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

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.