Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex
| Autor: | Xavier Periole, Tomas E. van den Berg, Clement Arnarez, Djurre H. de Jong, Nicoletta Liguori, Siewert J. Marrink |
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| Přispěvatelé: | Biophysics Photosynthesis/Energy, LaserLaB - Energy, Molecular Dynamics |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Pheophytin
Chlorophyll Octanols MOLECULAR-DYNAMICS SIMULATIONS Photosystem II Plastoquinone Protein Conformation Ubiquinone Lipid Bilayers Respiratory chain Heme Molecular Dynamics Simulation chemistry.chemical_compound Molecular dynamics BIOMOLECULAR SIMULATIONS PROTON-TRANSFER Materials Chemistry CRYSTAL-STRUCTURE Physical and Theoretical Chemistry Molecular Structure Chemistry CYTOCHROME BC(1) COMPLEX Chlorophyll A Pheophytins Photosystem II Protein Complex Water beta Carotene Electron transport chain Surfaces Coatings and Films Chloroplast FORCE-FIELD DEVELOPMENT Crystallography PARTITION-COEFFICIENTS Thylakoid Biophysics LIGAND COMPLEXES Thermodynamics MEMBRANE ATOM-ADDITIVE METHOD |
| Zdroj: | Journal of Physical Chemistry B, 119(25), 7791-7803. American Chemical Society de Jong, D H, Liguori, N, van den Berg, T E, Arnarez, C, Periole, X & Marrink, S J 2015, ' Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex ', Journal of Physical Chemistry B, vol. 119, no. 25, pp. 7791-7803 . https://doi.org/10.1021/acs.jpcb.5b00809 The Journal of Physical Chemistry B, 119(25), 7791-7803. AMER CHEMICAL SOC |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.5b00809 |
| Popis: | Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular Mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and beta-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin. |
| Databáze: | OpenAIRE |
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