Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II

Mechanism of Oxygen Evolution and Mn4CaO5 Cluster Restoration in the Natural Water-Oxidizing Catalyst

Water oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn₄Ca cluster located in the core of Photosystem II and proceeds along the five steps (S₀-S₄) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn₄Ca cluster in the S₀ state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S₀ state.

Chlorophyll excitation energies and structural stability of the CP47 antenna of photosystem II: a case study in the first-principles simulation of light-harvesting complexes

Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment-protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment-protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of "near-native" cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and β-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.

Molecular dynamics simulations in photosynthesis

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.

Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II

TyrZ oxidation state triggers hydrogen bond modification in the water oxidation catalysis.

trans-A2B-corrole bearing 2,3-di(2-pyridyl)quinoxaline (DPQ)/phenothiazine moieties: synthesis, characterization, electrochemistry and photophysics

Singlet–singlet energy transfer and electron transfer processes in corrole–phenothiazine and corrole–DPQ dyads were demonstrated by using electrochemical and fluorescence (steady-state and time-resolved) spectral studies.

SIBPA under the Tuscan sun: Introduction to the SIBPA XXIII Special Issue

The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIII National Congress in the gorgeous Tuscan town of Cortona, Italy, on September 18-21, 2016. This special issue features a selection of contributions from the Congress in the areas of molecular, applied, cellular and computational biophysics. Cutting-edge developments in nanoscale biophysics were introduced for the first time in the program. SIBPA continues its successful promotion of biophysical disciplines at the national and international levels, with added strength from its partnership with Biophysical Chemistry and Elsevier.