Deformation of Chlorin Rings in the Photosystem II Crystal Structure

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center

Using the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center from Blastochloris viridis that show light-induced time-dependent structural changes (Dods et al., (2021) Nature 589, 310-314), we investigated time-dependent changes in the energetics of the electron-transfer pathway, considering the entire protein environment of the protein structures and titrating the redox-active sites in the presence of all fully equilibrated titratable residues. In the dark and charge separation intermediate structures, the calculated redox potential (Em) values for the accessory bacteriochlorophyll and bacteriopheophytin in the electron-transfer-active branch (BL and HL) are higher than those in the electron-transfer-inactive branch (BM and HM). However, the stabilization of the charge-separated [PLPM]•+HL•- state owing to protein reorganization is not clearly observed in the Em(HL) values in the charge-separated 5 ps ([PLPM]•+HL•- state) structure. Furthermore, the expected chlorin ring deformation upon formation of HL•- (saddling mode) is absent in the HL geometry of the original 5 ps structure. These findings suggest that there is no clear link between the time-dependent structural changes and the electron-transfer events in the XFEL structures.

Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP

Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems.

The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.

Ultrafast structural changes within a photosynthetic reaction centre

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography¹ using an X-ray free-electron laser² to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

Acquirement of water-splitting ability and alteration of the charge-separation mechanism in photosynthetic reaction centers

In photosynthetic reaction centers from purple bacteria (PbRC) and the water-oxidizing enzyme, photosystem II (PSII), charge separation occurs along one of the two symmetrical electron-transfer branches. Here we report the microscopic origin of the unidirectional charge separation, fully considering electron-hole interaction, electronic coupling of the pigments, and electrostatic interaction with the polarizable entire protein environments. The electronic coupling between the pair of bacteriochlorophylls is large in PbRC, forming a delocalized excited state with the lowest excitation energy (i.e., the special pair). The charge-separated state in the active branch is stabilized by uncharged polar residues in the transmembrane region and charged residues on the cytochrome c ₂ binding surface. In contrast, the accessory chlorophyll in the D1 protein (Chl_D1) has the lowest excitation energy in PSII. The charge-separated state involves Chl_D1 ^•+ and is stabilized predominantly by charged residues near the Mn₄CaO₅ cluster and the proceeding proton-transfer pathway. It seems likely that the acquirement of water-splitting ability makes Chl_D1 the initial electron donor in PSII.

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I

Excited-state properties of α- and β-ligated chlorophyll dimers of photosystem I were studied at ab initio correlated levels of theory.

Geometric deconstruction of core and electron activation of a π-system in a series of deformed porphyrins: mimics of heme

The predominant distortion of heme is responsible for its electronic activity, catalytic ability and spectral properties. In this work, altogether 12 new X-ray structures of saddled, waved and ruffled porphyrins are reported. Three types of deformed porphyrins as mimics of heme were evaluated and analyzed by geometric deconstruction, spectral comparison, and electrochemical tracking, which shows a unique relationship of deformation fashions and distortion degree to the geometry of the core and electron transfer ability of rings in these enzyme containing porphyrins. These mimics can adjust their core geometry for changing the structures of potential metals; while for rings themselves, they can also regulate the electron activity by switching the HOMO of the large π systems. These deformed porphyrins can be used as ideal mimics for heme. These findings help us to understand the principle and contribution of these deformations to electron transfer in catalytic oxidation and photoreactions. The nonplanar mimics have been synthesized through a modular synthetic approach under Adler-Longo or Lindsey condensation conditions.

Electron Transfer and Geometric Conversion of Co-NO Moiety in Saddled Porphyrins: Implications for Trigger Role of Tetrapyrrole Distortion

The electrons of NO and Co are strongly delocalized in normal {Co-NO}⁸ species. In this work, {Co-NO}⁸ complexes are induced to convert from (Co^II)^+•-NO^• to Co^III-NO^- by a core contraction of 0.06 Å in saddled cobalt(II) porphyrins. This intramolecular electron transfer mechanism indicates that nonplanarity of porphyrin is involved in driving conversion of the NO units from electrophilic NO^• as a bent geometry to nucleophilic NO^- as a linear geometry. This implies that distortion acts as a trigger in enzymes containing tetrapyrrole. The electronic behaviors of the Co^II ions and Co-NO moieties were confirmed by X-ray crystallography, EPR spectroscopy, theoretical calculation, UV-vis and IR spectroscopy, and electrochemistry.

Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models

Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.

Fine Tuning of Chlorophyll Spectra by Protein-Induced Ring Deformation

The ability to tune the light-absorption properties of chlorophylls by their protein environment is the key to the robustness and high efficiency of photosynthetic light-harvesting proteins. Unfortunately, the intricacy of the natural complexes makes it very difficult to identify and isolate specific protein-pigment interactions that underlie the spectral-tuning mechanisms. Herein we identify and demonstrate the tuning mechanism of chlorophyll spectra in type II water-soluble chlorophyll binding proteins from Brassicaceae (WSCPs). By comparing the molecular structures of two natural WSCPs we correlate a shift in the chlorophyll red absorption band with deformation of its tetrapyrrole macrocycle that is induced by changing the position of a nearby tryptophan residue. We show by a set of reciprocal point mutations that this change accounts for up to 2/3 of the observed spectral shift between the two natural variants.

Dynamics of the Special Pair of Chlorophylls of Photosystem II

Cholophylls are at the basis of the photosynthetic energy conversion mechanisms in algae, plants, and cyanobacteria. In photosystem II, the photoproduced electrons leave a special pair of chlorophylls (namely, P(D1) and P(D2)) that becomes cationic. This oxidizing pair [P(D1),P(D2)](+), in turn, triggers a cascade of oxidative events, eventually leading to water splitting and oxygen evolution. In the present work, using quantum mechanics/molecular mechanics calculations, we investigate the electronic structure and the dynamics of the P(D1)P(D2) special pair in both its oxidized and reduced states. In agreement with previously reported static calculations, the symmetry between the two chlorophylls was found to be broken, the positive charge being preferentially located on P(D1). Nevertheless, this study reveals for the first time that large charge fluctuations occur along dynamics, temporarily inverting the charge preference for the two branches. Finally, a vibrational analysis pinpointed that such charge fluctuations are strongly coupled to specific modes of the special pair.

A comparison between plant photosystem I and photosystem II architecture and functioning

Oxygenic photosynthesis is indispensable both for the development and maintenance of life on earth by converting light energy into chemical energy and by producing molecular oxygen and consuming carbon dioxide. This latter process has been responsible for reducing the CO2 from its very high levels in the primitive atmosphere to the present low levels and thus reducing global temperatures to levels conducive to the development of life. Photosystem I and photosystem II are the two multi-protein complexes that contain the pigments necessary to harvest photons and use light energy to catalyse the primary photosynthetic endergonic reactions producing high energy compounds. Both photosystems are highly organised membrane supercomplexes composed of a core complex, containing the reaction centre where electron transport is initiated, and of a peripheral antenna system, which is important for light harvesting and photosynthetic activity regulation. If on the one hand both the chemical reactions catalysed by the two photosystems and their detailed structure are different, on the other hand they share many similarities. In this review we discuss and compare various aspects of the organisation, functioning and regulation of plant photosystems by comparing them for similarities and differences as obtained by structural, biochemical and spectroscopic investigations.