Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 Å resolution

Flavodiiron proteins associate pH-dependently with the thylakoid membrane for ferredoxin-1-powered O2 photoreduction

Flavodiiron proteins (FDPs) catalyse light-dependent reduction of oxygen to water in photosynthetic organisms, creating an electron sink on the acceptor side of Photosystem I that protects the photosynthetic apparatus. However, ambiguity about the electron donor(s) remains, and the molecular mechanisms regulating FDP activity have remained elusive. We employed spectroscopic and gas flux analysis of photosynthetic electron transport, bimolecular fluorescence complementation assays for in vivo protein-protein interactions in the model cyanobacterium Synechocystis sp. PCC 6803, and in silico surface charge modelling. We demonstrated that ferredoxin-1 interacts with Flv1, Flv2, and Flv3, and is the main electron donor to FDP heterooligomers, which are responsible for the photoreduction of oxygen. Moreover, we revealed that FDP heterooligomers dissociate from the thylakoid membrane upon alkalisation of the cytosol, providing the first in vivo evidence of a self-regulatory feedback mechanism allowing dynamic control of FDP activity and maintenance of photosynthetic redox balance in fluctuating environments. Our findings have direct implications for rationally directing electron flux towards desired reactions in biotechnological applications.

Enhanced photocurrent generation of a bio-photocathode based on photosystem I integrated in solvated redox polymers films nanostructured by SWCNTs

The most energetic light-induced charge-separation step in nature is driven by photosystem I (PSI), making this photosynthetic protein an attractive candidate for the development of semi-artificial energy conversion devices. Despite significant progress in semiconductor-free bio-photocathodes, the highest photocurrent density was only 322 ± 19 μA cm-2, achieved by integrating PSI within a pH-dependent poly(vinyl)imidazole Os(bispyridine)2Cl redox polymer (T Kothe et al., Chem. Eur. J., 2014, 20, 11029). This study presents a more efficient PSI-based bio-photocathode by incorporating single-walled carbon nanotubes (SWCNTs) into the redox hydrogel composed of the same Osmium-containing redox polymer. The nanostructured redox hydrogel film with SWCNTs serving as electric scaffolds significantly improves the stability, loading amount, and heterogeneous electron transfer rate, resulting in a substantial increase in photocurrent density exceeding 2 mA cm-2, the highest achieved in a semiconductor-free PSI based photocathode to date. Bioelectrodes constructed by pre-depositing SWCNTs on the electrode surface via covalent bonds outperform those formed by co-immobilizing SWCNTs with the redox hydrogel. The dependence of photocurrent on light intensity and the photocurrent spectrum action demonstrate that the photocurrent unequivocally arises from PSI charge separation. This research lays a promising foundation for the development of semi-artificial photoelectrochemical devices for light-to-energy conversion.

Distinct Aggregation Behavior of N-Terminally Truncated Aβ4-42 Over Aβ1-42 in the Presence of Zn(II)

The deposition of amyloid-β (Aβ) aggregates and metal ions within senile plaques is a hallmark of Alzheimer's disease (AD). Among the modifications observed in Aβ peptides, N-terminal truncation at Phe4, yielding Aβ4-x, is highly prevalent in AD-affected brains and significantly alters Aβ's metal-binding and aggregation profiles. Despite the abundance of Zn(II) in senile plaques, its impact on the aggregation and toxicity of Aβ4-x remains unexplored. Here, we report the distinct aggregation behavior of N-terminally truncated Aβ, specifically Aβ4-42, in the absence and presence of either Zn(II), Aβ seeds, or both, and compare it to that of full-length Aβ1-42. Our findings reveal notable differences in the aggregation profiles of Aβ4-42 and Aβ1-42, largely influenced by their different Zn(II)-binding properties. These results provide insights into the mechanisms underlying the distinct aggregation behavior of truncated and full-length Aβ in the presence of Zn(II), contributing to a deeper understanding of AD pathology.

Structural Characterization of the Platinum Nanoparticle Hydrogen-Evolving Catalyst Assembled on Photosystem I by Light-Driven Chemistry

Directed assembly of abiotic catalysts onto biological redox protein frameworks is of interest as an approach for the synthesis of biohybrid catalysts that combine features of both synthetic and biological materials. In this report, we provide a multiscale characterization of the platinum nanoparticle (NP) hydrogen-evolving catalysts that are assembled by light-driven reductive precipitation of platinum from an aqueous salt solution onto the photosystem I protein (PSI), isolated from cyanobacteria as trimeric PSI. The resulting PSI-NP assemblies were analyzed using a combination of X-ray energy-dispersive spectroscopy (XEDS), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), small-angle X-ray scattering (SAXS), and high-energy X-ray scattering with atomic pair distribution function (PDF) analyses. The results show that the PSI-supported NPs are approximately 1.8 nm diameter disk-shaped particles that assemble at discrete sites with 145 Å separation. This separation is too large to be consistent with NP nucleation and growth at a site adjacent to the FB cofactor site. Instead, we suggest a mechanism for NP growth at hydrophobic sites on the PSI stromal surface. The NPs photoreductively assembled on the PSI stromal surface are found to be analogous to the nanostructures produced by successive cycles of atomic layer deposition (ALD) of platinum onto 40 nm porous anodic alumina oxide supports, although the mechanisms for nucleation appear to differ. This work establishes a foundation for the investigation of the reductive assembly of abiotic metal catalysts at sites connected to photochemically reducing equivalent production in PSI.

A High-Resolution Crystallographic Study of Cytochrome c6: Structural Basis for Electron Transfer in Cyanobacterial Photosynthesis

Cyanobacterial cytochrome c6 (Cyt c6) is crucial for electron transfer between the cytochrome b6f complex and photosystem I (PSI), playing a key role in photosynthesis and enhancing adaptation to extreme environments. This study investigates the high-resolution crystal structures of Cyt c6 from Synechococcus elongatus PCC 7942 and Synechocystis PCC 6803, focusing on its dimerization mechanisms and functional implications for photosynthesis. Cyt c6 was expressed in Escherichia coli using a dual-plasmid co-expression system and characterized in both oxidized and reduced states. X-ray crystallography revealed three distinct crystal forms, with asymmetric units containing 2, 4, or 12 molecules, all of which consist of repeating dimeric structures. Structural comparisons across species indicated that dimerization predominantly occurs through hydrophobic interactions within a conserved motif around the heme crevice, despite notable variations in dimer positioning. We propose that the dimerization of Cyt c6 enhances structural stability, optimizes electron transfer kinetics, and protects the protein from oxidative damage. Furthermore, we used AlphaFold3 to predict the structure of the PSI-Cyt c6 complex, revealing specific interactions that may facilitate efficient electron transfer. These findings provide new insights into the functional role of Cyt c6 dimerization and its contribution to improving cyanobacterial photosynthetic electron transport.

Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I

BACKGROUND

All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A-1 and A0, which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites?

RESULTS

The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A-1 and A0; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A-1, A0 and A1 as well as their cofactor binding sites; (iv) the tryptophan residues close to A0 and A1 are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods.

CONCLUSIONS

The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.

Modeling Diffusive Motion of Ferredoxin and Plastocyanin on the PSI Domain of Procholorococcus marinus MIT9313

Diffusion of mobile charge carriers, such as ferredoxin and plastocyanin, often constitutes a rate-determining step in photosynthetic energy conversion. The diffusion time scales typically exceed that of other primary bioenergetic processes and remain beyond the reach of direct simulation at the molecular level. We characterize the diffusive kinetics of ferredoxin and plastocyanin upon the photosystem I-rich domain of Prochlorococcus, the most abundant phototroph on Earth by mass. A modeling approach for ferredoxin and plastocyanin diffusion is presented that uses ensembles of coarse-grained molecular dynamics simulations in Martini 2.2P with GROMACS 2021.2. The simulation ensembles are used to construct the diffusion coefficient and drift for ferredoxin and plastocyanin as spatial functions in the photosystem I domain of the MIT9313 ecotype. Four separate models are constructed, corresponding to ferredoxin and plastocyanin in reduced and oxidized states. A single scaling constant of 0.7 is found to be sufficient to adjust the diffusion coefficient obtained from the Martini simulation ensemble to match the in vitro values for both ferredoxin and plastocyanin. A comparison of Martini versions (2.2P, 2.2, 3) is presented with respect to diffusion scaling. The diffusion coefficient and drift together quantify the inhomogeneity of diffusive behavior. Notably, a funnel-like convergence toward the corresponding putative binding positions is observed for both ferredoxin and plastocyanin, even without such a priori foreknowledge supplied in the simulation protocol. The approach presented here is of relevance for studying diffusion kinetics in photosynthetic and other bioenergetic processes.

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst

Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

Investigating the Balance between Structural Conservation and Functional Flexibility in Photosystem I

Photosynthesis, as the primary source of energy for all life forms, plays a crucial role in maintaining the global balance of energy, entropy, and enthalpy in living organisms. Among its various building blocks, photosystem I (PSI) is responsible for light-driven electron transfer, crucial for generating cellular reducing power. PSI acts as a light-driven plastocyanin-ferredoxin oxidoreductase and is situated in the thylakoid membranes of cyanobacteria and the chloroplasts of eukaryotic photosynthetic organisms. Comprehending the structure and function of the photosynthetic machinery is essential for understanding its mode of action. New insights are offered into the structure and function of PSI and its associated light-harvesting proteins, with a specific focus on the remarkable structural conservation of the core complex and high plasticity of the peripheral light-harvesting complexes.

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.

Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin

Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.

Evolutionary implications from lipids in membrane bilayers and photosynthetic complexes in cyanobacteria and chloroplasts

In biomembranes, lipids form bilayer structures that serve as the fluid matrix for membrane proteins and other hydrophobic compounds. Additionally, lipid molecules associate with membrane proteins and impact their structures and functions. In both cyanobacteria and the chloroplasts of plants and algae, the lipid bilayer of the thylakoid membrane consists of four distinct glycerolipid classes: monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol, and phosphatidylglycerol. These lipids are also integral components of photosynthetic complexes such as photosystem II and photosystem I. The lipid-binding sites within the photosystems, as well as the lipid composition in the thylakoid membrane, are highly conserved between cyanobacteria and photosynthetic eukaryotes, and each lipid class has specific roles in oxygenic photosynthesis. This review aims to shed light on the potential evolutionary implications of lipid utilization in membrane lipid bilayers and photosynthetic complexes in oxygenic photosynthetic organisms.

Efficient Semi-Artificial Photosynthesis of Ethylene by a Self-Assembled InP-Cyanobacterial Biohybrid System

Biomanufacturing of ethylene is particularly important for modern society. Cyanobacterial cells are able to photosynthesize various valuable chemicals. A promising platform for next-generation biomanufacturing, the semiconductor-cyanobacterial hybrid systems are capable of enhancing the solar-to-chemical conversion efficiency. Herein, the native ethylene-producing capability of a filamentous cyanobacterium Nostoc sphaeroides is confirmed experimentally. The self-assembly characteristic of N. sphaeroides is exploited to facilitate its interaction with InP nanomaterial, and the resulting biohybrid system gave rise to further elevated photosynthetic ethylene production. Based on chlorophyll fluorescence measurement and metabolic analysis, the InP nanomaterial-augmented photosystem I activity and enhanced ethylene production metabolism of biohybrid cells are confirmed, the mechanism underlying the material-cell energy transduction as well as nanomaterial-modulated photosynthetic light and dark reactions are established. This work not only demonstrates the potential application of semiconductor-N. sphaeroides biohybrid system as a good platform for sustainable ethylene production but also provides an important reference for future studies to construct and optimize nano-cell biohybrid systems for efficient solar-driven valuable chemical production.

In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex

In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis1,2. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs)3. Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis4, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI.

A dimer-monomer transition captured by the crystal structures of cyanobacterial apo flavodoxin

In cyanobacteria and algae (but not plants), flavodoxin (Fld) replaces ferredoxin (Fd) under stress conditions to transfer electrons from photosystem I (PSI) to ferredoxin-NADP⁺ reductase (FNR) during photosynthesis. Fld constitutes a small electron carrier noncovalently bound to flavin mononucleotide (FMN), and also an ideal model for revealing the protein/flavin-binding mechanism because of its relative simplicity compared to other flavoproteins. Here, we report two crystal structures of apo-Fld from Synechococcus sp. PCC 7942, one dimeric structure of 2.09 Å and one monomeric structure of 1.84 Å resolution. Analytical ultracentrifugation showed that in solution, apo-Fld exists both as monomers and dimers. Our dimer structure contains two ligand-binding pockets separated by a distance of 45 Å, much longer than the previous structures of FMN-bound dimers. These results suggested a potential dimer-monomer transition mechanism of cyanobacterial apo-Fld. We further propose that the dimer represents the "standby" state to stabilize itself, while the monomer constitutes the "ready" state to bind FMN. Furthermore, we generated a new docking model of cyanobacterial Fld-FNR complex based on the recently reported cryo-EM structures, and mapped the special interactions between Fld and FNR in detail.

Structural insights into photosynthetic cyclic electron transport

During photosynthesis, light energy is utilized to drive sophisticated biochemical chains of electron transfers, converting solar energy into chemical energy that feeds most life on earth. Cyclic electron transfer/flow (CET/CEF) plays an essential role in efficient photosynthesis, as it balances the ATP/NADPH ratio required in various regulatory and metabolic pathways. Photosystem I, cytochrome b₆f, and NADH dehydrogenase (NDH) are large multisubunit protein complexes embedded in the thylakoid membrane of the chloroplast and key players in NDH-dependent CEF pathway. Furthermore, small mobile electron carriers serve as shuttles for electrons between these membrane protein complexes. Efficient electron transfer requires transient interactions between these electron donors and acceptors. Structural biology has been a powerful tool to advance our knowledge of this important biological process. A number of structures of the membrane-embedded complexes, soluble electron carrier proteins, and transient complexes composed of both have now been determined. These structural data reveal detailed interacting patterns of these electron donor-acceptor pairs, thus allowing us to visualize the different parts of the electron transfer process. This review summarizes the current state of structural knowledge of three membrane complexes and their interaction patterns with mobile electron carrier proteins.