The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas viridis

Intramolecular charge transfer and the function of vibronic excitons in photosynthetic light harvesting

A widely discussed explanation for the prevalence of pairs or clusters of closely spaced electronic chromophores in photosynthetic light-harvesting proteins is the presence of ultrafast and highly directional excitation energy transfer pathways mediated by vibronic excitons, the delocalized optical excitations derived from mixing of the electronic and vibrational states of the chromophores. We discuss herein the hypothesis that internal conversion processes between exciton states on the <100 fs timescale are possible when the excitonic potential energy surfaces are controlled by the vibrational modes that induce charge transfer character in a strongly coupled system of chromophores. We discuss two examples, the peridinin-chlorophyll protein from marine dinoflagellates and the intact phycobilisome from cyanobacteria, in which the intramolecular charge-transfer (ICT) character arising from out-of-plane distortion of the conjugation of carotenoid or bilin chromophores also results in localization of the initially delocalized optical excitation on the vibrational timescale. Tuning of the ground state conformations of the chromophores to manipulate their ICT character provides a natural photoregulatory mechanism, which would control the overall quantum yield of excitation energy transfer by turning on and off the delocalized character of the optical excitations.

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

Supramolecular Biohybrid Construct for Photoconversion Based on a Bacterial Reaction Center Covalently Bound to Cytochrome c by an Organic Light Harvesting Bridge

A supramolecular construct for solar energy conversion is developed by covalently bridging the reaction center (RC) from the photosynthetic bacterium Rhodobacter sphaeroides and cytochrome c (Cyt c) proteins with a tailored organic light harvesting antenna (hCy2). The RC-hCy2-Cyt c biohybrid mimics the working mechanism of biological assemblies located in the bacterial cell membrane to convert sunlight into metabolic energy. hCy2 collects visible light and transfers energy to the RC, increasing the rate of photocycle between a RC and Cyt c that are linked in such a way that enhances proximity without preventing protein mobility. The biohybrid obtained with average 1 RC/10 hCy2/1.5 Cyt c molar ratio features an almost doubled photoactivity versus the pristine RC upon illumination at 660 nm, and ∼10 times higher photocurrent versus an equimolar mixture of the unbound proteins. Our results represent an interesting insight into photoenzyme chemical manipulation, opening the way to new eco-sustainable systems for biophotovoltaics.

Axial vs equatorial: Capturing the intramolecular charge transfer state geometry in conformational polymorphic crystals of a donor-bridge-acceptor dyad in nanosecond-time-scale

Two conformational polymorphs of a donor-bridge-acceptor (D-B-A) dyad, p-(CH3)2N-C6H4-(CH2)2-(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH3)2N-C6H4/DMA is connected through a bridging group (B), -CH2-CH2-, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ∼3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ∼7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C-N-(CH3)2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.

Concerning the enigmatic cytochrome b-559 of oxygenic photosynthesis

Although there is an extensive literature on the properties and possible electron transfer pathways of cytochrome b-559, which is a prominent subunit of the multi-subunit photosystem II complex which functions in oxygenic photosynthesis, there is presently no consensus on the function of b-559 in the photosynthetic electron transport chain. The inability in earlier times to define a redox-linked function of this cytochrome was, to a large extent, a consequence of an absence of biochemical and structure information to complement an extensive array of spectrophotometric studies of the cytochrome in situ. Based on the location of hetero-dimeric b-559 in the photosystem II reaction center complex, derived from crystal crystallographic structure analysis, and the absence of a necessary redox function for the cytochrome in PSII, it is proposed that the main function of cytochrome b-559 is linked to its role as a structure component in the PSII reaction center complex. This function resides in the association of b-559 through its heme histidine residues in the trans-membrane domains of the PsbE and PsbF subunits of the PSII reaction center. These subunits, along with PsbJ, are inferred, from the analysis of structure, to define the intra-membrane portal in the PSII reaction center for plastoquinol (PQH₂) export which, through the PSII complex, provides the redox link to the cytochrome b₆f complex in the electron transfer chain.

Nonplanar porphyrins: synthesis, properties, and unique functionalities

Porphyrins are variously substituted tetrapyrrolic macrocycles, with wide-ranging biological and chemical applications derived from metal chelation in the core and the 18π aromatic surface. Under suitable conditions, the porphyrin framework can deform significantly from regular planar shape, owing to steric overload on the porphyrin periphery or steric repulsion in the core, among other structure modulation strategies. Adopting this nonplanar porphyrin architecture allows guest molecules to interact directly with an exposed core, with guest-responsive and photoactive electronic states of the porphyrin allowing energy, information, atom and electron transfer within and between these species. This functionality can be incorporated and tuned by decoration of functional groups and electronic modifications, with individual deformation profiles adapted to specific key sensing and catalysis applications. Nonplanar porphyrins are assisting breakthroughs in molecular recognition, organo- and photoredox catalysis; simultaneously bio-inspired and distinctly synthetic, these molecules offer a new dimension in shape-responsive host-guest chemistry. In this review, we have summarized the synthetic methods and design aspects of nonplanar porphyrin formation, key properties, structure and functionality of the nonplanar aromatic framework, and the scope and utility of this emerging class towards outstanding scientific, industrial and environmental issues.

Preparation of Photo-Bioelectrochemical Cells With the RC-LH Complex From Roseiflexus castenholzii

Roseiflexus castenholzii is an ancient green non-sulfur bacteria that absorbs the solar energy through bacteriochlorophylls (BChls) bound in the only light harvesting (LH) complex, and transfers to the reaction center (RC), wherein primary charge separation occurs and transforms the energy into electrochemical potentials. In contrast to purple bacteria, R. castenholzii RC-LH (rcRC-LH) does not contain an H subunit. Instead, a tightly bound tetraheme cytochrome c subunit is exposed on the P-side of the RC, which contains three BChls, three bacteriopheophytins (BPheos), two menaquinones, and one iron for electron transfer. These novel structural features of the rcRC-LH are advantageous for enhancing the electron transfer efficiency and subsequent photo-oxidation of the c-type hemes. However, the photochemical properties of rcRC-LH and its applications in developing the photo-bioelectrochemical cells (PBECs) have not been characterized. Here, we prepared a PBEC using overlapped fluorine-doped tin oxide (FTO) glass and Pt-coated glass as electrodes, and rcRC-LH mixed with varying mediators as the electrolyte. Absence of the H subunit allows rcRC-LH to be selectively adhered onto the hydrophilic surface of the front electrode with its Q-side. Upon illumination, the photogenerated electrons directly enter the front electrode and transfer to the counter electrode, wherein the accepted electrons pass through the exposed c-type hemes to reduce the excited P⁺, generating a steady-state current of up to 320 nA/cm² when using 1-Methoxy-5-methylphenazinium methyl sulfate (PMS) as mediator. This study demonstrated the novel photoelectric properties of rcRC-LH and its advantages in preparing effective PBECs, showcasing a potential of this complex in developing new type PBECs.

Stepwise Oxidative C-C Coupling and/or C-N Fusion of Zn(II) meso-Pyridin-2-ylthio-porphyrins

The synthesis and characterization of zinc(II) meso-pyridin-2-ylthio-porphyrins are presented in this manuscript. The (electro)chemical oxidation of [5-(pyridin-2-ylthio)-10,20-bis(p-tolyl)-15-phenylporphyrinato] zinc(II) or [5,15-bis(pyridin-2-ylthio)-10,20-bis(p-tolyl)porphyrinato] zinc(II) leads to the formation of one or two C-N bond(s) by intramolecular nucleophilic attack of the peripheral thiopyridinyl fragment(s) on the neighboring β-pyrrolic position(s) (C-N fusion reaction). In addition, the chemical oxidation of [5-(pyridin-2-ylthio)-10,20-bis(p-tolyl)porphyrinato] zinc(II), i.e., bearing one free meso position, mainly affords the meso,meso-dimer. Further stepwise electrochemical oxidation selectively produces the mono and bis C-N fused meso,meso-dimer. The resulting pyridinium derivatives exhibit important changes in their physicochemical properties (NMR, UV-vis, CV) as compared to their initial unfused precursors. Also, the X-ray crystallographic structures of three unfused monomers, one unfused meso,meso-dimer, and two C-N fused monomers are presented.

Using photocaging for fast time-resolved structural biology studies

Careful selection of photocaging approaches is critical to achieve fast and well synchronized reaction initiation and perform successful time-resolved structural biology experiments. This review summarizes the best characterized and most relevant photocaging groups previously described in the literature. It also provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions, focusing on photocaging groups with well characterized spectroscopic properties. The relationships between decay rates (k in s-1), quantum yields (ϕ) and molar extinction coefficients (ϵmax in M-1 cm-1) are highlighted for different groups. The effects of the nature of the photocaged group on these properties is also discussed. Four main photocaging scaffolds are presented in detail, o-nitrobenzyls, p-hydroxyphenyls, coumarinyls and nitrodibenzofuranyls, along with three examples of the use of this technology. Furthermore, a subset of specialty photocages are highlighted: photoacids, molecular photoswitches and metal-containing photocages. These extend the range of photocaging approaches by, for example, controlling pH or generating conformationally locked molecules.

Dimeric Corrole Analogs of Chlorophyll Special Pairs

Chlorophyll special pairs in photosynthetic reaction centers function as both exciton acceptors and primary electron donors. Although the macrocyclic natural pigments contain Mg(II), the central metal in most synthetic analogs is Zn(II). Here we report that insertion of either Al(III) or Ga(III) into an imidazole-substituted corrole affords an exceptionally robust photoactive dimer. Notably, attractive electronic interactions between dimer subunits are relatively strong, as documented by signature changes in NMR and electronic absorption spectra, as well as by cyclic voltammetry, where two well-separated reversible redox couples were observed. EPR spectra of one-electron oxidized dimers closely mimic those of native special pairs, and strong through-space interactions between corrole subunits inferred from spectroscopic and electrochemical data are further supported by crystal structure analyses (3 Å interplanar distances, 5 Å lateral shifts, and 6 Å metal to metal distances).

Solvent-regulated biomorphs from the intense π,π-mediated assemblies of tetracenequinone fused porphyrin

Tetracenequninone fused porphyrin exhibits remarkable π,π-stacking, which can be regulated by solvents to afford various biomorphs or cubic-shaped architectures.

Single Particle Analysis for High-Resolution 2D Electron Crystallography

Electron crystallography has been used for decades to determine three-dimensional structures of membrane proteins embedded in a lipid bilayer. However, high-resolution information could only be retrieved from samples where the 2D crystals were well ordered and perfectly flat. This is rarely the case in practice. We implemented in the FOCUS package a module to export transmission electron microscopy images of 2D crystals for 3D reconstruction by single particle algorithms. This approach allows for correcting local distortions of the 2D crystals, yielding much higher resolution reconstructions than otherwise expected from the observable diffraction spots. In addition, the single particle framework enables classification of heterogeneous structures coexisting within the 2D crystals. We provide here a detailed guide on single particle analysis of 2D crystal data based on the FOCUS and FREALIGN packages.

Modulation of the optical properties of chiral porphyrin dimers by introducing bridged chiral amide-bonds

The d/l-enantiomers of a series of three Zn(II)tetraarylporphyrin dimers were synthesized and isolated by incorporating a bridging amide-bonded xanthene moiety at the para-position of one of the meso-aryl rings. The electronic structures and optical properties were modulated by incorporating chiral amino acid moieties into the amide-bonding moieties of the xanthene bridge that contain methyl, tolyl and 2-methylindole substituents. A cofacial dimer was formed in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) resulting in a significant red shift of the B band, due to a relative destabilization of the HOMO, which has large MO coefficients on the pyrrole nitrogens. The sign sequences observed in the B band region of the CD spectra due to the presence of the chiral amino acid moieties were modified due to this change in geometry. Significant CD intensity is also observed in the B band region of the CD spectra of anion radical species during in situ spectroelectrochemical measurements.

Introduction of the Menaquinone Biosynthetic Pathway into Rhodobacter sphaeroides and de Novo Synthesis of Menaquinone for Incorporation into Heterologously Expressed Integral Membrane Proteins

Quinones are redox-active molecules that transport electrons and protons in organelles and cell membranes during respiration and photosynthesis. In addition to the fundamental importance of these processes in supporting life, there has been considerable interest in exploiting their mechanisms for diverse applications ranging from medical advances to innovative biotechnologies. Such applications include novel treatments to target pathogenic bacterial infections and fabricating biohybrid solar cells as an alternative renewable energy source. Ubiquinone (UQ) is the predominant charge-transfer mediator in both respiration and photosynthesis. Other quinones, such as menaquinone (MK), are additional or alternative redox mediators, for example in bacterial photosynthesis of species such as Thermochromatium tepidum and Chloroflexus aurantiacus. Rhodobacter sphaeroides has been used extensively to study electron transfer processes, and recently as a platform to produce integral membrane proteins from other species. To expand the diversity of redox mediators in R. sphaeroides, nine Escherichia coli genes encoding the synthesis of MK from chorismate and polyprenyl diphosphate were assembled into a synthetic operon in a newly designed expression plasmid. We show that the menFDHBCE, menI, menA, and ubiE genes are sufficient for MK synthesis when expressed in R. sphaeroides cells, on the basis of high performance liquid chromatography and mass spectrometry. The T. tepidum and C. aurantiacus photosynthetic reaction centers produced in R. sphaeroides were found to contain MK. We also measured in vitro charge recombination kinetics of the T. tepidum reaction center to demonstrate that the MK is redox-active and incorporated into the Q_A pocket of this heterologously expressed reaction center.

Ultrafast Dynamics of Nonrigid Zinc-Porphyrin Arrays Mimicking the Photosynthetic "Special Pair"

Conjugated porphyrin arrays are heavily investigated as efficient molecular systems for photosynthesis and photocatalysis. Recently, a series of one-, two-, and six-zinc-porphyrin arrays, noncovalently linked through benzene-based hubs, have been synthesized with the aim of mimicking the structure and function of the bacteriochlorophyll "special pair" in photosynthetic reaction centers. The excitonically coupled porphyrin subunits are expected to activate additional excited state relaxation channels with respect to the monomer. Here, we unveil the appearance of such supramolecular electronic interactions using ultrafast transient absorption spectroscopy with sub-25 fs time resolution. Upon photoexcitation of the Soret band, we resolve energy trapping within ∼150 fs in a delocalized dark excitonic manifold. Moreover, excitonic interactions promote an additional fast internal conversion from the Q-band to the ground state with an efficiency of up to 60% in the hexamer. These relaxation pathways appear to be common loss channels that limit the lifetime of the exciton states in noncovalently bound molecular aggregates.

Unfolding pathway and intermolecular interactions of the cytochrome subunit in the bacterial photosynthetic reaction center

Precise folding of photosynthetic proteins and organization of multicomponent assemblies to form functional entities are fundamental to efficient photosynthetic electron transfer. The bacteriochlorophyll b-producing purple bacterium Blastochloris viridis possesses a simplified photosynthetic apparatus. The light-harvesting (LH) antenna complex surrounds the photosynthetic reaction center (RC) to form the RC-LH1 complex. A non-membranous tetraheme cytochrome (4Hcyt) subunit is anchored at the periplasmic surface of the RC, functioning as the electron donor to transfer electrons from mobile electron carriers to the RC. Here, we use atomic force microscopy (AFM) and single-molecule force spectroscopy (SMFS) to probe the long-range organization of the photosynthetic apparatus from Blc. viridis and the unfolding pathway of the 4Hcyt subunit in its native supramolecular assembly with its functional partners. AFM images reveal that the RC-LH1 complexes are densely organized in the photosynthetic membranes, with restricted lateral protein diffusion. Unfolding of the 4Hcyt subunit represents a multi-step process and the unfolding forces of the 4Hcyt α-helices are approximately 121 picoNewtons. Pulling of 4Hcyt could also result in the unfolding of the RC L subunit that binds with the N-terminus of 4Hcyt, suggesting strong interactions between RC subunits. This study provides new insights into the protein folding and interactions of photosynthetic multicomponent complexes, which are essential for their structural and functional integrity to conduct photosynthetic electron flow.

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AFM and single-molecule force spectroscopy reveal the membrane organization and unfolding process of Blastochloris viridis RC

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RC-light-harvesting 1 complexes are densely organized in photosynthetic membranes, with restricted lateral diffusion

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Unfolding of the non-membranous cytochrome (4Hcyt) subunit represents a multi-step process;

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The average unfolding forces of the 4Hcyt α-helices are ~121 pN;

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Pulling of 4Hcyt from the RC suggests strong interactions (> 150 pN) between 4Hcyt and L subunits in the RC structure.

Structural basis of light-harvesting in the photosystem II core complex

Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.

Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment

Calcium ions (Ca2+) are major messengers in cell signaling, impacting nearly every aspect of cellular life. Those signals are generated within a wide spatial and temporal range through a large variety of Ca2+ channels, pumps, and exchangers. More and more evidences suggest that Ca2+ exchanges are regulated by their surrounding lipid environment. In this review, we point out the technical challenges that are currently being overcome and those that still need to be defeated to analyze the Ca2+ transport protein-lipid interactions. We then provide evidences for the modulation of Ca2+ transport proteins by lipids, including cholesterol, acidic phospholipids, sphingolipids, and their metabolites. We also integrate documented mechanisms involved in the regulation of Ca2+ transport proteins by the lipid environment. Those include: (i) Direct interaction inside the protein with non-annular lipids; (ii) close interaction with the first shell of annular lipids; (iii) regulation of membrane biophysical properties (e.g., membrane lipid packing, thickness, and curvature) directly around the protein through annular lipids; and (iv) gathering and downstream signaling of several proteins inside lipid domains. We finally discuss recent reports supporting the related alteration of Ca2+ and lipids in different pathophysiological events and the possibility to target lipids in Ca2+-related diseases.

On the use of oxygenic photosynthesis for the sustainable production of commodity chemicals

A sustainable society will have to largely refrain from the use of fossil carbon deposits. In such a regime, renewable electricity can be harvested as a primary source of energy. However, as for the synthesis of carbon-based materials from bulk chemicals, an alternative is required. A sustainable approach towards this is the synthesis of commodity chemicals from CO₂ , water and sunlight. Multiple paths to achieve this have been designed and tested in the domains of chemistry and biology. In the latter, the use of both chemotrophic and phototrophic organisms has been advocated. 'Direct conversion' of CO₂ and H₂ O, catalyzed by an oxyphototroph, has excellent prospects to become the most economically competitive of these transformations, because of the relative ease of scale-up of this process. Significantly, for a wide range of energy and commodity products, a proof of principle via engineering of the corresponding production organism has been provided. In the optimization of a cyanobacterial production organism, a wide range of aspects has to be addressed. Of these, here we will put our focus on: (1) optimizing the (carbon) flux to the desired product; (2) increasing the genetic stability of the producing organism and (3) maximizing its energy conversion efficiency. Significant advances have been made on all these three aspects during the past 2 years and these will be discussed: (1) increasing the carbon partitioning to >50%; (2) aligning product formation with the growth of the cells and (3) expanding the photosynthetically active radiation region for oxygenic photosynthesis.

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.

Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote

Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC–LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.

Filamentous anoxygenic phototrophs (FAPs) are phylogenetically distant from other anoxygenic photosynthetic bacteria. Here the authors present the 4.1 Å cryo-EM structure of the photosynthetic core complex from the FAP Roseiflexus castenholzii and propose a model for energy and electron transfer.

Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins

A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.

Interactions of Metal-Based and Ligand-Based Electronic Spins in Neutral Tripyrrindione π Dimers

The ability of tetrapyrrolic macrocycles to stabilize unpaired electrons and engage in π-π interactions is essential for many electron-transfer processes in biology and materials engineering. Herein, we demonstrate that the formation of π dimers is recapitulated in complexes of a linear tripyrrolic analogue of naturally occurring pigments derived from heme decomposition. Hexaethyltripyrrindione (H₃TD1) coordinates divalent transition metals (i.e., Pd, Cu, Ni) as a stable dianionic radical and was recently described as a robust redox-active ligand. The resulting planar complexes, which feature a delocalized ligand-based electronic spin, are stable at room temperature in air and support ligand-based one-electron processes. We detail the dimerization of neutral tripyrrindione complexes in solution through electron paramagnetic resonance (EPR) and visible absorption spectroscopic methods. Variable-temperature measurements using both EPR and absorption techniques allowed determination of the thermodynamic parameters of π dimerization, which resemble those previously reported for porphyrin radical cations. The inferred electronic structure, featuring coupling of ligand-based electronic spins in the π dimers, is supported by density functional theory (DFT) calculations.

Electrostatic Asymmetry in the Reaction Center of Photosystem II

The exciton Hamiltonian of the chlorophyll (Chl) and pheophytin (Pheo) pigments in the reaction center (RC) of photosystem II is computed based on recent crystal structures by using the Poisson-Boltzmann/quantum-chemical method. Computed site energies largely confirm a previous model inferred from fits of optical spectra, in which Chl_D1 has the lowest site energy, while that of Pheo_D1 is higher than that of Pheo_D2. The latter assignment has been challenged recently under reference to mutagenesis experiments. We argue that these data are not in contradiction to our results. We conclude that Chl_D1 is the primary electron donor in both isolated RCs and intact core complexes at least at cryogenic temperatures. The main source of asymmetry in site energies is the charge distribution in the protein. Because many small contributions from various structural elements have to be taken into account, it can be assumed that this asymmetry was established in evolution by global optimization of the RC protein.

Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria

Porphyrin-based photosynthetic reaction centre (PRC) mimics, ZnPQ-Q2HP-C60 and MP2Q-Q2HP-C60 (M = Zn or 2H), designed to have a similar special-pair electron donor and similar charge-separation distances, redox processes and photochemical reaction rates to those in the natural PRC from purple bacteria, have been synthesised and extensive photochemical studies performed. Mechanisms of electron-transfer reactions are fully investigated using femtosecond and nanosecond transient absorption spectroscopy. In benzonitrile, all models show picosecond-timescale charge-separations and the final singlet charge-separations with the microsecond-timescale. The established lifetimes are long compared to other processes in organic solar cells or other organic light harvesting systems. These rigid, synthetically flexible molecules provide the closest mimics to the natural PRC so far synthesised and present a future direction for the design of light harvesters with controllable absorption, redox, and kinetics properties.

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.

Fluorophore Absorption Size Exclusion Chromatography (FA-SEC): An Alternative Method for High-Throughput Detergent Screening of Membrane Proteins

Membrane proteins play key roles in many fundamental functions in cells including ATP synthesis, ion and molecule transporter, cell signalling and enzymatic reactions, accounting for ~30% genes of whole genomes. However, the hydrophobic nature of membrane proteins frequently hampers the progress of structure determination. Detergent screening is the critical step in obtaining stable detergent-solubilized membrane proteins and well-diffracting protein crystals. Fluorescence Detection Size Exclusion Chromatography (FSEC) has been developed to monitor the extraction efficiency and monodispersity of membrane proteins in detergent micelles. By tracing the FSEC profiles of GFP-fused membrane proteins, this method significantly enhances the throughput of detergent screening. However, current methods to acquire FSEC profiles require either an in-line fluorescence detector with the SEC equipment or an off-line spectrofluorometer microplate reader. Here, we introduce an alternative method detecting the absorption of GFP (FA-SEC) at 485 nm, thus making this methodology possible on conventional SEC equipment through the in-line absorbance spectrometer. The results demonstrate that absorption is in great correlation with fluorescence of GFP. The comparably weaker absorption signal can be improved by using a longer path-length flow cell. The FA-SEC profiles were congruent with the ones plotted by FSEC, suggesting FA-SEC could be a comparable and economical setup for detergent screening of membrane proteins.

Optically Active Porphyrin and Phthalocyanine Systems

This review highlights and summarizes various optically active porphyrin and phthalocyanine molecules prepared using a wide range of structural modification methods to improve the design of novel structures and their applications. The induced chirality of some illustrative achiral bis-porphyrins with a chiral guest molecule is introduced because these systems are ideal for the identification and separation of chiral biologically active substrates. In addition, the relationship between CD signal and the absolute configuration of the molecule is analyzed through an analysis of the results of molecular modeling calculations. Possible future research directions are also discussed.

Development and dynamics of the photosynthetic apparatus in purple phototrophic bacteria

The purple bacterium Rhodobacter sphaeroides provides a useful model system for studies of the assembly and dynamics of bacterial photosynthetic membranes. For the nascent developing membrane, proteomic analyses showed an ~2-fold enrichment in general membrane assembly factors, compared to chromatophores. When the protonophore carbonyl-cyanide m-chlorophenyl-hydrazone (CCCP) was added to an ICM inducing culture, an ~2-fold elevation in spectral counts vs. the control was seen for the SecA translocation ATPase, the preprotein translocase SecY, SecD and SecF insertion components, and chaperonins DnaJ and DnaK, which act early in the assembly process. It is suggested that these factors accumulated with their nascent polypeptides, as putative assembly intermediates in a functionally arrested state. Since in Synechocystis PCC 6803, a link has been established between Chl delivery involving the high-light HilD protein and the SecY/YidC-requiring cotranslational insertion of nascent polypeptides, such a connection between BChl biosynthesis and insertion and folding of nascent Rba. sphaeroides BChl binding proteins is likely to also occur. AFM imaging studies of the formation of the reaction center (RC)-light harvesting 1 (LH1) complex suggested a cooperative assembly mechanism in which, following the association between the RC template and the initial LH1 unit, addition of successive LH1 units to the RC drives the assembly process to completion. Alterations in membrane dynamics as the developing membrane becomes filled with LH2-rings were assessed by fluorescence induction/relaxation kinetics, which showed a slowing in RC electron transfer rate thought to mainly reflect alterations in donor side electron transfer. This was attributed to an increased distance for electron flow in cytochrome c2 between the RC and cytochrome bc1 complexes, as suggested in the current structural models. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof Conrad Mullineaux.

Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves

Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable.

Large photocurrent response and external quantum efficiency in biophotoelectrochemical cells incorporating reaction center plus light harvesting complexes

Bacterial photosynthetic reaction centers (RCs) are promising materials for solar energy harvesting, due to their high ratio of photogenerated electrons to absorbed photons and long recombination time of generated charges. In this work, photoactive electrodes were prepared from a bacterial RC-light-harvesting 1 (LH1) core complex, where the RC is encircled by the LH1 antenna, to increase light capture. A simple immobilization method was used to prepare RC-LH1 photoactive layer. Herein, we demonstrate that the combination of pretreatment of the RC-LH1 protein complexes with quinone and the immobilization method results in biophotoelectrochemical cells with a large peak transient photocurrent density and photocurrent response of 7.1 and 3.5 μA cm(-2), respectively. The current study with monochromatic excitation showed maximum external quantum efficiency (EQE) and photocurrent density of 0.21% and 2 μA cm(-2), respectively, with illumination power of ∼6 mW cm(-2) at ∼875 nm, under ambient conditions. This work provides new directions to higher performance biophotoelectrochemical cells as well as possibly other applications of this broadly functional photoactive material.

Crystallization of membrane proteins by vapor diffusion

X-ray crystallography remains the most robust method to determine protein structure at the atomic level. However, the bottlenecks of protein expression and purification often discourage further study. In this chapter, we address the most common problems encountered at these stages. Based on our experiences in expressing and purifying antimicrobial efflux proteins, we explain how a pure and homogenous protein sample can be successfully crystallized by the vapor diffusion method. We present our current protocols and methodologies for this technique. Case studies show step-by-step how we have overcome problems related to expression and diffraction, eventually producing high-quality membrane protein crystals for structural determinations. It is our hope that a rational approach can be made of the often anecdotal process of membrane protein crystallization.

Synthesis and photophysical properties of new catenated electron donor-acceptor materials with magnesium and free base porphyrins as donors and C60 as the acceptor

A new series of nanoscale electron donor-acceptor systems with [2]catenane architectures has been synthesized, incorporating magnesium porphyrin (MgP) or free base porphyrin (H2P) as electron donor and C60 as electron acceptor, surrounding a central tetrahedral Cu(I)-1,10-phenanthroline (phen) complex. Model catenated compounds incorporating only one or none of these photoactive moieties were also prepared. The synthesis involved the use of Sauvage's metal template protocol in combination with the 1,3-dipolar cycloaddition of azides and alkynes ("click chemistry"), as in other recent reports from our laboratories. Ground state electron interactions between the individual constituents was probed using electrochemistry and UV-vis absorption spectroscopy, while events occurring following photoexcitation in tetrahydrofuran (under both aerobic and anaerobic conditions) at various wavelengths were followed by means of time-resolved transient absorption and emission spectroscopies on the femtosecond and nanosecond time scales, respectively, complemented by measurements of quantum yields for generation of singlet oxygen. From similar studies with model catenates containing one or neither of the chromophores, the events following photoexcitation could be elucidated. The results were compared with those previously reported for analogous catenates based on zinc porphyrin (ZnP). It was determined that a series of energy transfer (EnT) and electron transfer (ET) processes take place in the present catenates, ultimately generating long-distance charge separated (CS) states involving oxidized porphyrin and reduced C60 moieties, with lifetimes ranging from 400 to 1060 nanoseconds. Shorter lived short-distance CS states possessing oxidized copper complexes and reduced C60, with lifetimes ranging from 15 to 60 ns, were formed en route to the long-distance CS states. The dynamics of the ET processes were analyzed in terms of their thermodynamic driving forces. It was clear that intramolecular back ET was occurring in the inverted region of the Marcus parabola correlating rates and driving forces for electron transfer processes. In addition, evidence for triplet excited states as a product of either incomplete ET or back ET was found. The differences in behavior of the three catenates upon photoexcitation are analyzed in terms of the energy levels of the various intermediate states and the driving forces for EnT and ET processes.

Light harvesting by lamellar chromatophores in Rhodospirillum photometricum

Purple photosynthetic bacteria harvest light using pigment-protein complexes which are often arranged in pseudo-organelles called chromatophores. A model of a chromatophore from Rhodospirillum photometricum was constructed based on atomic force microscopy data. Molecular-dynamics simulations and quantum-dynamics calculations were performed to characterize the intercomplex excitation transfer network and explore the interplay between close-packing and light-harvesting efficiency.

Multiporphyrin arrays with π-π interchromophore interactions

A recently reported synthetic method has been employed to prepare several arrays of free base and zinc porphyrins. In the arrays, the porphyrins are arranged around a central benzene ring. The lack of aryl rings in the linkages to the central benzene ring, coupled with the presence of only one meso-aryl substituent on each porphyrin, allows strong electronic interactions between the porphyrin macrocycles. In arrays containing two or six porphyrins, a variety of evidence indicates that the porphyrins exist as twist-stacked dimers reminiscent of the special pairs of bacteriochlorophylls found in some photosynthetic bacteria. These dimers feature van der Waals contact between the macrocycles, and demonstrate excitonic splitting due to π-π interactions. The excitonic effects split and blue-shift the Soret absorptions, and slightly broaden the Q-band absorptions and shift them to longer wavelengths. The interactions also lower the first oxidation potentials by ca. 100 mV, and the arrays show evidence for delocalization of the radical cation over both porphyrins in the dimer. The arrays demonstrate singlet-singlet energy transfer among the chromophores. Arrays of this type will be good models for some aspects of the interactions of photosynthetic pigments, including those of reaction center special pairs and possibly quantum coherence effects. They can also be useful in artificial photosynthetic constructs.

Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes

Neutron reflectometry (NR) is an emerging experimental technique for the structural characterization of proteins interacting with fluid bilayer membranes under conditions that mimic closely the cellular environment. Thus, cellular processes can be emulated in artificial systems and their molecular basis studied by adding cellular components one at a time in a well-controlled environment while the resulting structures, or structural changes in response to external cues, are monitored with neutron reflection. In recent years, sample environments, data collection strategies and data analysis were continuously refined. The combination of these improvements increases the information which can be obtained from NR to an extent that enables structural characterization of protein-membrane complexes at a length scale that exceeds the resolution of the measurement by far. Ultimately, the combination of NR with molecular dynamics (MD) simulations can be used to cross-validate the results of the two techniques and provide atomic-scale structural models. This review discusses these developments in detail and demonstrates how they provide new windows into relevant biomedical problems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.

Photo- and electro-functional self-assembled architectures of porphyrins

Recent developments in supramolecular strategies have enabled us to construct novel well-defined assemblies of dye molecules. These fundamental researches of such organic materials also entail the synthetic and photophysical processes of molecular aggregates at the nano- and micro-meter scale, since their optical properties significantly differ from those of monomeric species. One of the promising candidates for such functional molecules is a porphyrin dye, which acts as an electron donor as well as a sensitizer. In this perspective, the focus is on the recent advances in the construction of optically and electronically functionalized molecular architectures of porphyrins for light energy conversion and electronics. First, porphyrin aggregates with morphologies such as cube, rod and fiber, which are prepared by three different supramolecular techniques, are reported. Then, we discuss composite molecular nanoarchitectures of porphyrins and carbon nanotubes such as single-wall carbon nanotubes (SWCNTs), stacked-cup carbon nanotubes (SCCNTs) and carbon nanohorns (CNHs). Finally, the structural and photophysical properties of the composite assemblies of porphyrins and graphenes including polycyclic aromatic hydrocarbons (PAH) are presented.

Versatile redox reactivity of triaryl-meso-substituted Ni(ii) porphyrin

The electrochemical oxidation of a Ni(ii) tri-arylporphyrin leads to the 5-Cl and 5-OH-porphyrins, the meso–meso, meso-β and meso-β/meso-β doubly fused dimers depending on the experimental conditions. Among them, the Ni(ii) 5-Cl-porphyrin is isolated in good yield and its formation mechanism is elucidated.

The nonheme iron in photosystem II

Photosystem II (PSII), the light-driven water:plastoquinone (PQ) oxidoreductase of oxygenic photosynthesis, contains a nonheme iron (NHI) at its electron acceptor side. The NHI is situated between the two PQs QA and QB that serve as one-electron transmitter and substrate of the reductase part of PSII, respectively. Among the ligands of the NHI is a (bi)carbonate originating from CO2, the substrate of the dark reactions of oxygenic photosynthesis. Based on recent advances in the crystallography of PSII, we review the structure of the NHI in PSII and discuss ideas concerning its function and the role of bicarbonate along with a comparison to the reaction center of purple bacteria and other enzymes containing a mononuclear NHI site.

Selective and differential optical spectroscopies in photosynthesis

Photosynthetic pigments are inherently intense optical absorbers and have strong polarisation characteristics. They can also luminesce strongly. These properties have led optical spectroscopies to be, quite naturally, key techniques in photosynthesis. However, there are typically many pigments in a photosynthetic assembly, which when combined with the very significant inhomogeneous and homogeneous linewidths characteristic of optical transitions, leads to spectral congestion. This in turn has made it difficult to provide a definitive and detailed electronic structure for many photosynthetic assemblies. An electronic structure is, however, necessary to provide a foundation for any complete description of fundamental processes in photosynthesis, particularly those in reaction centres. A wide range of selective and differential spectral techniques have been developed to help overcome the problems of spectral complexity and congestion. The techniques can serve to either reduce spectral linewidths and/or extract chromophore specific information from unresolved spectral features. Complementary spectral datasets, generated by a number of techniques, may then be combined in a 'multi-dimensional' theoretical analysis so as to constrain and define effective models of photosynthetic assemblies and their fundamental processes. A key example is the work of Renger and his group (Raszewski, Biophys J 88(2):986-998, 2005) on PS II reaction centre assemblies. This article looks to provide an overview of some of these techniques and indicate where their strengths and weaknesses may lie. It highlights some of our own contributions and indicates areas where progress may be possible.

Evolution of photosystem I and the control of global enthalpy in an oxidizing world

Life on earth is governed by light, chemical reactions, and the second law of thermodynamics, which defines the tendency for increasing entropy as an expression of disorder or randomness. Life is an expression of increasing order, and a constant influx of energy and loss of entropic wastes are required to maintain or increase order in living organisms. Most of the energy for life comes from sunlight and, thus, photosynthesis underlies the survival of all life forms. Oxygenic photosynthesis determines not only the global amount of enthalpy in living systems, but also the composition of the Earth's atmosphere and surface. Photosynthesis was established on the Earth more than 3.5 billion years ago. The primordial reaction center has been suggested to comprise a homodimeric unit resembling the core complex of the current reaction centers in Chlorobi, Heliobacteria, and Acidobacteria. Here, an evolutionary scenario based on the known structures of the current reaction centers is proposed.