. [PMID: 28587931 PMCID: PMC5538271 DOI: 10.1016/j.bbabio.2017.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 11/22/2022]
Abstract
In bacterial photosynthesis reaction center-light-harvesting 1 (RC-LH1) complexes trap absorbed solar energy by generating a charge separated state. Subsequent electron and proton transfers form a quinol, destined to diffuse to the cytochrome bc1 complex. In bacteria such as Rhodobacter (Rba.) sphaeroides and Rba. capsulatus the PufX polypeptide creates a channel for quinone/quinol traffic across the LH1 complex that surrounds the RC, and it is therefore essential for photosynthetic growth. PufX also plays a key role in dimerization of the RC-LH1-PufX core complex, and the structure of the Rba. sphaeroides complex shows that the PufX C-terminus, particularly the region from X49-X53, likely mediates association of core monomers. To investigate this putative interaction we analysed mutations PufX R49L, PufX R53L, PufX R49/53L and PufX G52L by measuring photosynthetic growth, fractionation of detergent-solubilised membranes, formation of 2-D crystals and electron microscopy. We show that these mutations do not affect assembly of PufX within the core or photosynthetic growth but they do prevent dimerization, consistent with predictions from the RC-LH1-PufX structure. We obtained low resolution structures of monomeric core complexes with and without PufX, using electron microscopy of negatively stained single particles and 3D reconstruction; the monomeric complex with PufX corresponds to one half of the dimer structure whereas LH1 completely encloses the RC if the gene encoding PufX is deleted. On the basis of the insights gained from these mutagenesis and structural analyses we propose a sequence for assembly of the dimeric RC-LH1-PufX complex.
Collapse
|
14
|
Bohuszewicz O, Liu J, Low HH. Membrane remodelling in bacteria. J Struct Biol 2016; 196:3-14. [PMID: 27265614 PMCID: PMC6168058 DOI: 10.1016/j.jsb.2016.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 01/10/2023]
Abstract
In bacteria the ability to remodel membrane underpins basic cell processes such as growth, and more sophisticated adaptations like inter-cell crosstalk, organelle specialisation, and pathogenesis. Here, selected examples of membrane remodelling in bacteria are presented and the diverse mechanisms for inducing membrane fission, fusion, and curvature discussed. Compared to eukaryotes, relatively few curvature-inducing proteins have been characterised so far. Whilst it is likely that many such proteins remain to be discovered, it also reflects the importance of alternative membrane remodelling strategies in bacteria where passive mechanisms for generating curvature are utilised.
Collapse
Affiliation(s)
- Olga Bohuszewicz
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Jiwei Liu
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Harry H Low
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK.
| |
Collapse
|
15
|
Sener M, Strumpfer J, Singharoy A, Hunter CN, Schulten K. Overall energy conversion efficiency of a photosynthetic vesicle. eLife 2016; 5. [PMID: 27564854 PMCID: PMC5001839 DOI: 10.7554/elife.09541] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/11/2016] [Indexed: 11/25/2022] Open
Abstract
The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytbc1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12–0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination. DOI:http://dx.doi.org/10.7554/eLife.09541.001 Photosynthesis, or the conversion of light energy into chemical energy, is a process that powers almost all life on Earth. Plants and certain bacteria share similar processes to perform photosynthesis, though the purple bacterium Rhodobacter sphaeroides uses a photosynthetic system that is much less complex than that in plants. Light harvesting inside the bacterium takes place in up to hundreds of compartments called chromatophores. Each chromatophore in turn contains hundreds of cooperating proteins that together absorb the energy of sunlight and convert and store it in molecules of ATP, the universal energy currency of all cells. The chromatophore of primitive purple bacteria provides a model for more complex photosynthetic systems in plants. Though researchers had characterized its individual components over the years, less was known about the overall architecture of the chromatophore and how its many components work together to harvest light energy efficiently and robustly. This knowledge would provide insight into the evolutionary pressures that shaped the chromatophore and its ability to work efficiently at different light intensities. Sener et al. now present a highly detailed structural model of the chromatophore of purple bacteria based on the findings of earlier studies. The model features the position of every atom of the constituent proteins and is used to examine how energy is transferred and converted. Sener et al. describe the sequence of energy conversion steps and calculate the overall energy conversion efficiency, namely how much of the light energy arriving at the microorganism is stored as ATP. These calculations show that the chromatophore is optimized to produce chemical energy at low light levels typical of purple bacterial habitats, and dissipate excess energy to avoid being damaged under brighter light. The chromatophore’s architecture also displays robustness against perturbations of its components. In the future, the approach used by Sener et al. to describe light harvesting in this bacterial compartment can be applied to more complex systems, such as those in plants. DOI:http://dx.doi.org/10.7554/eLife.09541.002
Collapse
Affiliation(s)
- Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Johan Strumpfer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| |
Collapse
|
16
|
Aydin F, Dutt M. Surface Reconfiguration of Binary Lipid Vesicles via Electrostatically Induced Nanoparticle Adsorption. J Phys Chem B 2016; 120:6646-56. [DOI: 10.1021/acs.jpcb.6b02334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fikret Aydin
- Department
of Chemical and
Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department
of Chemical and
Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| |
Collapse
|
17
|
Kahraman O, Koch PD, Klug WS, Haselwandter CA. Bilayer-thickness-mediated interactions between integral membrane proteins. Phys Rev E 2016; 93:042410. [PMID: 27176332 DOI: 10.1103/physreve.93.042410] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.
Collapse
Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - Christoph A Haselwandter
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
18
|
Kahraman O, Koch PD, Klug WS, Haselwandter CA. Architecture and Function of Mechanosensitive Membrane Protein Lattices. Sci Rep 2016; 6:19214. [PMID: 26771082 PMCID: PMC4725903 DOI: 10.1038/srep19214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/07/2015] [Indexed: 12/04/2022] Open
Abstract
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular organization and collective function of membrane proteins remain largely unknown. Here we show that bilayer-mediated elastic interactions between membrane proteins can yield regular and distinctive lattice architectures of protein clusters, and may provide a link between lattice architecture and lattice function. Using the mechanosensitive channel of large conductance (MscL) as a model system, we obtain relations between the shape of MscL and the supramolecular architecture of MscL lattices. We predict that the tetrameric and pentameric MscL symmetries observed in previous structural studies yield distinct lattice architectures of MscL clusters and that, in turn, these distinct MscL lattice architectures yield distinct lattice activation barriers. Our results suggest general physical mechanisms linking protein symmetry, the lattice architecture of membrane protein clusters, and the collective function of membrane protein lattices.
Collapse
Affiliation(s)
- Osman Kahraman
- Departments of Physics &Astronomy and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
| | - Christoph A Haselwandter
- Departments of Physics &Astronomy and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
19
|
Mothersole DJ, Jackson PJ, Vasilev C, Tucker JD, Brindley AA, Dickman MJ, Hunter CN. PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides. Mol Microbiol 2015; 99:307-27. [PMID: 26419219 PMCID: PMC4949548 DOI: 10.1111/mmi.13235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2015] [Indexed: 01/21/2023]
Abstract
The mature architecture of the photosynthetic membrane of the purple phototroph Rhodobacter sphaeroides has been characterised to a level where an atomic-level membrane model is available, but the roles of the putative assembly proteins LhaA and PucC in establishing this architecture are unknown. Here we investigate the assembly of light-harvesting LH2 and reaction centre-light-harvesting1-PufX (RC-LH1-PufX) photosystem complexes using spectroscopy, pull-downs, native gel electrophoresis, quantitative mass spectrometry and fluorescence lifetime microscopy to characterise a series of lhaA and pucC mutants. LhaA and PucC are important for specific assembly of LH1 or LH2 complexes, respectively, but they are not essential; the few LH1 subunits found in ΔlhaA mutants assemble to form normal RC-LH1-PufX core complexes showing that, once initiated, LH1 assembly round the RC is cooperative and proceeds to completion. LhaA and PucC form oligomers at sites of initiation of membrane invagination; LhaA associates with RCs, bacteriochlorophyll synthase (BchG), the protein translocase subunit YajC and the YidC membrane protein insertase. These associations within membrane nanodomains likely maximise interactions between pigments newly arriving from BchG and nascent proteins within the SecYEG-SecDF-YajC-YidC assembly machinery, thereby co-ordinating pigment delivery, the co-translational insertion of LH polypeptides and their folding and assembly to form photosynthetic complexes.
Collapse
Affiliation(s)
- David J Mothersole
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.,ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jaimey D Tucker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| |
Collapse
|
20
|
D'Haene SE, Crouch LI, Jones MR, Frese RN. Organization in photosynthetic membranes of purple bacteria in vivo: the role of carotenoids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1665-73. [PMID: 25017691 DOI: 10.1016/j.bbabio.2014.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 11/19/2022]
Abstract
Photosynthesis in purple bacteria is performed by pigment-protein complexes that are closely packed within specialized intracytoplasmic membranes. Here we report on the influence of carotenoid composition on the organization of RC-LH1 pigment-protein complexes in intact membranes and cells of Rhodobacter sphaeroides. Mostly dimeric RC-LH1 complexes could be isolated from strains expressing native brown carotenoids when grown under illuminated/anaerobic conditions, or from strains expressing green carotenoids when grown under either illuminated/anaerobic or dark/semiaerobic conditions. However, mostly monomeric RC-LH1 complexes were isolated from strains expressing the native photoprotective red carotenoid spheroidenone, which is synthesized during phototrophic growth in the presence of oxygen. Despite this marked difference, linear dichroism (LD) and light-minus-dark LD spectra of oriented intact intracytoplasmic membranes indicated that RC-LH1 complexes are always assembled in ordered arrays, irrespective of variations in the relative amounts of isolated dimeric and monomeric RC-LH1 complexes. We propose that part of the photoprotective response to the presence of oxygen mediated by synthesis of spheroidenone may be a switch of the structure of the RC-LH1 complex from dimers to monomers, but that these monomers are still organized into the photosynthetic membrane in ordered arrays. When levels of the dimeric RC-LH1 complex were very high, and in the absence of LH2, LD and ∆LD spectra from intact cells indicated an ordered arrangement of RC-LH1 complexes. Such a degree of ordering implies the presence of highly elongated, tubular membranes with dimensions requiring orientation along the length of the cell and in a proportion larger than previously observed.
Collapse
Affiliation(s)
- Sandrine E D'Haene
- Biophysics of photosynthesis/Physics of Energy, Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands.
| | - Lucy I Crouch
- School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Michael R Jones
- School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.
| | - Raoul N Frese
- Biophysics of photosynthesis/Physics of Energy, Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands.
| |
Collapse
|
21
|
Llorente-Garcia I, Lenn T, Erhardt H, Harriman OL, Liu LN, Robson A, Chiu SW, Matthews S, Willis NJ, Bray CD, Lee SH, Shin JY, Bustamante C, Liphardt J, Friedrich T, Mullineaux CW, Leake MC. Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:811-24. [DOI: 10.1016/j.bbabio.2014.01.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 02/04/2023]
|
22
|
Hormel TT, Kurihara SQ, Brennan MK, Wozniak MC, Parthasarathy R. Measuring lipid membrane viscosity using rotational and translational probe diffusion. PHYSICAL REVIEW LETTERS 2014; 112:188101. [PMID: 24856725 DOI: 10.1103/physrevlett.112.188101] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Indexed: 05/23/2023]
Abstract
The two-dimensional fluidity of lipid bilayers enables the motion of membrane-bound macromolecules and is therefore crucial to biological function. Microrheological methods that measure fluid viscosity via the translational diffusion of tracer particles are challenging to apply and interpret for membranes, due to uncertainty about the local environment of the tracers. Here, we demonstrate a new technique in which determination of both the rotational and translational diffusion coefficients of membrane-linked particles enables quantification of viscosity, measurement of the effective radii of the tracers, and assessment of theoretical models of membrane hydrodynamics. Surprisingly, we find a wide distribution of effective tracer radii, presumably due to a variable number of lipids linked to each tracer particle. Furthermore, we show for the first time that a protein involved in generating membrane curvature, the vesicle trafficking protein Sar1p, dramatically increases membrane viscosity. Using the rheological method presented here, therefore, we are able to reveal a class of previously unknown couplings between protein activity and membrane mechanics.
Collapse
Affiliation(s)
- Tristan T Hormel
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Sarah Q Kurihara
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - M Kathleen Brennan
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Matthew C Wozniak
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Raghuveer Parthasarathy
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| |
Collapse
|
23
|
Scheuring S, Nevo R, Liu LN, Mangenot S, Charuvi D, Boudier T, Prima V, Hubert P, Sturgis JN, Reich Z. The architecture of Rhodobacter sphaeroides chromatophores. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1263-70. [PMID: 24685429 DOI: 10.1016/j.bbabio.2014.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 12/18/2022]
Abstract
The chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bc1 complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bc1 complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bc1 complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs.
Collapse
Affiliation(s)
- Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique de Luminy, Marseille F-13009, France.
| | - Reinat Nevo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lu-Ning Liu
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique de Luminy, Marseille F-13009, France
| | | | - Dana Charuvi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thomas Boudier
- Sorbonne Universités, UPMC Univ Paris 06, IBPS, F-75005 Paris, France
| | - Valerie Prima
- LISM CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Pierre Hubert
- LISM CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - James N Sturgis
- LISM CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
24
|
Sznee K, Crouch LI, Jones MR, Dekker JP, Frese RN. Variation in supramolecular organisation of the photosynthetic membrane of Rhodobacter sphaeroides induced by alteration of PufX. PHOTOSYNTHESIS RESEARCH 2014; 119:243-256. [PMID: 24197265 DOI: 10.1007/s11120-013-9949-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/24/2013] [Indexed: 06/02/2023]
Abstract
In purple bacteria of the genus Rhodobacter (Rba.), an LH1 antenna complex surrounds the photochemical reaction centre (RC) with a PufX protein preventing the LH1 complex from completely encircling the RC. In membranes of Rba. sphaeroides, RC-LH1 complexes associate as dimers which in turn assemble into longer range ordered arrays. The present work uses linear dichroism (LD) and dark-minus-light difference LD (ΔLD) to probe the organisation of genetically altered RC-LH1 complexes in intact membranes. The data support previous proposals that Rba. capsulatus, and Rba. sphaeroides heterologously expressing the PufX protein from Rba. capsulatus, produce monomeric core complexes in membranes that lack long-range order. Similarly, Rba. sphaeroides with a point mutation in the Gly 51 residue of PufX, which is located on the membrane-periplasm interface, assembles mainly non-ordered RC-LH1 complexes that are most likely monomeric. All the Rba. sphaeroides membranes in their ΔLD spectra exhibited a spectral fingerprint of small degree of organisation implying the possibility of ordering influence of LH1, and leading to an important conclusion that PufX itself has no influence on ordering RC-LH1 complexes, as long-range order appears to be induced only through its role of configuring RC-LH1 complexes into dimers.
Collapse
Affiliation(s)
- Kinga Sznee
- Division of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands,
| | | | | | | | | |
Collapse
|
25
|
Schneider AR, Geissler PL. Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities. FRONTIERS IN PLANT SCIENCE 2014; 4:555. [PMID: 24478781 PMCID: PMC3896813 DOI: 10.3389/fpls.2013.00555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/30/2013] [Indexed: 06/03/2023]
Abstract
Coarse-grained simulation is a powerful and well-established suite of computational methods for studying structure and dynamics in nanoscale biophysical systems. As our understanding of the plant photosynthetic apparatus has become increasingly nuanced, opportunities have arisen for coarse-grained simulation to complement experiment by testing hypotheses and making predictions. Here, we give an overview of best practices in coarse-grained simulation, with a focus on techniques and results that are applicable to the plant thylakoid membrane-protein system. We also discuss current research topics for which coarse-grained simulation has the potential to play a key role in advancing the field.
Collapse
Affiliation(s)
- Anna R. Schneider
- Biophysics Graduate Group, University of CaliforniaBerkeley, CA, USA
- Department of Chemistry, University of CaliforniaBerkeley, CA, USA
| | - Phillip L. Geissler
- Department of Chemistry, University of CaliforniaBerkeley, CA, USA
- Chemical Sciences and Physical Biosciences Divisions, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| |
Collapse
|
26
|
Duneau JP, Sturgis JN. Lateral organization of biological membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:843-50. [DOI: 10.1007/s00249-013-0933-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/13/2013] [Accepted: 09/26/2013] [Indexed: 11/24/2022]
|
27
|
Qian P, Papiz MZ, Jackson PJ, Brindley AA, Ng IW, Olsen JD, Dickman MJ, Bullough PA, Hunter CN. Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX. Biochemistry 2013; 52:7575-85. [DOI: 10.1021/bi4011946] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pu Qian
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Miroslav Z. Papiz
- Institute
of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Philip J. Jackson
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Amanda A. Brindley
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Irene W. Ng
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - John D. Olsen
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Mark J. Dickman
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Per A. Bullough
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| |
Collapse
|
28
|
Sumino A, Dewa T, Noji T, Nakano Y, Watanabe N, Hildner R, Bösch N, Köhler J, Nango M. Influence of Phospholipid Composition on Self-Assembly and Energy-Transfer Efficiency in Networks of Light-Harvesting 2 Complexes. J Phys Chem B 2013; 117:10395-404. [DOI: 10.1021/jp4047819] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ayumi Sumino
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Takehisa Dewa
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Tomoyasu Noji
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yuki Nakano
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Natsuko Watanabe
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Richard Hildner
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Nils Bösch
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Jürgen Köhler
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Mamoru Nango
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
29
|
Liu LN, Scheuring S. Investigation of photosynthetic membrane structure using atomic force microscopy. TRENDS IN PLANT SCIENCE 2013; 18:277-86. [PMID: 23562040 DOI: 10.1016/j.tplants.2013.03.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/21/2013] [Accepted: 03/01/2013] [Indexed: 05/26/2023]
Abstract
Photosynthetic processes, including light capture, electron transfer, and energy conversion, are not only ensured by the activities of individual photosynthetic complexes but also substantially determined and regulated by the composition and assembly of the overall photosynthetic apparatus at the supramolecular level. In recent years, atomic force microscopy (AFM) has matured as a unique and powerful tool for directly assessing the supramolecular assembly of integral membrane protein complexes in their native membrane environment at submolecular resolution. This review highlights the major contributions and advances of AFM studies to our understanding of the structure of the bacterial photosynthetic machinery and its regulatory arrangement during chromatic adaptation. AFM topographs of other biological membrane systems and potential future applications of AFM are also discussed.
Collapse
Affiliation(s)
- Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | | |
Collapse
|
30
|
Kusumaatmaja H, Wales DJ. Defect motifs for constant mean curvature surfaces. PHYSICAL REVIEW LETTERS 2013; 110:165502. [PMID: 23679616 DOI: 10.1103/physrevlett.110.165502] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 12/13/2012] [Indexed: 06/02/2023]
Abstract
The energy landscapes of electrostatically charged particles embedded on constant mean curvature surfaces are analyzed for a wide range of system size, curvature, and interaction potentials. The surfaces are taken to be rigid, and the basin-hopping method is used to locate the putative global minimum structures. The defect motifs favored by potential energy agree with experimental observations for colloidal systems: extended defects (scars and pleats) for weakly positive and negative Gaussian curvatures, and isolated defects for strongly negative Gaussian curvatures. Near the phase boundary between these regimes, the two motifs are in strong competition, as evidenced from the appearance of distinct funnels in the potential energy landscape. We also report a novel defect motif consisting of pentagon pairs.
Collapse
Affiliation(s)
- Halim Kusumaatmaja
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | |
Collapse
|
31
|
Goose JE, Sansom MSP. Reduced lateral mobility of lipids and proteins in crowded membranes. PLoS Comput Biol 2013; 9:e1003033. [PMID: 23592975 PMCID: PMC3623704 DOI: 10.1371/journal.pcbi.1003033] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/28/2013] [Indexed: 12/31/2022] Open
Abstract
Coarse-grained molecular dynamics simulations of the E. coli outer membrane proteins FhuA, LamB, NanC, OmpA and OmpF in a POPE/POPG (3∶1) bilayer were performed to characterise the diffusive nature of each component of the membrane. At small observation times (<10 ns) particle vibrations dominate phospholipid diffusion elevating the calculated values from the longer time-scale bulk value (>50 ns) of 8.5×10−7 cm2 s−1. The phospholipid diffusion around each protein was found to vary based on distance from protein. An asymmetry in the diffusion of annular lipids in the inner and outer leaflets was observed and correlated with an asymmetry in charged residues in the vicinity of the inner and outer leaflet head-groups. Protein rotational and translational diffusion were also found to vary with observation time and were inversely correlated with the radius of gyration of the protein in the plane of the bilayer. As the concentration of protein within the bilayer was increased, the overall mobility of the membrane decreased reflected in reduced lipid diffusion coefficients for both lipid and protein components. The increase in protein concentration also resulted in a decrease in the anomalous diffusion exponent α of the lipid. Formation of extended clusters and networks of proteins led to compartmentalisation of lipids in extreme cases. Biological membranes are selective barriers which control the entry/exit of molecules to/from the interior of a cell. They are composed of a lipid bilayer in which are embedded many membrane proteins. Whilst the individual components of membranes are relatively well characterised, the lateral organization and dynamics of the membrane remain less well understood. The lateral mobility of constituent membrane species affects many processes, including how quickly proteins complexes form and protein recruitment occurs, how quickly lipids can be modified/lysed, and the formation of disordered and ordered microdomains. Biological membranes can contain as much as 50% protein. The dynamics of these crowded environments differ greatly from the sparsely populated membranes often studied in silico or in vitro. We use molecular dynamics computer simulations to quantify how mobility within the membrane decreases as the protein concentration increases. We calculate a baseline diffusion of both lipids and selected bacterial outer membrane proteins in the simplest of systems, namely a single protein in a large lipid bilayer patch. In this case diffusion can be correlated with the size of the protein. We observe how proteins affect the mobility of adjacent lipids. As the protein concentration within our systems increases we show that diffusion of both the proteins and lipids is reduced.
Collapse
Affiliation(s)
- Joseph E. Goose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
32
|
Alessandrini A, Viero G, Dalla Serra M, Prévost G, Facci P. γ-Hemolysin oligomeric structure and effect of its formation on supported lipid bilayers: an AFM investigation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:405-11. [PMID: 23036932 DOI: 10.1016/j.bbamem.2012.09.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/05/2012] [Accepted: 09/25/2012] [Indexed: 11/28/2022]
Abstract
γ-Hemolysins are bicomponent β-barrel pore forming toxins produced by Staphylococcus aureus as water-soluble monomers, which assemble into oligomeric pores on the surface of lipid bilayers. Here, after investigating the oligomeric structure of γ-hemolysins on supported lipid bilayers (SLBs) by atomic force microscopy (AFM), we studied the effect produced by this toxin on the structure of SLBs. We found that oligomeric structures with different number of monomers can assemble on the lipid bilayer being the octameric form the stablest one. Moreover, in this membrane model we found that γ-hemolysins can form clusters of oligomers inducing a curvature in the lipid bilayer, which could probably enhance the aggressiveness of these toxins at high concentrations.
Collapse
Affiliation(s)
- Andrea Alessandrini
- Centro S3, CNR-Istituto di Nanoscienze, Via Campi 213/A, 41125 Modena, Italy.
| | | | | | | | | |
Collapse
|
33
|
Adams PG, Hunter CN. Adaptation of intracytoplasmic membranes to altered light intensity in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1616-27. [PMID: 22659614 DOI: 10.1016/j.bbabio.2012.05.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/18/2012] [Accepted: 05/25/2012] [Indexed: 11/19/2022]
Abstract
The model photosynthetic bacterium Rhodobacter sphaeroides uses a network of bacteriochlorophyll (BChl)-protein complexes embedded in spherical intracytoplasmic membranes (ICM) to collect and utilise solar energy. We studied the effects of high- and low-light growth conditions, where BChl levels increased approximately four-fold from 1.6×10(6) to 6.5×10(6) molecules per cell. Most of this extra pigment is accommodated in the proliferating ICM system, which increases from approximately 274 to 1468 vesicles per cell. Thus, 16×10(6)nm(2) of specialised membrane surface area is made available for harvesting and utilising solar energy compared to 3×10(6)nm(2) under high-light conditions. Membrane mapping using atomic force microscopy revealed closely packed dimeric and monomeric reaction centre-light harvesting 1-PufX (RC-LH1-PufX) complexes in high-light ICM with room only for small clusters of LH2, whereas extensive LH2-only domains form during adaptation to low light, with the LH2/RC ratio increasing three-fold. The number of upper pigmented band (UPB) sites where membrane invagination is initiated hardly varied; 704 (5.8×10(5) BChls/cell) and 829 (4.9×10(5) BChls/cell) UPB sites per cell were estimated under high- and low-light conditions, respectively. Thus, the lower ICM content in high-light cells is a consequence of fewer ICM invaginations reaching maturity. Taking into account the relatively poor LH2-to-LH1 energy transfer in UPB membranes it is likely that high-light cells are relatively inefficient at energy trapping, but can grow well enough without the need to fully develop their photosynthetic membranes from the relatively inefficient UPB to highly efficient mature ICM.
Collapse
Affiliation(s)
- Peter G Adams
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | |
Collapse
|
34
|
Sarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. PHYSICAL REVIEW LETTERS 2012; 108:118101. [PMID: 22540513 DOI: 10.1103/physrevlett.108.118101] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Indexed: 05/18/2023]
Abstract
Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.
Collapse
Affiliation(s)
- Anđela Sarić
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | |
Collapse
|
35
|
Sznee K, Dekker JP, Dame RT, van Roon H, Wuite GJL, Frese RN. Jumping mode atomic force microscopy on grana membranes from spinach. J Biol Chem 2011; 286:39164-71. [PMID: 21911498 DOI: 10.1074/jbc.m111.284844] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thylakoid membrane system is a complex membrane system that organizes and reorganizes itself to provide plants optimal chemical energy from sunlight under different and varying environmental conditions. Grana membranes are part of this system and contain the light-driven water-splitting enzyme Photosystem II (PSII) and light-harvesting antenna complexes. Here, we present a direct visualization of PSII complexes within grana membranes from spinach. By means of jumping mode atomic force microscopy in liquid, minimal forces were applied between the scanning tip and membrane or protein, allowing complexes to be imaged with high detail. We observed four different packing arrangements of PSII complexes, which occur primarily as dimers: co-linear crystalline rows, nanometric domains of straight or skewed rows, and disordered domains. Upon storing surface-adhered membranes at low temperature prior to imaging, large-scale reorganizations of supercomplexes between PSII and light-harvesting complex II could be induced. The highest resolution images show the existence of membrane domains without obvious topography extending beyond supercomplexes. These observations illustrate the possibility for diffusion of proteins and smaller molecules within these densely packed membranes.
Collapse
Affiliation(s)
- Kinga Sznee
- Faculty of Sciences, Department of Physics and Astronomy, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
36
|
Şener M, Strümpfer J, Hsin J, Chandler D, Scheuring S, Hunter CN, Schulten K. Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems. Chemphyschem 2011; 12:518-31. [PMID: 21344591 DOI: 10.1002/cphc.201000944] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Förster’s theory of resonant energy transfer underlies a fundamental process in nature, namely the harvesting of sunlight by photosynthetic life forms. The theoretical framework developed by Förster and others describes how electronic excitation migrates in the photosynthetic apparatus of plants, algae, and bacteria from light absorbing pigments to reaction centers where light energy is utilized for the eventual conversion into chemical energy. The demand for highest possible efficiency of light harvesting appears to have shaped the evolution of photosynthetic species from bacteria to plants which, despite a great variation in architecture, display common structural themes founded on the quantum physics of energy transfer as described first by Förster. Herein, Förster’s theory of excitation transfer is summarized, including recent extensions, and the relevance of the theory to photosynthetic systems as evolved in purple bacteria, cyanobacteria, and plants is demonstrated. Förster’s energy transfer formula, as used widely today in many fields of science, is also derived.
Collapse
Affiliation(s)
- Melih Şener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | | | | | | | |
Collapse
|
37
|
Ramanan V, Agrawal NJ, Liu J, Engles S, Toy R, Radhakrishnan R. Systems biology and physical biology of clathrin-mediated endocytosis. Integr Biol (Camb) 2011; 3:803-15. [PMID: 21792431 PMCID: PMC3153420 DOI: 10.1039/c1ib00036e] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this review, we describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time. However, recent experimental, theoretical, and computational tools have proved to be critical in establishing a sequence of events, cooperative dynamics, and energetics of the intracellular process. On the experimental front, total internal reflection fluorescence microscopy, photo-activated localization microscopy, and spinning-disk confocal microscopy have focused on assembly and patterning of endocytic proteins at the membrane, while on the theory front, minimal theoretical models for clathrin nucleation, biophysical models for membrane curvature and bending elasticity, as well as methods from computational structural and systems biology, have proved insightful in describing membrane topologies, curvature mechanisms, and energetics.
Collapse
Affiliation(s)
- Vyas Ramanan
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| | - Neeraj J. Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| | - Jin Liu
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| | - Sean Engles
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| | - Randall Toy
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, USA
| |
Collapse
|
38
|
Sumino A, Dewa T, Takeuchi T, Sugiura R, Sasaki N, Misawa N, Tero R, Urisu T, Gardiner AT, Cogdell RJ, Hashimoto H, Nango M. Construction and structural analysis of tethered lipid bilayer containing photosynthetic antenna proteins for functional analysis. Biomacromolecules 2011; 12:2850-8. [PMID: 21650465 DOI: 10.1021/bm200585y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAP), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.
Collapse
Affiliation(s)
- Ayumi Sumino
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Woronowicz K, Sha D, Frese RN, Sturgis JN, Nanda V, Niederman RA. The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c2 oxidoreductase. Metallomics 2011; 3:765-74. [PMID: 21691621 DOI: 10.1039/c1mt00034a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Atomic force microscopy (AFM) of the native architecture of the intracytoplasmic membrane (ICM) of a variety of species of purple photosynthetic bacteria, obtained at submolecular resolution, shows a tightly packed arrangement of light harvesting (LH) and reaction center (RC) complexes. Since there are no unattributed structures or gaps with space sufficient for the cytochrome bc(1) or ATPase complexes, they are localized in membrane domains distinct from the flat regions imaged by AFM. This has generated a renewed interest in possible long-range pathways for lateral diffusion of UQ redox species that functionally link the RC and the bc(1) complexes. Recent proposals to account for UQ flow in the membrane bilayer are reviewed, along with new experimental evidence provided from an analysis of intrinsic near-IR fluorescence emission that has served to test these hypotheses. The results suggest that different mechanism of UQ flow exist between species such as Rhodobacter sphaeroides, with a highly organized arrangement of LH and RC complexes and fast RC electron transfer turnover, and Phaeospirillum molischianum with a more random organization and slower RC turnover. It is concluded that packing density of the peripheral LH2 antenna in the Rba. sphaeroides ICM imposes constraints that significantly slow the diffusion of UQ redox species between the RC and cytochrome bc(1) complex, while in Phs. molischianum, the crowding of the ICM with LH3 has little effect upon UQ diffusion. This supports the proposal that in this type of ICM, a network of RC-LH1 core complexes observed in AFM provides a pathway for long-range quinone diffusion that is unaffected by differences in LH complex composition or organization.
Collapse
Affiliation(s)
- Kamil Woronowicz
- Department of Molecular Biology and Biochemistry, Rutgers University, Busch Campus, 604 Allison Road, Piscataway, NJ 08854-8082, USA
| | | | | | | | | | | |
Collapse
|
40
|
Adams PG, Mothersole DJ, Ng IW, Olsen JD, Hunter CN. Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1044-55. [PMID: 21663730 DOI: 10.1016/j.bbabio.2011.05.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 10/18/2022]
Abstract
In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation.
Collapse
Affiliation(s)
- Peter G Adams
- Department of Molecular Biology and Biochemistry, University of Sheffield, United Kingdom
| | | | | | | | | |
Collapse
|
41
|
Sumino A, Dewa T, Kondo M, Morii T, Hashimoto H, Gardiner AT, Cogdell RJ, Nango M. Selective assembly of photosynthetic antenna proteins into a domain-structured lipid bilayer for the construction of artificial photosynthetic antenna systems: structural analysis of the assembly using surface plasmon resonance and atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1092-1099. [PMID: 21204531 DOI: 10.1021/la103281q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Two types of photosynthetic membrane proteins, the peripheral antenna complex (LH2) and the core antenna/reaction center complex (LH1-RC), play an essential role in the primary process of purple bacterial photosynthesis, that is, capturing light energy, transferring it to the RC where it is used in subsequent charge separation. Establishment of experimental platforms is required to understand the function of the supramolecular assembly of LH2 and LH1-RC molecules into arrays. In this study, we assembled LH2 and LH1-RC arrays into domain-structured planar lipid bilayers placed on a coverglass using stepwise combinations of vesicle-to-planar membrane formation and vesicle fusion methods. First, it was shown that assembly of LH2 and LH1-RC in planar lipid bilayers, through vesicle-to-planar membrane formation, could be confirmed by absorption spectroscopy and high resolution atomic force microscopy (AFM). Second, formation of a planar membrane incorporating LH2 molecules made by the vesicle fusion method was corroborated by AFM together with quantitative analysis by surface plasmon resonance (SPR). By combining planar membrane formation and vesicle fusion, in a stepwise manner, LH2 and LH1-RC were successfully organized in the domain-structured planar lipid membrane. This methodology for construction of LH2/LH1-RC assemblies will be a useful experimental platform with which to investigate energy transfer from LH2 to LH1-RC where the relative arrangement of these two complexes can be controlled.
Collapse
Affiliation(s)
- Ayumi Sumino
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Pàmies JC, Cacciuto A. Reshaping elastic nanotubes via self-assembly of surface-adhesive nanoparticles. PHYSICAL REVIEW LETTERS 2011; 106:045702. [PMID: 21405335 DOI: 10.1103/physrevlett.106.045702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Indexed: 05/30/2023]
Abstract
Elastic sheets with macroscopic dimensions are easy to deform by bending and stretching. Yet shaping nanometric sheets by mechanical manipulation is hard. Here we show that nanoparticle self-assembly could be used to this end. We demonstrate that spherical nanoparticles adhering to the outer surface of an elastic nanotube can self-assemble into linear structures: rings or helices on stretchable nanotubes, and axial strings on nanotubes with high rigidity to stretching. These self-assembled structures are inextricably linked to a variety of deformed nanotube profiles, which can be controlled by tuning the concentration of nanoparticles, the nanoparticle-nanotube diameter ratio and the elastic properties of the nanotube. Our results open the possibility of designing nanoparticle-laden tubular nanostructures with tailored shapes, for potential applications in materials science and nanomedicine.
Collapse
Affiliation(s)
- Josep C Pàmies
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | |
Collapse
|
43
|
Ratcliffe EC, Tunnicliffe RB, Ng IW, Adams PG, Qian P, Holden-Dye K, Jones MR, Williamson MP, Hunter CN. Experimental evidence that the membrane-spanning helix of PufX adopts a bent conformation that facilitates dimerisation of the Rhodobacter sphaeroides RC-LH1 complex through N-terminal interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:95-107. [PMID: 20937243 DOI: 10.1016/j.bbabio.2010.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 10/19/2022]
Abstract
The PufX polypeptide is an integral component of some photosynthetic bacterial reaction center-light harvesting 1 (RC-LH1) core complexes. Many aspects of the structure of PufX are unresolved, including the conformation of its long membrane-spanning helix and whether C-terminal processing occurs. In the present report, NMR data recorded on the Rhodobacter sphaeroides PufX in a detergent micelle confirmed previous conclusions derived from equivalent data obtained in organic solvent, that the α-helix of PufX adopts a bent conformation that would allow the entire helix to reside in the membrane interior or at its surface. In support of this, it was found through the use of site-directed mutagenesis that increasing the size of a conserved glycine on the inside of the bend in the helix was not tolerated. Possible consequences of this bent helical structure were explored using a series of N-terminal deletions. The N-terminal sequence ADKTIFNDHLN on the cytoplasmic face of the membrane was found to be critical for the formation of dimers of the RC-LH1 complex. It was further shown that the C-terminus of PufX is processed at an early stage in the development of the photosynthetic membrane. A model in which two bent PufX polypeptides stabilise a dimeric RC-LH1 complex is presented, and it is proposed that the N-terminus of PufX from one half of the dimer engages in electrostatic interactions with charged residues on the cytoplasmic surface of the LH1α and β polypeptides on the other half of the dimer.
Collapse
Affiliation(s)
- Emma C Ratcliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Agrawal NJ, Nukpezah J, Radhakrishnan R. Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis. PLoS Comput Biol 2010. [PMID: 20838575 DOI: 10.1371/journal.pcbi.1000926.s008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an important regulatory process required for many essential cellular functions. The role of cooperative protein-protein and protein-membrane interactions in the ubiquitous endocytic pathway in mammalian cells, namely the clathrin-dependent endocytosis, remains unresolved. We employ the Helfrich membrane Hamiltonian together with surface evolution methodology to address how the shapes and energetics of vesicular-bud formation in a planar membrane are stabilized by presence of the clathrin-coat assembly. Our results identify a unique dual role for the tubulating protein epsin: multiple epsins localized spatially and orientationally collectively play the role of a curvature inducing capsid; in addition, epsin serves the role of an adapter in binding the clathrin coat to the membrane. Our results also suggest an important role for the clathrin lattice, namely in the spatial- and orientational-templating of epsins. We suggest that there exists a critical size of the coat above which a vesicular bud with a constricted neck resembling a mature vesicle is stabilized. Based on the observed strong dependence of the vesicle diameter on the bending rigidity, we suggest that the variability in bending stiffness due to variations in membrane composition with cell type can explain the experimentally observed variability on the size of clathrin-coated vesicles, which typically range 50-100 nm. Our model also provides estimates for the number of epsins involved in stabilizing a coated vesicle, and without any direct fitting reproduces the experimentally observed shapes of vesicular intermediates as well as their probability distributions quantitatively, in wildtype as well as CLAP IgG injected neuronal cell experiments. We have presented a minimal mesoscale model which quantitatively explains several experimental observations on the process of vesicle nucleation induced by the clathrin-coated assembly prior to vesicle scission in clathrin dependent endocytosis.
Collapse
Affiliation(s)
- Neeraj J Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | | |
Collapse
|
45
|
Agrawal NJ, Nukpezah J, Radhakrishnan R. Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis. PLoS Comput Biol 2010; 6:e1000926. [PMID: 20838575 PMCID: PMC2936510 DOI: 10.1371/journal.pcbi.1000926] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 08/09/2010] [Indexed: 11/21/2022] Open
Abstract
In eukaryotic cells, the internalization of extracellular cargo via the endocytic machinery is an important regulatory process required for many essential cellular functions. The role of cooperative protein-protein and protein-membrane interactions in the ubiquitous endocytic pathway in mammalian cells, namely the clathrin-dependent endocytosis, remains unresolved. We employ the Helfrich membrane Hamiltonian together with surface evolution methodology to address how the shapes and energetics of vesicular-bud formation in a planar membrane are stabilized by presence of the clathrin-coat assembly. Our results identify a unique dual role for the tubulating protein epsin: multiple epsins localized spatially and orientationally collectively play the role of a curvature inducing capsid; in addition, epsin serves the role of an adapter in binding the clathrin coat to the membrane. Our results also suggest an important role for the clathrin lattice, namely in the spatial- and orientational-templating of epsins. We suggest that there exists a critical size of the coat above which a vesicular bud with a constricted neck resembling a mature vesicle is stabilized. Based on the observed strong dependence of the vesicle diameter on the bending rigidity, we suggest that the variability in bending stiffness due to variations in membrane composition with cell type can explain the experimentally observed variability on the size of clathrin-coated vesicles, which typically range 50-100 nm. Our model also provides estimates for the number of epsins involved in stabilizing a coated vesicle, and without any direct fitting reproduces the experimentally observed shapes of vesicular intermediates as well as their probability distributions quantitatively, in wildtype as well as CLAP IgG injected neuronal cell experiments. We have presented a minimal mesoscale model which quantitatively explains several experimental observations on the process of vesicle nucleation induced by the clathrin-coated assembly prior to vesicle scission in clathrin dependent endocytosis.
Collapse
Affiliation(s)
- Neeraj J. Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jonathan Nukpezah
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
46
|
Hsin J, Strümpfer J, Sener M, Qian P, Hunter CN, Schulten K. Energy Transfer Dynamics in an RC-LH1-PufX Tubular Photosynthetic Membrane. NEW JOURNAL OF PHYSICS 2010; 12:085005. [PMID: 21152381 PMCID: PMC2997751 DOI: 10.1088/1367-2630/12/8/085005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Light absorption and the subsequent transfer of excitation energy are the first two steps of the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of light-harvesting complexes II, the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet computationally costly, treat the coupling between BChls and their protein environment. A widely employed description, generalized Förster theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rhodobacter sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced in the BChl organization. It is shown that the energy transfer dynamics is not affected by the considered changes in the BChl organization, and that generalized Förster theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.
Collapse
Affiliation(s)
- Jen Hsin
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strümpfer
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Melih Sener
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| |
Collapse
|
47
|
Şener M, Strümpfer J, Timney JA, Freiberg A, Hunter CN, Schulten K. Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Biophys J 2010; 99:67-75. [PMID: 20655834 PMCID: PMC2895385 DOI: 10.1016/j.bpj.2010.04.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 11/24/2022] Open
Abstract
Photosynthetic chromatophore vesicles found in some purple bacteria constitute one of the simplest light-harvesting systems in nature. The overall architecture of chromatophore vesicles and the structural integration of vesicle function remain poorly understood despite structural information being available on individual constituent proteins. An all-atom structural model for an entire chromatophore vesicle is presented, which improves upon earlier models by taking into account the stoichiometry of core and antenna complexes determined by the absorption spectrum of intact vesicles in Rhodobacter sphaeroides, as well as the well-established curvature-inducing properties of the dimeric core complex. The absorption spectrum of low-light-adapted vesicles is shown to correspond to a light-harvesting-complex 2 to reaction center ratio of 3:1. A structural model for a vesicle consistent with this stoichiometry is developed and used in the computation of excitonic properties. Considered also is the packing density of antenna and core complexes that is high enough for efficient energy transfer and low enough for quinone diffusion from reaction centers to cytochrome bc(1) complexes.
Collapse
Affiliation(s)
- Melih Şener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Johan Strümpfer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John A. Timney
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| |
Collapse
|
48
|
Hsin J, Chandler DE, Gumbart J, Harrison CB, Şener M, Strumpfer J, Schulten K. Self-assembly of photosynthetic membranes. Chemphyschem 2010; 11:1154-9. [PMID: 20183845 PMCID: PMC3086839 DOI: 10.1002/cphc.200900911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Indexed: 11/08/2022]
Abstract
Bacterial photosynthetic membranes, also known as chromatophores, are tightly packed with integral membrane proteins that work together to carry out photosynthesis. Chromatophores display a wide range of cellular morphologies; spherical, tubular, and lamellar chromatophores have all been observed in different bacterial species, or with different protein constituents. Through recent computational modeling and simulation, it has been demonstrated that the light-harvesting complexes abundant in chromatophores induce local membrane curvature via multiple mechanisms. These protein complexes assemble to generate a global curvature and sculpt the chromatophores into various cellular-scale architectures.
Collapse
Affiliation(s)
- Jen Hsin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Danielle E. Chandler
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - James Gumbart
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | | | - Melih Şener
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Johan Strumpfer
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| |
Collapse
|
49
|
Tucker JD, Siebert CA, Escalante M, Adams PG, Olsen JD, Otto C, Stokes DL, Hunter CN. Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles. Mol Microbiol 2010; 76:833-47. [PMID: 20444085 DOI: 10.1111/j.1365-2958.2010.07153.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The purple phototrophic bacteria synthesize an extensive system of intracytoplasmic membranes (ICM) in order to increase the surface area for absorbing and utilizing solar energy. Rhodobacter sphaeroides cells contain curved membrane invaginations. In order to study the biogenesis of ICM in this bacterium mature (ICM) and precursor (upper pigmented band - UPB) membranes were purified and compared at the single membrane level using electron, atomic force and fluorescence microscopy, revealing fundamental differences in their morphology, protein organization and function. Cryo-electron tomography demonstrates the complexity of the ICM of Rba. sphaeroides. Some ICM vesicles have no connection with other structures, others are found nearer to the cytoplasmic membrane (CM), often forming interconnected structures that retain a connection to the CM, and possibly having access to the periplasmic space. Near-spherical single invaginations are also observed, still attached to the CM by a 'neck'. Small indents of the CM are also seen, which are proposed to give rise to the UPB precursor membranes upon cell disruption. 'Free-living' ICM vesicles, which possess all the machinery for converting light energy into ATP, can be regarded as bacterial membrane organelles.
Collapse
Affiliation(s)
- Jaimey D Tucker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, UK
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Magis GJ, den Hollander MJ, Onderwaater WG, Olsen JD, Hunter CN, Aartsma TJ, Frese RN. Light harvesting, energy transfer and electron cycling of a native photosynthetic membrane adsorbed onto a gold surface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:637-45. [DOI: 10.1016/j.bbamem.2009.12.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 11/26/2022]
|