title: Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.
abstract: 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 β-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.
authors.forename: Djurre H
authors.initials: DH
authors.lastname: de Jong
authors.affiliation: ‡Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Liguori
authors.forename: Tom
authors.initials: T
authors.lastname: van den Berg
authors.forename: Clement
authors.initials: C
authors.lastname: Arnarez
authors.forename: Xavier
authors.initials: X
authors.lastname: Periole
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink
mesh_terms: D002734:Chlorophyll / Q000378:metabolism; D000077194:Chlorophyll A; D006418:Heme / Q000378:metabolism; D008051:Lipid Bilayers / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D000442:Octanols / Q000737:chemistry; D010674:Pheophytins / Q000378:metabolism; D045332:Photosystem II Protein Complex / Q000378:metabolism*; D010971:Plastoquinone / Q000031:analogs & derivatives / Q000378:metabolism; D011487:Protein Conformation; D013816:Thermodynamics; D014451:Ubiquinone / Q000031:analogs & derivatives / Q000378:metabolism; D014867:Water / Q000737:chemistry; D019207:beta Carotene / Q000378:metabolism
chemical_list: D008051:Lipid Bilayers; D000442:Octanols; D010674:Pheophytins; D045332:Photosystem II Protein Complex; D019207:beta Carotene; D014867:Water; D014451:Ubiquinone; D002734:Chlorophyll; C003165:plastoquinol; D006418:Heme; C003741:ubiquinol; D010971:Plastoquinone; D000077194:Chlorophyll A