X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis

The diversity of physiology and metabolism in chlorophototrophic bacteria

Photosynthesis by (bacterio)chlorophyll-producing organisms ("chlorophototrophy") sustains virtually all life on Earth, providing the biosphere with food and energy. The oxygenic process carried out by plants, algae and cyanobacteria also generates the oxygen we breathe, and ancient cyanobacteria were responsible for oxygenating the atmosphere, creating the conditions that allowed the evolution of complex life. Cyanobacteria were also the endosymbiotic progenitors of chloroplasts, play major roles in biogeochemical cycles and as primary producers in aquatic ecosystems, and act as genetically tractable model organisms for studying oxygenic photosynthesis. In addition to the Cyanobacteriota, eight other bacterial phyla, namely Proteobacteria/Pseudomonadota, Chlorobiota, Chloroflexota, Bacillota, Acidobacteriota, Gemmatimonadota, Vulcanimicrobiota and Myxococcota contain at least one putative chlorophototrophic species, all of which perform a variant of anoxygenic photosynthesis, which does not yield oxygen as a by-product. These chlorophototrophic organisms display incredible diversity in the habitats that they colonise, and in their biochemistry, physiology and metabolism, with variation in the light-harvesting complexes and pigments they produce to utilise solar energy. Whilst some are very well understood, such as the proteobacterial 'purple bacteria', others have only been identified in the last few years and therefore relatively little is known about them - especially those that have not yet been isolated and cultured. In this chapter, we aim to summarise and compare the photosynthetic physiology and central metabolic processes of chlorophototrophic members from the nine phyla in which they are found, giving both a short historical perspective and highlighting gaps in our understanding.

Synthesis, structure, and properties of antiaromatic PVO complexes of triphyrins(2.1.1)

A series of antiaromatic stable PVO complexes of meso-tetra(p-tolyl) triphyrin(2.1.1) and its β-substituted derivatives were synthesized in 38-48% yields by treating an appropriate aromatic free base triphyrin(2.1.1) with PCl3 in toluene/Et3N at reflux for 4-6 h. During the reaction, 14π aromatic meso-tetra(p-tolyl) triphyrin(2.1.1) is reduced to a 16π macrocycle and complexes with PVO to form antiaromatic PVO complexes of meso-tetra(p-tolyl) triphyrins(2.1.1). The X-ray structure obtained for one of the PVO triphyrin(2.1.1) complexes revealed that unlike the almost planar structure of free base meso-tetraaryl triphyrin(2.1.1), PVO triphyrin(2.1.1) was highly distorted and adopted a domed structure with P(V) placed at a distance of 0.927 Å above the mean plane defined by the four meso-carbon atoms. NMR studies indicated the paratropic ring current effect in the PVO triphyrin(2.1.1) complexes and the outer β-pyrrole protons which appear in the downfield region of 7.50-8.20 ppm in free base triphyrin(2.1.1) experienced significant upfield shifts and appeared in the region of 3.50-4.50 ppm in PVO triphyrin(2.1.1) complexes, supporting the switching of aromatic 14π free base triphyrin(2.1.1) to antiaromatic 16π PVO triphyrin(2.1.1) complexes. The PVO triphyrin(2.1.1) complexes show one intense absorption band in the 300-350 nm region and an antiaromatic characteristic broad band in the lower energy region of 450-1000 nm. The electrochemical studies revealed that the PVO triphyrin(2.1.1) complexes undergo very easy oxidations and difficult reductions compared to their corresponding free base triphyrins(2.1.1). DFT/TD-DFT calculations were carried out to support the experimental observations.

Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum

Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The apoproteins of these antennas, encoded respectively by the genes pufBA and pucBA within and outside the photosynthetic gene cluster, respectively, exhibit conserved amino acid sequences and structural topologies suggesting they were derived from a shared ancestor. Here we present the structures of two photosynthetic complexes from Roseospirillum (Rss.) parvum 930I: an LH1-RC complex and a variant of the LH1 complex also encoded by pufBA that we designate as LH1'. The LH1-RC complex forms a closed elliptical structure consisting of 16 pairs of αβ-polypeptides that surrounds the RC. By contrast, the LH1' complex is a closed ring structure composed of 14 pairs of αβ-polypeptides, and it shows significant similarities to LH2 complexes both spectrally and structurally. Although LH2-like, the LH1' complex is larger than any known LH2 complexes, and genomic analyses of Rss. parvum revealed the absence of pucBA, genes that encode classical LH2 complexes. Characterization of the unique Rss. parvum photocomplexes not only underscores the diversity of such structures but also sheds new light on the evolution of light-harvesting complexes from phototrophic bacteria.

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.

In Situ Self-Inflating-Modeled Giant-Vesicle-Like Quantum Dot Assembly for Biomimetic Artificial Photosynthesis

The study of biomimetic self-assembly is crucial for scientists aiming to understand the origin of life and construct biomimetic functional structures. In our endeavor to create a biomimetic photosynthetic assembly, we discover a self-inflation behavior that drives the components, MPA-CdSe quantum dots (QDs) and a solid cationic polyelectrolyte, CPPA, to form a giant-vesicle-like (GVL) architecture, termed GVL-QDs@CPPA. The in situ generation of osmotic pressure during the self-assembly of QDs onto swollen CPPA in water was found to cause this self-inflation process. The resulting vesicle-like structure exhibits spatial characteristics similar to those of natural photosynthetic cells, with QDs acting as pigments uniformly distributed on the CPPA membranes, which have embedded cobalt catalytic centers. This architecture ensures optimal absorption of visible light and facilitates efficient electron transfer between the QDs and catalytic centers. As a result, GVL-QDs@CPPA assemblies efficiently harness photogenerated electrons and holes to convert protons and isopropanol into hydrogen (H2) and acetone, respectively, achieving a nearly 1:1 ratio of the reduction product (H2) to the oxidation product (acetone).

Excited Charge Transfer Promoted Electron Transfer in all Perylenediimide Derived, Wide-Band Capturing Conjugates: A Mimicry of the Early Events of Natural Photosynthesis

Fundamental discoveries in electron transfer advance scientific and technological advancements. It is suggested that in plant and bacterial photosynthesis, the primary donor, a chlorophyll or bacteriochlorophyll dimer, forms an initial excited symmetry-breaking charge transfer state (1CT*) upon photoexcitation that subsequently promotes sequential electron transfer (ET) events. This is unlike monomeric photosensitizer-bearing donor-acceptor dyads where ET occurs from the excited donor or acceptor (1D* or 1A*). In the present study, we successfully demonstrated the former photochemical event using an excited charge transfer molecule as a donor. Electron-deficient perylenediimide (PDI) is functionalized with three electron-rich piperidine entities at the bay positions, resulting in a far-red emitting CT molecule (DCT). Further, this molecule is covalently linked to another PDI (APDI) carrying no substituents at the bay positions, resulting in wide-band capturing DCT-APDI conjugates. Selective excitation of the CT band of DCT in these conjugates leads to an initial 1DCT* that undergoes subsequent ET involving APDI, resulting in DCT +-APDI - charge separation product (kCS~109 s-1). Conversely, when APDI was directly excited, ultrafast energy transfer (ENT) from 1APDI* to DCT (kENT~1011 s-1) followed by ET from 1DCT* to PDI is witnessed. While increasing solvent polarity improved kCS rates, for a given solvent, the magnitude of the kCS values was almost the same, irrespective of the excitation wavelengths. The present findings demonstrate ET from an initial CT state to an acceptor is key to understanding the intricate ET events in complex natural and bacterial photosynthetic systems possessing multiple redox- and photoactive entities.

Downhill excitation energy flow in reaction centers of purple bacteria Rhodospirillum rubrum G9

Using femtosecond differential spectroscopy, excitation energy transfer in reaction centers (RCs) of the carotenoidless strain of purple bacteria Rhodospirillum rubrum G9 was studied at room temperature. Excitation and probing of the Qy, Qx and Soret absorption bands of the RCs were carried out by pulses with duration of 25-30 fs. Modeling of ΔA (light - dark) kinetics made it possible to estimate the characteristic time of various stages of excitation energy transformation. It is shown that the dynamics of the downhill energy flow in the RCs is determined both by the internal energy conversion Soret→ Qx → Qy in each cofactor and by the energy transfer H* → B* → P* (H - bacteriopheophytin, B - bacteriochlorophyll a, P - bacteriochlorophyll a dimer) between cofactors. The transfer of energy between the upper excited levels (Soret and Qx) of the cofactors accelerates its arrival to the lower exciton level of the P, from where charge separation begins. It turned out that all conversion and energy transfer processes occur within 40-160 fs: the conversion Soret → Qx occurs in 40-50 fs, the conversion Qx → Qy occurs in 100-140 fs, the transfer H* → B* has a time constant of 80-120 fs, and the transfer B* → P* has a time constant of 130-160 fs. The rate of energy transfer between the upper excited levels is close to the rate of transfer between Qy levels.

Antioxidative Triplet Excitation Energy Transfer in Bacterial Reaction Center Using a Screened Range Separated Hybrid Functional

Excess energy absorbed by photosystems (PSs) can result in photoinduced oxidative damage. Transfer of such energy within the core pigments of the reaction center in the form of triplet excitation is important in regulating and preserving the functionality of PSs. In the bacterial reaction center (BRC), the special pair (P) is understood to act as the electron donor in a photoinduced charge transfer process, triggering the charge separation process through the photoactive branch A pigments that experience a higher polarizing environment. At this work, triplet excitation energy transfer (TEET) in BRC is studied using a computational perspective to gain insights into the roles of the dielectric environment and interpigment orientations. We find in agreement with experimental observations that TEET proceeds through branch B. The TEET process toward branch B pigment is found to be significantly faster than the hypothetical process proceeding through branch A pigments with ps and ms time scales, respectively. Our calculations find that conformational differences play a major role in this branch asymmetry in TEET, where the dielectric environment asymmetry plays only a secondary role in directing the TEET to proceed through branch B. We also address TEET processes asserting the role of carotenoid as the final triplet energy acceptor and in a mutant form, where the branch pigments adjacent to P are replaced by bacteriopheophytins. The necessary electronic excitation energies and electronic state couplings are calculated by the recently developed polarization-consistent framework combining a screened range-separated hybrid functional and a polarizable continuum mode. The polarization-consistent potential energy surfaces are used to parametrize the quantum mechanical approach, implementing Fermi's golden rule expression of the TEET rate calculations.

Use of bacterial photosynthetic vesicles to evaluate the effect of ionic liquids on the permeability of biological membranes

Ionic liquids (ILs) are salts composed of a combination of organic or inorganic cations and anions characterized by a low melting point, often below 100 °C. This property, together with an extremely low vapor pressure, low flammability and high thermal stability, makes them suitable for replacing canonical organic solvents, with a reduction of industrial activities impact on the environment. Although in the last decades the eco-compatibility of ILs has been extensively verified through toxicological tests performed on model organisms, a detailed understanding of the interaction of these compounds with biological membranes is far from being exhaustive. In this context, we have chosen to evaluate the effect of some ILs on native membranes by using chromatophores, photosynthetic vesicles that can be isolated from Rhodobacter capsulatus, a member of the purple non‑sulfur bacteria. Here, carotenoids associated with the light-harvesting complex II, act as endogenous spectral probes of the transmembrane electrical potential (ΔΨ). By measuring through time-resolved absorption spectroscopy the evolution of the carotenoid band shift induced by a single excitation of the photosynthetic reaction center, information on the ΔΨ dissipation due to ionic currents across the membrane can be obtained. We found that some ILs cause a rather fast dissipation of the transmembrane ΔΨ even at low concentrations, and that this behavior is dose-dependent. By using two different models to analyze the decay of the carotenoid signals, we attempted to interpret at a mechanistic level the marked increase of ionic permeability caused by specific ILs.

Structural diversity and modularity of photosynthetic RC-LH1 complexes

Bacterial photosynthesis is essential for sustaining life on Earth as it aids in carbon assimilation, atmospheric composition, and ecosystem maintenance. Many bacteria utilize anoxygenic photosynthesis to convert sunlight into chemical energy while producing organic matter. The core machinery of anoxygenic photosynthesis performed by purple photosynthetic bacteria and Chloroflexales is the reaction center-light-harvesting 1 (RC-LH1) pigment-protein supercomplex. In this review, we discuss recent structural studies of RC-LH1 core complexes based on the advancement in structural biology techniques. These studies have provided fundamental insights into the assembly mechanisms, structural variations, and modularity of RC-LH1 complexes across different bacterial species, highlighting their functional adaptability. Understanding the natural architectures of RC-LH1 complexes will facilitate the design and engineering of artificial photosynthetic systems, which can enhance photosynthetic efficiency and potentially find applications in sustainable energy production and carbon capture.

Panchromatic Light-Capturing Bis-styryl BODIPY-Perylenediimide Donor-Acceptor Constructs: Occurrence of Sequential Energy Transfer Followed by Electron Transfer

Two wide-band-capturing donor-acceptor conjugates featuring bis-styrylBODIPY and perylenediimide (PDI) have been newly synthesized, and the occurrence of ultrafast excitation transfer from the 1 PDI* to BODIPY, and a subsequent electron transfer from the 1 BODIPY* to PDI have been demonstrated. Optical absorption studies revealed panchromatic light capture but offered no evidence of ground-state interactions between the donor and acceptor entities. Steady-state fluorescence and excitation spectral recordings provided evidence of singlet-singlet energy transfer in these dyads, and quenched fluorescence of bis-styrylBODIPY emission in the dyads suggested additional photo-events. The facile oxidation of bis-styrylBODIPY and facile reduction of PDI, establishing their relative roles of electron donor and acceptor, were borne out by electrochemical studies. The electrostatic potential surfaces of the S1 and S2 states, derived from time-dependent DFT calculations, supported excited charge transfer in these dyads. Spectro-electrochemical studies on one-electron-oxidized and one-electron-reduced dyads and the monomeric precursor compounds were also performed in a thin-layer optical cell under corresponding applied potentials. From this study, both bis-styrylBODIPY⋅+ and PDI⋅- could be spectrally characterizes and were subsequently used in characterizing the electron-transfer products. Finally, pump-probe spectral studies were performed in dichlorobenzene under selective PDI and bis-styrylBODIPY excitation to secure energy and electron-transfer evidence. The measured rate constants for energy transfer, kENT , were in the range of 1011  s-1 , while the electron transfer rate constants, kET , were in the range of 1010  s-1 , thus highlighting their potential use in solar energy harvesting and optoelectronic applications.

A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases

Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.

Membrane protein isolation and structure determination in cell-derived membrane vesicles

Integral membrane protein structure determination traditionally requires extraction from cell membranes using detergents or polymers. Here, we describe the isolation and structure determination of proteins in membrane vesicles derived directly from cells. Structures of the ion channel Slo1 from total cell membranes and from cell plasma membranes were determined at 3.8 Å and 2.7 Å resolution, respectively. The plasma membrane environment stabilizes Slo1, revealing an alteration of global helical packing, polar lipid, and cholesterol interactions that stabilize previously unresolved regions of the channel and an additional ion binding site in the Ca2+ regulatory domain. The two methods presented enable structural analysis of both internal and plasma membrane proteins without disrupting weakly interacting proteins, lipids, and cofactors that are essential to biological function.

Unveiling the Cerium(III)/(IV) Structures and Charge-Transfer Mechanism in Sulfuric Acid

The Ce³⁺/Ce⁴⁺ redox couple has a charge transfer (CT) with extreme asymmetry and a large shift in redox potential depending on electrolyte composition. The redox potential shift and CT behavior are difficult to understand because neither the cerium structures nor the CT mechanism are well understood, limiting efforts to improve the Ce³⁺/Ce⁴⁺ redox kinetics in applications such as energy storage. Herein, we identify the Ce³⁺ and Ce⁴⁺ structures and CT mechanism in sulfuric acid via extended X-ray absorption fine structure spectroscopy (EXAFS), kinetic measurements, and density functional theory (DFT) calculations. We show EXAFS evidence that confirms that Ce³⁺ is coordinated by nine water molecules and suggests that Ce⁴⁺ is complexed by water and three bisulfates in sulfuric acid. Despite the change in complexation within the first coordination shell between Ce³⁺ and Ce⁴⁺, we show that the kinetics are independent of the electrode, suggesting outer-sphere electron-transfer behavior. We identify a two-step mechanism where Ce⁴⁺ exchanges the bisulfate anions with water in a chemical step followed by a rate-determining electron transfer step that follows Marcus theory (MT). This mechanism is consistent with all experimentally observed structural and kinetic data. The asymmetry of the Ce³⁺/Ce⁴⁺ CT and the observed shift in the redox potential with acid is explained by the addition of the chemical step in the CT mechanism. The fitted parameters from this rate law qualitatively agree with DFT-predicted free energies and the reorganization energy. The combination of a two-step mechanism with MT should be considered for other metal ion CT reactions whose kinetics have not been appropriately described.

The role of the γ subunit in the photosystem of the lowest-energy phototrophs

Purple phototrophic bacteria use a 'photosystem' consisting of light harvesting complex 1 (LH1) surrounding the reaction centre (RC) that absorbs far-red-near-infrared light and converts it to chemical energy. Blastochloris species, which harvest light >1000 nm, use bacteriochlorophyll b rather than the more common bacteriochlorophyll a as their major photopigment, and assemble LH1 with an additional polypeptide subunit, LH1γ, encoded by multiple genes. To assign a role to γ, we deleted the four encoding genes in the model Blastochloris viridis. Interestingly, growth under halogen bulbs routinely used for cultivation yielded cells displaying an absorption maximum of 825 nm, similar to that of the RC only, but growth under white light yielded cells with an absorption maximum at 972 nm. HPLC analysis of pigment composition and sucrose gradient fractionation demonstrate that the white light-grown mutant assembles RC-LH1, albeit with an absorption maximum blue-shifted by 46 nm. Wavelengths between 900-1000 nm transmit poorly through the atmosphere due to absorption by water, so our results provide an evolutionary rationale for incorporation of γ; this polypeptide red-shifts absorption of RC-LH1 to a spectral range in which photons are of lower energy but are more abundant. Finally, we transformed the mutant with plasmids encoding natural LH1γ variants and demonstrate that the polypeptide found in the wild type complex red-shifts absorption back to 1018 nm, but incorporation of a distantly related variant results in only a moderate shift. This result suggests that tuning the absorption of RC-LH1 is possible and may permit photosynthesis past its current low-energy limit.

In memory of Vladimir Anatolievich Shuvalov (1943-2022): an outstanding biophysicist

We present here a tribute to one of the foremost biophysicists of our time, Vladimir Anatolievich Shuvalov, who made important contributions in bioenergetics, especially on the primary steps of conversion of light energy into charge-separated states in both anoxygenic and oxygenic photosynthesis. For this, he and his research team exploited pico- and femtosecond transient absorption spectroscopy, photodichroism & circular dichroism spectroscopy, light-induced FTIR (Fourier-transform infrared) spectroscopy, and hole-burning spectroscopy. We remember him for his outstanding leadership and for being a wonderful mentor to many scientists in this area. Reminiscences by many [Suleyman Allakhverdiev (Russia); Robert Blankenship (USA); Richard Cogdell (UK); Arvi Freiberg (Estonia); Govindjee Govindjee (USA); Alexander Krasnovsky, jr, (Russia); William Parson (USA); Andrei Razjivin (Russia); Jian- Ren Shen (Japan); Sergei Shuvalov (Russia); Lyudmilla Vasilieva (Russia); and Andrei Yakovlev (Russia)] have included not only his wonderful personal character, but his outstanding scientific research.

Controlling Symmetry Breaking Charge Transfer in BODIPY Pairs

ConspectusSymmetry breaking charge transfer (SBCT) is a process in which a pair of identical chromophores absorb a photon and use its energy to transfer an electron from one chromophore to the other, breaking the symmetry of the chromophore pair. This excited state phenomenon is observed in photosynthetic organisms where it enables efficient formation of separated charges that ultimately catalyze biosynthesis. SBCT has also been proposed as a means for developing photovoltaics and photocatalytic systems that operate with minimal energy loss. It is known that SBCT in both biological and artificial systems is in part made possible by the local environment in which it occurs, which can move to stabilize the asymmetric SBCT state. However, how environmental degrees of freedom act in concert with steric and structural constraints placed on a chromophore pair to dictate its ability to generate long-lived charge pairs via SBCT remain open topics of investigation.In this Account, we compare a broad series of dipyrrin dimers that are linked by distinct bridging groups to discern how the spatial separation and mutual orientation of linked chromophores and the structural flexibility of their linker each impact SBCT efficiency. Across this material set, we observe a general trend that SBCT is accelerated as the spatial separation between dimer chromophores decreases, consistent with the expectation that the electronic coupling between these units varies exponentially with their separation. However, one key observation is that the rate of charge recombination following SBCT was found to slow with decreasing interchromophore separation, rather than speed up. This stems from an enhancement of the dimer's structural rigidity due to increasing steric repulsion as the length of their linker shrinks. This rigidity further inhibits charge recombination in systems where symmetry has already enforced zero HOMO-LUMO overlap. Additionally, for the forward transfer, the active torsion is shown to increase LUMO-LUMO coupling, allowing for faster SBCT within bridging groups.By understanding trends for how rates of SBCT and charge recombination depend on a dimer's internal structure and its environment, we identify design guidelines for creating artificial systems for driving sustained light-induced charge separation. Such systems can find application in solar energy technologies and photocatalytic applications and can serve as a model for light-induced charge separation in biological systems.

Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile QB pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.

Exploiting neutron scattering contrast variation in biological membrane studies

Biological membranes composed of lipids and proteins are central for the function of all cells and individual components, such as proteins, that are readily studied by a range of structural approaches, including x-ray crystallography and cryo-electron microscopy. However, the study of complex molecular mixtures within the biological membrane structure and dynamics requires techniques that can study nanometer thick molecular bilayers in an aqueous environment at ambient temperature and pressure. Neutron methods, including scattering and spectroscopic approaches, are useful since they can measure structure and dynamics while also being able to penetrate sample holders and cuvettes. The structural approaches, such as small angle neutron scattering and neutron reflectometry, detect scattering caused by the difference in neutron contrast (scattering length) between different molecular components such as lipids or proteins. Usually, the bigger the contrast, the clearer the structural data, and this review uses examples from our research to illustrate how contrast can be increased to allow the structures of individual membrane components to be resolved. Most often this relies upon the use of deuterium in place of hydrogen, but we also discuss the use of magnetic contrast and other elements with useful scattering length values.

Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO₂-concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

Systematic phenotyping of 58,101 mutants of the model eukaryotic alga Chlamydomonas reinhardtii under 121 environmental and chemical stress conditions provides a large resource for characterizing gene function.

Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept

At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.

Isomerization kinetics of bacteriochlorophyll b and bacteriopheophytin b under acidic conditions

Bacteriochlorophyll (BChl) b has a unique π-conjugation system, in which the bacteriochlorin macrocycle is conjugated with the C8-ethylidene group. This π-system is converted easily to the chlorin macrocycle. However, the effects of the central magnesium in BChl b on this conversion are unclear. In this study, the isomerization kinetics of BChl b and its demetalated pigment, bacteriopheophytin (BPhe) b, was analyzed under weakly acidic conditions. BChl b exhibited faster acid-induced isomerization than BPhe b. These results were attributed to the stabilization of a cationic intermediate, whose C8-ethylidene group is protonated, during the isomerization of BChl b compared to BPhe b because of a difference in the electron densities of the π-conjugation systems between BChl b and BPhe b. High-performance liquid chromatography analyses indicated that BChl b was primarily isomerized to 3-acetyl Chl a, followed by demetalation. The reaction order was due to the slower demetalation kinetics of metallobacteriochlorins than metallochlorins. These results will be helpful for handling unstable BChl b and BPhe b. The reaction properties of BChl b and BPhe b demonstrated here will be helpful for understanding the in vivo formation of BPhe b, which acts as the primary electron acceptor in photosynthetic reaction center complexes in BChl b-containing purple photosynthetic bacteria.

Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen

In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.

Charge-Transfer in Panchromatic Porphyrin-Tetracyanobuta-1,3-Diene-Donor Conjugates: Switching the Role of Porphyrin in the Charge Separation Process

Using a combination of cycloaddition-retroelectrocyclization reaction, free-base and zinc porphyrins (H₂ P and ZnP) are decorated at their β-pyrrole positions with strong charge transfer complexes, viz., tetracyanobuta-1,3-diene (TCBD)-phenothiazine (3 and 4) or TCBD-aniline (7 and 8), novel class of push-pull systems. The physico-chemical properties of these compounds (MP-Donor and MP-TCBD-Donor) have been investigated using a range of electrochemical, spectroelectrochemical, DFT as well as steady-state and time-resolved spectroscopic techniques. Ground-state charge transfer interactions between the porphyrin and the electron-withdrawing TCBD directly attached to the porphyrin π-system extended the absorption features well into the near-infrared region. To visualize the photo-events, energy level diagrams with the help of free-energy calculations have been established. Switching the role of porphyrin from the initial electron acceptor to electron donor was possible to envision. Occurrence of photoinduced charge separation has been established by complementary transient absorption spectral studies followed by global and target data analyses. Better charge stabilization in H₂ P derived over ZnP derived conjugates, and in phenothiazine derived over aniline derived conjugates has been possible to establish. These findings highlight the importance of the nature of porphyrins and second electron donor in governing the ground and excited state charge transfer events in closely positioned donor-acceptor conjugates.

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).

Donor-acceptor conjugates derived from cobalt porphyrin and fullerene via metal-ligand axial coordination: Formation and excited state charge separation

Two types of cobalt porphyrins, viz., meso-tetrakis(tolylporphyrinato)cobalt(II), (TTP)Co (1), and meso-tetrakis(triphenylamino porphyrinato)cobalt(II), [(TPA)4P]Co, (2) were self-assembled via metal-ligand axial coordination of phenyl imidazole functionalized fulleropyrrolidine, ImC[Formula: see text] to form a new series of donor–acceptor constructs. A 1:2 complex formation with ImC[Formula: see text] was established in the case of (TTP)Co while for [(TPA)4P]Co only a 1:1 complex was possible to positively identify. The binding constants [Formula: see text] and [Formula: see text] for step-wise addition of ImC[Formula: see text] to (TTP)Co were found to be 1.07 × 105 and 3.20 × 104 M[Formula: see text], respectively. For [(TPA)4P]Co:ImC[Formula: see text], the measured [Formula: see text] values was found to be 6.48 × 104 M[Formula: see text], slightly smaller than that observed for (TTP)Co. Although both cobalt porphyrins were non-fluorescent, they were able to quench the fluorescence of ImC[Formula: see text] indicating occurrence of excited state events in the supramolecular donor-acceptor complexes. Electrochemistry coupled with spectroelectrochemistry, revealed the formation of cobalt(III) porphyrin cation instead of a cobalt(II) porphyrin radical cation, as the main product, during oxidation of phenyl imidazole coordinated cobalt porphyrin. With the help of computational and electrochemical results, an energy level diagram was constructed to witness excited state photo-events. Competitive energy and electron transfer from excited CoP to coordinated ImC[Formula: see text], and electron transfer from Im1C[Formula: see text]* to cobalt(II) porphyrin resulting into the formation of PCo[Formula: see text]:ImC[Formula: see text] charge separated state was possible to envision from the energy diagram. Finally, using femtosecond transient absorption spectroscopy and data analysis by Glotaran, it was possible to establish sequential occurrence of energy transfer and charge separation processes. The lifetime of the final charge separated state was [Formula: see text] 2 ns. A slightly better charge stabilization was observed in the case of [(TPA)4P]Co:ImC[Formula: see text] due to the presence of electron rich, peripheral triphenylamine substituents on the cobalt porphyrin.

Meso-Biphenyl-Linked, Near- and Far-Infrared Emitting, Chlorin and Bacteriochlorin Dimers: Synthesis, Excitation Transfer, and Singlet Oxygen Production

A series of meso-biphenyl linked chlorin and bacteriochlorin dimers, derived from naturally occurring chlorophyll (Chl-a) and bacteriochlorophyll (BChl-a) were synthesized in 32 % to 44 % yields and characterized, as photosynthetic antenna mimics, and a new class of singlet oxygen producing agents. The dimers are characterized by absorption, fluorescence, electrochemical, spectroelectrochemical and computational methods to evaluate their physico-chemical properties, and to identify ground and excited state interactions. Evidence of excited energy exchange among the chromophores in the dimer is derived from femtosecond transient absorption spectral studies. Rate constants for excitation hopping were in the order of 1011  s-1 , indicating occurrence of efficient processes. Nanosecond transient absorption studies confirmed relaxation of the singlet excited chlorin and bacteriochlorin dimers to their corresponding triplet states (3 Chl* and 3 Bchl*). As predicted by the established energy level diagrams, both 3 Chl* and 3 Bchl* are shown to be capable of producing singlet oxygen with appreciable quantum yields (ϕSO ∼0.3).

The modified Q-cycle: A look back at its development and forward to a functional model

On looking back at a lifetime of research, it is interesting to see, in the light of current progress, how things came to be, and to speculate on how things might be. I am delighted in the context of the Mitchell prize to have that excuse to present this necessarily personal view of developments in areas of my interests. I have focused on the Q-cycle and a few examples showing wider ramifications, since that had been the main interest of the lab in the 20 years since structures became available, - a watershed event in determining our molecular perspective. I have reviewed the evidence for our model for the mechanism of the first electron transfer of the bifurcated reaction at the Q_o-site, which I think is compelling. In reviewing progress in understanding the second electron transfer, I have revisited some controversies to justify important conclusions which appear, from the literature, not to have been taken seriously. I hope this does not come over as nitpicking. The conclusions are important to the final section in which I develop an internally consistent mechanism for turnovers of the complex leading to a state similar to that observed in recent rapid-mix/freeze-quench experiments, reported three years ago. The final model is necessarily speculative but is open to test.

Formation of a tris(catecholato) iron(III) complex with a nature-inspired cyclic peptoid ligand

Siderophore-mimicking macrocyclic peptoids were synthesized. Peptoid 3 with intramolecular hydrogen bonds showed an optimally arranged primary coordination sphere leading to a stable catecholate-iron complex. The tris(catecholato) structure of 3-Fe(iii) was determined with UV-vis, fluorescence, and EPR spectroscopies and DFT calculations. The iron binding affinity was comparable to that of deferoxamine, with enhanced stability upon air exposure.

The Mechanisms of Electrogenic Reactions in Bacterial Photosynthetic Reaction Centers: Studies in Collaboration with Alexander Konstantinov

In this review, we discuss our studies conducted in 1985-1988 in collaboration with A. A. Konstantinov, one of the top scientists in the field of membrane bioenergetics. Studying fast kinetics of membrane potential generation in photosynthetic reaction centers (RCs) of purple bacteria in response to a laser flash has made it possible to examine in detail the mechanisms of electrogenic reactions at the donor and acceptor sides of RCs. Electrogenesis associated with the intraprotein electron transfer from the exogenous secondary donors, redox dyes, and soluble cytochrome (cyt) c to the photooxidized dimer of bacteriochlorophyll P₈₇₀ was studied using proteoliposomes containing RCs from the non-sulfur purple bacterium Rhodospirillum rubrum. It was found that reduction of the secondary quinone electron acceptor Q_B accompanied by its protonation in the chromatophores from R. rubrum in response to every second light flash was electrogenic. Spectral characteristics and redox potentials of the four hemes in the tightly bound cyt c in the RC of Blastochloris viridis and electrogenic reactions associated with the electron transfer within the RC complex were identified. For the first time, relative amplitudes of the membrane potential generated in the course of individual electrogenic reactions were compared with the distances between the redox cofactors determined based on the three-dimensional structure of the Bl. viridis RC.

X-ray diffraction analysis of matter taking into account the second harmonic in the scattering of powerful ultrashort pulses of an electromagnetic field

It is well known that the scattering of ultrashort pulses (USPs) of an electromagnetic field in the X-ray frequency range can be used in diffraction analysis. When such USPs are scattered by various polyatomic objects, a diffraction pattern appears from which the structure of the object can be determined. Today, there is a technical possibility of creating powerful USP sources and the analysis of the scattering spectra of such pulses is a high-precision instrument for studying the structure of matter. As a rule, such scattering occurs at a frequency close to the carrier frequency of the incident USP. In this work, it is shown that for high-power USPs, where the magnetic component of USPs cannot be neglected, scattering at the second harmonic appears. The scattering of USPs by the second harmonic has a characteristic diffraction pattern which can be used to judge the structure of the scattering object; combining the scattering spectra at the first and second harmonics therefore greatly enhances the diffraction analysis of matter. Scattering spectra at the first and second harmonics are shown for various polyatomic objects: examples considered are 2D and 3D materials such as graphene, carbon nanotubes, and hybrid structures consisting of nanotubes. The theory developed in this work can be applied to various multivolume objects and is quite simple for X-ray structural analysis, because it is based on analytical expressions.

The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways

We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from Marichromatium (Mch.) purpuratum determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.

Membrane lipids and transporter function

Transport proteins are essential for cells in allowing the exchange of substances between cells and their environment across the lipid bilayer forming a tight barrier. Membrane lipids modulate the function of transmembrane proteins such as transporters in two ways: Lipids are tightly and specifically bound to transport proteins and in addition they modulate from the bulk of the lipid bilayer the function of transport proteins. This overview summarizes currently available information at the ultrastructural level on lipids tightly bound to transport proteins and the impact of altered bulk membrane lipid composition. Human diseases leading to altered lipid homeostasis will lead to altered membrane lipid composition, which in turn affect the function of transporter proteins.

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank

Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.

Pd-Catalyzed Cross Coupling Strategy for Functional Porphyrin Arrays

Porphyrin arrays are an important class of compounds to study interporphyrin electronic interactions that are crucial in determining the rates of energy transfer and electron transfer reactions. When the electronic interactions become stronger, porphyrin arrays exhibit significantly altered optical and electronic properties owing to large oscillator strength and flexible electronic nature of porphyrins. In addition, porphyrins accept various metal cation in their cavities and the interporphyrin interactions depend upon the coordinated metal. With these in the background, porphyrin arrays have been extensively explored as sensors, multielectron catalysts, photodynamic therapy reagents, artificial photosynthetic antenna, nonlinear optical materials, and so on. Here, we review the synthesis of porphyrin arrays by palladium-catalyzed cross-coupling reactions, which are quite effective to construct carbon-carbon bonds and carbon-nitrogen bonds in porphyrin substrates. Palladium-catalyzed cross coupling reactions employed so far are Suzuki-Miyaura coupling reaction, Sonogashira coupling reaction, Buchwald-Hartwig amination, Mizoroki-Heck reaction, Migita-Kosugi-Stille coupling reaction, and so on. In each case, the representative examples and synthetic advantages are discussed.

One-Photon Excitation Followed by a Three-Step Sequential Energy-Energy-Electron Transfer Leading to a Charge-Separated State in a Supramolecular Tetrad Featuring Benzothiazole-Boron-Dipyrromethene-Zinc Porphyrin-C60

A panchromatic triad, consisting of benzothiazole (BTZ) and BF₂ -chelated boron-dipyrromethene (BODIPY) moieties covalently linked to a zinc porphyrin (ZnP) core, has been synthesized and systematically characterized by using ¹ H NMR spectroscopy, ESI-MS, UV-visible, steady-state fluorescence, electrochemical, and femtosecond transient absorption techniques. The absorption band of the triad, BTZ-BODIPY-ZnP, and dyads, BTZ-BODIPY and BODIPY-ZnP, along with the reference compounds BTZ-OMe, BODIPY-OMe, and ZnP-OMe exhibited characteristic bands corresponding to individual chromophores. Electrochemical measurements on BTZ-BODIPY-ZnP exhibited redox behavior similar to that of the reference compounds. Upon selective excitation of BTZ (≈290 nm) in the BTZ-BODIPY-ZnP triad, the fluorescence of the BTZ moiety is quenched, due to photoinduced energy transfer (PEnT) from ¹ BTZ^* to the BODIPY moiety, followed by quenching of the BODIPY emission due to sequential PEnT from the ¹ BODIPY* moiety to ZnP, resulting in the appearance of the ZnP emission, indicating the occurrence of a two-step singlet-singlet energy transfer. Further, a supramolecular tetrad, BTZ-BODIPY-ZnP:ImC₆₀ , was formed by axially coordinating the triad with imidazole-appended fulleropyrrolidine (ImC₆₀ ), and parallel steady-state measurements displayed the diminished emission of ZnP, which clearly indicated the occurrence of photoinduced electron transfer (PET) from ¹ ZnP* to ImC₆₀ . Finally, femtosecond transient absorption spectral studies provided evidence for the sequential occurrence of PEnT and PET events, namely, ¹ BTZ^* -BODIPY-ZnP:ImC₆₀ →BTZ-¹ BODIPY^* -ZnP:ImC₆₀ →BTZ-BODIPY-¹ ZnP^* :ImC₆₀ →BTZ-BODIPY-ZnP^.+ :ImC₆₀ ^.- in the supramolecular tetrad. The evaluated rate of energy transfer, k_EnT , was found to be 3-5×10¹⁰  s^-1 , which was slightly faster than that observed in the case of BODIPY-ZnP and BTZ-BODIPY-ZnP, lacking the coordinated ImC₆₀ . The rate constants for charge separation and recombination, k_CS and k_CR , respectively, calculated by monitoring the rise and decay of C₆₀ ^.- were found to be 5.5×10¹⁰ and 4.4×10⁸  s^-1 , respectively, for the BODIPY-ZnP:ImC₆₀ triad, and 3.1×10¹⁰ and 4.9×10⁸  s^-1 , respectively, for the BTZ-BODIPY-ZnP:ImC₆₀ tetrad. Initial excitation of the tetrad, promoting two-step energy transfer and a final electron-transfer event, has been successfully demonstrated in the present study.

Vibrational Coupling in Solvated H3O+: Interplay between Fermi Resonance and Combination Band

Complex vibrational features of solvated hydronium ion, H₃O⁺, in 3 μm enable us to look into the vibrational coupling among O-H stretching modes and other degrees of freedom. Two anharmonic coupling schemes have often been engaged to explain observed spectra: coupling with the OH bending overtone, known as Fermi resonance (FR), has been proposed to account for the splitting of the OH stretch band at ∼3300 cm^-1 in H₃O⁺···Ar₃, but an additional peak in H₃O⁺···(N₂)₃ at the similar frequency region has been assigned to a combination band (CB) with the low-frequency intermolecular stretches. While even stronger vibrational coupling is expected in H₃O⁺···(H₂O)₃, such pronounced peaks are absent. In the present study, vibrational spectra of H₃O⁺···Kr₃ and H₃O⁺···(CO)₃ are measured to complement the existing spectra. Using ab initio anharmonic algorithms, we are able to assign the observed complex spectral features, to resolve seemingly contradictory notions in the interpretations, and to reveal simple pictures of the interplay between FR and CB.

Charge stabilization via electron exchange: excited charge separation in symmetric, central triphenylamine derived, dimethylaminophenyl-tetracyanobutadiene donor-acceptor conjugates

Photoinduced charge separation in donor-acceptor conjugates plays a pivotal role in technology breakthroughs, especially in the areas of efficient conversion of solar energy into electrical energy and fuels. Extending the lifetime of the charge separated species is a necessity for their practical utilization, and this is often achieved by following the mechanism of natural photosynthesis where the process of electron/hole migration occurs distantly separating the radical ion pairs. Here, we hypothesize and demonstrate a new mechanism to stabilize the charge separated states via the process of electron exchange among the different acceptor entities in multimodular donor-acceptor conjugates. For this, star-shaped, central triphenylamine derived, dimethylamine-tetracyanobutadiene conjugates have been newly designed and characterized. Electron exchange was witnessed upon electroreduction in conjugates having multiple numbers of electron acceptors. Using ultrafast spectroscopy, the occurrence of excited state charge separation, and the effect of electron exchange in prolonging the lifetime of charge separated states in the conjugates having multiple acceptors have been successfully demonstrated. This work constitutes the first example of stabilizing charge-separated states via the process of electron exchange.

Protein Matrix Control of Reaction Center Excitation in Photosystem II

Photosystem II (PSII) is a multisubunit pigment-protein complex that uses light-induced charge separation to power oxygenic photosynthesis. Its reaction center chromophores, where the charge transfer cascade is initiated, are arranged symmetrically along the D1 and D2 core polypeptides and comprise four chlorophyll (PD1, PD2, ChlD1, ChlD2) and two pheophytin molecules (PheoD1 and PheoD2). Evolution favored productive electron transfer only via the D1 branch, with the precise nature of primary excitation and the factors that control asymmetric charge transfer remaining under investigation. Here we present a detailed atomistic description for both. We combine large-scale simulations of membrane-embedded PSII with high-level quantum-mechanics/molecular-mechanics (QM/MM) calculations of individual and coupled reaction center chromophores to describe reaction center excited states. We employ both range-separated time-dependent density functional theory and the recently developed domain based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD), the first coupled cluster QM/MM calculations of the reaction center. We find that the protein matrix is exclusively responsible for both transverse (chlorophylls versus pheophytins) and lateral (D1 versus D2 branch) excitation asymmetry, making ChlD1 the chromophore with the lowest site energy. Multipigment calculations show that the protein matrix renders the ChlD1 → PheoD1 charge-transfer the lowest energy excitation globally within the reaction center, lower than any pigment-centered local excitation. Remarkably, no low-energy charge transfer states are located within the "special pair" PD1-PD2, which is therefore excluded as the site of initial charge separation in PSII. Finally, molecular dynamics simulations suggest that modulation of the electrostatic environment due to protein conformational flexibility enables direct excitation of low-lying charge transfer states by far-red light.

Perturbation of the primary acceptor chlorophyll site in the heliobacterial reaction center by coordinating amino acid substitution

All known Type I photochemical reaction center protein complexes contain a form of the pigment chlorophyll a in their primary electron acceptor site (termed ec3). In the reaction center from the primitive heliobacteria (HbRC), all of the pigment cofactors are bacteriochlorophyll g except in the ec3 sites, which contain 8¹-hydroxychlorophyll a. To explore the energetic flexibility of this site, we performed site-directed mutagenesis on two of the amino acids of the PshA core polypeptide responsible for coordinating the 8¹-hydroxychlorophyll a. These two amino acids are serine-545, which coordinates the central Mg(II) through an intermediary water molecule, and serine-553, which participates in a hydrogen bond with the 13¹-keto O atom. Mutagenesis of serine-545 to histidine (S545H) changes how the chlorophyll's central Mg(II) is coordinated, with the result of decreasing the chlorophyll's site energy. Mutagenesis of serine-545 to methionine (S545M), which was made to mimic the ec3 site of Photosystem I, abolishes chlorophyll binding and charge separation altogether. Mutagenesis of serine-553 to alanine (S553A) removes the aforementioned hydrogen bond, increasing the site energy of the chlorophyll. In the S545H and S553A mutants, the forward and reverse electron transfer rates from ec3 are both faster. This coincides with a decrease in both the quantum yield of initial charge separation and the overall photochemical quantum yield. Taken together, these data indicate that wild-type HbRC is optimized for overall photochemical efficiency, rather than just for maximizing the forward electron transfer rate. The necessity for a chlorophyll a derivative at the ec3 site is also discussed.

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.

Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments

Serial crystallography is having an increasing impact on structural biology. This emerging technique opens up new possibilities for studying protein structures at room temperature and investigating structural dynamics using time-resolved X-ray diffraction. A limitation of the method is the intrinsic need for large quantities of well ordered micrometre-sized crystals. Here, a method is presented to screen for conditions that produce microcrystals of membrane proteins in the lipidic cubic phase using a well-based crystallization approach. A key advantage over earlier approaches is that the progress of crystal formation can be easily monitored without interrupting the crystallization process. In addition, the protocol can be scaled up to efficiently produce large quantities of crystals for serial crystallography experiments. Using the well-based crystallization methodology, novel conditions for the growth of showers of microcrystals of three different membrane proteins have been developed. Diffraction data are also presented from the first user serial crystallography experiment performed at MAX IV Laboratory.

Covalently Linked Bis(Amido-Corroles): Inter- and Intramolecular Hydrogen-Bond-Driven Supramolecular Assembly

Four bis-corroles linked by diamide bridges were synthesized through peptide-type coupling of a trans-A₂ B-corrole acid with aliphatic and aromatic diamines. In the solid state, the hydrogen-bond pattern in these bis-corroles is strongly affected by the type of solvent used in the crystallization process. Although intramolecular hydrogen bonds play a decisive role, they are supported by intermolecular hydrogen bonds and weak N-H⋅⋅⋅π interactions between molecules of toluene and the corrole cores. In an analogy to mono(amido-corroles), both in crystalline state and in solutions, the aliphatic or aromatic bridge is located directly above the corrole ring. When either ethylenediamine or 2,3-diaminonaphthalene are used as linkers, incorporation of polar solvents into the crystalline lattice causes a roughly parallel orientation of the corrole rings. At the same time, both NHCO⋅⋅⋅NH corrole hydrogen bonds are intramolecular. In contrast, solvation in toluene causes a distortion with one of the hydrogen bonds being intermolecular. Interestingly, intramolecular hydrogen bonds are always formed between the -NHCO- functionality located further from the benzene ring present at the position 10-meso. In solution, the hydrogen-bonds pattern of the bis(amido-corroles) is strongly affected by the type of the solvent. Compared with toluene (strongly high-field shifted signals), DMSO and pyridine disrupt self-assembly, whereas hexafluoroisopropanol strengthens intramolecular hydrogen bonds.

Coordination self-assembly through weak interactions in meso-dialkoxyphosphoryl-substituted zinc porphyrinates

The self-assembly of seven zinc 10-(dialkoxyphosphoryl)-5,15-diarylporphyrinates Zn5-Zn11 containing different substituents at the phosphonate and aryl groups was investigated. Single crystals of Zn5-Zn9 complexes were grown under the same conditions and analyzed by X-ray structural analysis. A supramolecular self-assembly is observed in all crystals through weak coordinative bonding of the phosphoryl group of one porphyrin molecule to the zinc(ii) ion of a second molecule. The geometry of the porphyrin macrocycle is similar in all of the studied crystals and the central zinc atom in each case adopts a distorted tetragonal pyramidal environment. However, the Zn5-Zn7 porphyrins display a 1D polymeric structure while the Zn8 and Zn9 complexes exist as discrete cyclotetramers in the crystals. This data demonstrates that the non-coordinating meso-aryl substituents of meso-(dialkoxyphosphoryl)porphyrins influence their crystalline organization. A self-assembly of the Zn5-Zn11 complexes is also observed in toluene and chloroform solutions over a large temperature range (223-323 K). According to NMR studies, the associates exhibit dynamic behavior. A well-defined supramolecular aggregate of complex Zn10 at 10-3 M in toluene and chloroform solutions was unambiguously characterized as a cyclotetramer [Zn10]4 by 1H NMR spectroscopy at 223 K. The structure of the Zn10 association in toluene and chloroform shows a concentration dependence. When a solution of Zn10 in toluene was diluted from 10-3 M to 10-5 M, the average number of molecules in the associated unit decreased to about two.