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.

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

“…Again taking into account the amount and time spent in the cavity, we estimate a lower bound of the reorientation time scale of 200 μs. The lower flip-flop rate of PLQol compared to PLQ is in line with the lower flip-flop rate for PLQol versus PLQ in bulk membranes (at least one order difference1721), and can be attributed to the more polar nature of the reduced cofactor.…”

“…Reorientation is possible in the membrane environment as well. The indicated time scales of the individual steps are estimates based on the current work (channel entrance t in and exit t out times, reorientation time t reor inside the exchange cavity, and binding/unbinding time scales t bind , t unb to Q B site), on previous simulations1721 (flip-flop time t flip inside the bulk thylakoid membrane), or on existing experimental data2627 (time scale t red of PLQ reduction to PLQol). Note that the reduction step in reality takes place within the same Q B site.…”

Molecular dynamics simulations in photosynthesis

“…The mobility of BCR in the membrane is as high as the one of lipids (see above), and it was computed to be between ~ 30 and ~ 50 μm 2 /s, depending both on the atomistic force field used (respectively, GROMOS (de Jong et al 2015) and OPLS (Jemioła-Rzemińska et al 2005) FF) and the lipid types present in the membrane (DPPC (de Jong et al 2015) vs POPC (Jemioła-Rzemińska et al 2005)). As expected, the diffusion rates at CG resolution resulted to be about four times higher than the ones with atomistic force fields (de Jong et al 2015). To the best of our knowledge, no experimental data are currently available on the diffusion coefficient of BCR in membranes.…”

“…In the case of the Amber force field for Cars (Prandi et al 2016), this set of parameters has been specifically validated to reproduce selected spectral properties. The UA FF available for the pigments, cofactors, and lipids associated to photosystem II (PSII) and the LHCs (López et al 2013;van Eerden et al 2015;de Jong et al 2015;Liguori et al 2015) have been developed based on the building blocks of GROMOS. Respecting the guiding rules of this FF (Oostenbrink et al 2004(Oostenbrink et al , 2005Schmid et al 2011), they have been validated against experimental data.…”

Effects of lipid composition on membrane distribution and permeability of natural quinones

“…38 The distribution of natural quinones in membranes with mixed lipid composition was also investigated with more approximate coarse-grained simulations. 39,40 Here, we employ MD simulations with an all-atom force-eld carefully calibrated for Q molecules 26 to investigate the effects of lipid composition and unsaturation of acyl chains on Q distribution and permeation using a multi-component bilayer mimicking membranes involved in bioenergetic processes. Ubiquinone, ubiquinol, menaquinone and plastoquinone ( Fig.…”