The effects of light-induced reduction of the photosystem II reaction center

Abstract

Accumulation of reduced pheophytin a (Pheo-D1) in photosystem II reaction center (PSII RC) under illumination at low redox potential is accompanied by changes in absorbance and circular dichroism spectra. The temperature dependences of these spectral changes have the potential to distinguish between changes caused by the excitonic interaction and temperature-dependent processes. We observed a conformational change in the PSII RC protein part and changes in the spatial positions of the PSII RC pigments of the active D1 branch upon reduction of Pheo-D1 only in the case of high temperature (298 K) dynamics. The resulting absorption difference spectra of PSII RC models equilibrated at temperatures of 77 K and 298 K were highly consistent with our previous experiments in which light-induced bleaching of the PSII RC absorbance spectrum was observable only at 298 K. These results support our previous hypothesis that Pheo-D1 does not interact excitonically with the other chlorins of the PSII RC, since the reduced form of Pheo-D1 causes absorption spectra bleaching only due to temperature-dependent processes.

Folding of Polyalanine into Helical Hairpins

“…Very complex model of such protein assembly that functions in photosynthesis was lately studied by MD simulation. [22] The helix-turn-helix structural motif is also of a much importance in structural biology for binding of protein to DNA through the major groove of DNA.…”

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

“…In general, one would like to question whether the static crystal structure alone—without considering the protein ensemble under physiological conditions—would suffice to discern between the active and inactive chains in terms of the electron transfer processes. Previous theoretical studies4445 involving molecular dynamics (MD) simulations (based on low-resolution crystal structures of PSII) have investigated the influence of protein dynamics on energy transfer within PSII. However, none of them addressed the pathway selection for either the energy or electron transfer processes.…”

Force field development for cofactors in the photosystem II

“…[6, 14] However, these structures are only static snapshots, whereas protein dynamics may play important roles in the electron transfer process. [10, 15, 16, 17] Therefore, molecular dynamics (MD) simulations that can model the dynamics at atomic resolution may complement experiments and provide useful dynamic information. Indeed, MD simulations have been shown to be a powerful tool to study the absorption spectrum and the electron transfer processes in the PSII core chromophores.…”

“…Indeed, MD simulations have been shown to be a powerful tool to study the absorption spectrum and the electron transfer processes in the PSII core chromophores. [16, 17] To perform MD simulations, force field (FF) parameters for both the PSII proteins and cofactors are necessary. Many commonly used FFs such as AMBER,[18, 19] CHARMM,[20, 21] GROMOS,[22] and OPLS[23] have been developed to simulate proteins.…”

“…[24–29] Recently, a couple of research groups have put together FF parameters for all the cofactors in PSII and simulated the whole complex. [16, 17, 30] For example, Vasil'ev et al [16] parameterized the FF for BCR, and took the parameters for other cofactors either from the existing atom types in AMBER94 FF[18] or from those of the bacterial cofactors[25] without further validation. Palencar et al [27, 28] developed FF parameters compatible with CHARMM for three PSII cofactors (CLA, PL9, and PHO) based on the bacterial FF.…”