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Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

de Jong, D. H., Liguori, N., van den Berg, T., Arnarez, C., Periole, X. & Marrink, S. J., 25-Jun-2015, In : The Journal of Physical Chemistry B. 119, 25, p. 7791-7803 13 p.

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  • Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

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DOI

  • Djurre H. de Jong
  • Nicoletta Liguori
  • Tom van den Berg
  • Clement Arnarez
  • Xavier Periole
  • Siewert J. Marrink

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.

Original languageEnglish
Pages (from-to)7791-7803
Number of pages13
JournalThe Journal of Physical Chemistry B
Volume119
Issue number25
Publication statusPublished - 25-Jun-2015

    Keywords

  • MOLECULAR-DYNAMICS SIMULATIONS, CYTOCHROME BC(1) COMPLEX, FORCE-FIELD DEVELOPMENT, ATOM-ADDITIVE METHOD, CRYSTAL-STRUCTURE, BIOMOLECULAR SIMULATIONS, PARTITION-COEFFICIENTS, LIGAND COMPLEXES, PROTON-TRANSFER, MEMBRANE

ID: 22983113