Structural basis for the assembly and electron transport mechanisms of the dimeric photosynthetic RC–LH1 supercomplex

[1]  M. Madigan,et al.  A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex , 2021, Nature Communications.

[2]  C. Hunter,et al.  Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation , 2021, The Biochemical journal.

[3]  C. Hunter,et al.  Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC–LH1 core complex at 2.5 Å , 2021, The Biochemical journal.

[4]  N. Moriarty,et al.  Cryo-EM structure of the Rhodospirillum rubrum RC–LH1 complex at 2.5 Å , 2021, The Biochemical journal.

[5]  M. Madigan,et al.  Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum. , 2021, Biochemistry.

[6]  M. Shirouzu,et al.  Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution , 2021, Science Advances.

[7]  N. Ranson,et al.  Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels , 2021, Science Advances.

[8]  M. Madigan,et al.  Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides , 2020, Nature Communications.

[9]  Conrad C. Huang,et al.  UCSF ChimeraX: Structure visualization for researchers, educators, and developers , 2020, Protein science : a publication of the Protein Society.

[10]  C. Mullineaux,et al.  Membrane Dynamics in Phototrophic Bacteria. , 2020, Annual review of microbiology.

[11]  R. Cogdell,et al.  A comparative look at structural variation among RC–LH1 ‘Core’ complexes present in anoxygenic phototrophic bacteria , 2020, Photosynthesis Research.

[12]  Lu-Ning Liu,et al.  Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center , 2020, Biochimica et biophysica acta. Bioenergetics.

[13]  Miguel Teixeira Faculty Opinions recommendation of Atoms to phenotypes: molecular design principles of cellular energy metabolism. , 2019 .

[14]  Paul Emsley,et al.  Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data , 2019, Protein science : a publication of the Protein Society.

[15]  K. Schulten,et al.  Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism , 2019, Cell.

[16]  Jasenko Zivanov,et al.  Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1 , 2019, bioRxiv.

[17]  Christopher J. Williams,et al.  Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix , 2019, Acta crystallographica. Section D, Structural biology.

[18]  Xinzheng Zhang,et al.  High-quality, high-throughput cryo-electron microscopy data collection via beam tilt and astigmatism-free beam-image shift. , 2019, Journal of structural biology.

[19]  Thorsten Wagner,et al.  SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM , 2019, Communications Biology.

[20]  Erik Lindahl,et al.  New tools for automated high-resolution cryo-EM structure determination in RELION-3 , 2018, eLife.

[21]  Robert Eugene Blankenship,et al.  Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote , 2018, Nature Communications.

[22]  C. A. Siebert,et al.  Cryo-EM structure of the Blastochloris viridis LH1–RC complex at 2.9 Å , 2018, Nature.

[23]  Jian-Ren Shen,et al.  Structure of photosynthetic LH1–RC supercomplex at 1.9 Å resolution , 2018, Nature.

[24]  Pu Qian,et al.  Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex , 2018, Biochimica et biophysica acta. Bioenergetics.

[25]  C. Hunter,et al.  The C-terminus of PufX plays a key role in dimerisation and assembly of the reaction center light-harvesting 1 complex from Rhodobacter sphaeroides , 2017, Biochimica et biophysica acta. Bioenergetics.

[26]  D. Agard,et al.  MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy , 2017, Nature Methods.

[27]  J. Olsen,et al.  The PufX quinone channel enables the light‐harvesting 1 antenna to bind more carotenoids for light collection and photoprotection , 2017, FEBS letters.

[28]  C. Hunter,et al.  Dimerization of core complexes as an efficient strategy for energy trapping in Rhodobacter sphaeroides. , 2016, Biochimica et biophysica acta.

[29]  Alexander D. MacKerell,et al.  CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field , 2015, Journal of chemical theory and computation.

[30]  N. Grigorieff,et al.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs , 2015, bioRxiv.

[31]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[32]  S. Marrink,et al.  Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. , 2015, The journal of physical chemistry. B.

[33]  Helgi I. Ingólfsson,et al.  Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. , 2015, Journal of chemical theory and computation.

[34]  Sunhwan Jo,et al.  CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations , 2014, J. Comput. Chem..

[35]  Peter G. Adams,et al.  Aberrant Assembly Complexes of the Reaction Center Light-harvesting 1 PufX (RC-LH1-PufX) Core Complex of Rhodobacter sphaeroides Imaged by Atomic Force Microscopy* , 2014, The Journal of Biological Chemistry.

[36]  Thomas Boudier,et al.  The architecture of Rhodobacter sphaeroides chromatophores. , 2014, Biochimica et biophysica acta.

[37]  K. Miki,et al.  Structure of the LH1–RC complex from Thermochromatium tepidum at 3.0 Å , 2014, Nature.

[38]  P. Bullough,et al.  Three-dimensional structure of the Rhodobacter sphaeroides RC-LH1-PufX complex: dimerization and quinone channels promoted by PufX. , 2013, Biochemistry.

[39]  Simon Scheuring,et al.  Investigation of photosynthetic membrane structure using atomic force microscopy. , 2013, Trends in plant science.

[40]  J. Chauvin,et al.  Structure of the dimeric RC–LH1–PufX complex from Rhodobaca bogoriensis investigated by electron microscopy , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[41]  Alexander D. MacKerell,et al.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. , 2012, Journal of chemical theory and computation.

[42]  Michael R. Jones,et al.  Cross-species investigation of the functions of the Rhodobacter PufX polypeptide and the composition of the RC-LH1 core complex. , 2012, Biochimica et biophysica acta.

[43]  Hyeon Joo,et al.  OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..

[44]  Peter G. Adams,et al.  Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides. , 2011, Biochimica et biophysica acta.

[45]  S. Scheuring,et al.  Forces guiding assembly of light-harvesting complex 2 in native membranes , 2011, Proceedings of the National Academy of Sciences.

[46]  Alexander D. MacKerell,et al.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.

[47]  A. Maliniak,et al.  Mechanical Properties of Coarse-Grained Bilayers Formed by Cardiolipin and Zwitterionic Lipids. , 2010, Journal of chemical theory and computation.

[48]  Xavier Periole,et al.  Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. , 2009, Journal of chemical theory and computation.

[49]  Alexander D. MacKerell,et al.  CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..

[50]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[51]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[52]  F. Gubellini,et al.  Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes. , 2007, Structure.

[53]  Yuan Zhao,et al.  Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge , 2007, J. Chem. Inf. Model..

[54]  Juergen Koepke,et al.  pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. , 2007, Journal of molecular biology.

[55]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[56]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[57]  F. Gubellini,et al.  Functional and structural analysis of the photosynthetic apparatus of Rhodobacter veldkampii. , 2006, Biochemistry.

[58]  Pu Qian,et al.  The 8.5A projection structure of the core RC-LH1-PufX dimer of Rhodobacter sphaeroides. , 2005, Journal of molecular biology.

[59]  Simon Scheuring,et al.  Structure of the Dimeric PufX-containing Core Complex of Rhodobacter blasticus by in Situ Atomic Force Microscopy* , 2005, Journal of Biological Chemistry.

[60]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[61]  Cees Otto,et al.  The native architecture of a photosynthetic membrane , 2004, Nature.

[62]  A. Engel,et al.  Molecular architecture of photosynthetic membranes in Rhodobacter sphaeroides: the role of PufX , 2004, The EMBO journal.

[63]  S. Scheuring,et al.  Structural Role of PufX in the Dimerization of the Photosynthetic Core Complex of Rhodobacter sphaeroides* , 2004, Journal of Biological Chemistry.

[64]  N. Isaacs,et al.  Crystal Structure of the RC-LH1 Core Complex from Rhodopseudomonas palustris , 2003, Science.

[65]  H. Zischka,et al.  Role of the N- and C-terminal regions of the PufX protein in the structural organization of the photosynthetic core complex of Rhodobacter sphaeroides. , 2002, European journal of biochemistry.

[66]  D. Engelman,et al.  The GxxxG motif: a framework for transmembrane helix-helix association. , 2000, Journal of molecular biology.

[67]  A. Verméglio,et al.  Supramolecular organization of the photosynthetic apparatus of Rhodobacter sphaeroides , 1999, The EMBO journal.

[68]  T. Walz,et al.  Projection structures of three photosynthetic complexes from Rhodobacter sphaeroides: LH2 at 6 A, LH1 and RC-LH1 at 25 A. , 1998, Journal of molecular biology.

[69]  P. McGlynn,et al.  The LH1-RC core complex of Rhodobacter sphaeroides: interaction between components, time-dependent assembly, and topology of the PufX protein. , 1998, Biochimica et biophysica acta.

[70]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[71]  D. Oesterhelt,et al.  Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex. , 1995, Biochemistry.

[72]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[73]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[74]  P. McGlynn,et al.  The Rhodobacter sphaeroides PufX protein is not required for photosynthetic competence in the absence of a light harvesting system , 1994, FEBS letters.

[75]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[76]  D. Oesterhelt,et al.  Studies on the expression of the pufX polypeptide and its requirement for photoheterotrophic growth in Rhodobacter sphaeroides. , 1992, The EMBO journal.

[77]  T. Lilburn,et al.  Pleiotropic effects of pufX gene deletion on the structure and function of the photosynthetic apparatus of Rhodobacter capsulatus. , 1992, Biochimica et biophysica acta.

[78]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[79]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[80]  S. Nosé A molecular dynamics method for simulations in the canonical ensemble , 1984 .

[81]  S. Nosé,et al.  Constant pressure molecular dynamics for molecular systems , 1983 .

[82]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[83]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[84]  Lu-Ning Liu,et al.  Composition, Organisation and Function of Purple Photosynthetic Machinery , 2020 .

[85]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[86]  É. Bonnet,et al.  Designing RNA Secondary Structures Is Hard , 2017, RECOMB.

[87]  M. Williamson,et al.  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. , 2011, Biochimica et biophysica acta.

[88]  Berk Hess,et al.  P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.

[89]  T. Carpenter Energy metabolism. , 1946, Annual Review of Physiology.