Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems

A Molecular Level Approach To Elucidate the Supramolecular Packing of Light-Harvesting Antenna Systems

The molecular geometry and supramolecular packing of two bichromophoric prototypic light harvesting compounds D1A2 and D2A2, consisting of two naphthylimide energy donors that were attached to the 1,7 bay positions of a perylene monoimide diester energy acceptor, have been determined by a hybrid approach using magic angle spinning NMR spectroscopy and electron nano-crystallography (ENC), followed by modelling. NMR shift constraints, combined with the P 1 ‾ space group obtained from ENC, were used to generate a centrosymmetric dimer of truncated perylene fragments. This racemic packing motif is used in a biased molecular replacement approach to generate a partial 3D electrostatic scattering potential map. Resolving the structure of the bay substituents is guided by the inversion symmetry, and the distance constraints obtained from heteronuclear correlation spectra. The antenna molecules form a pseudocrystalline lattice of antiparallel centrosymmetric dimers with pockets of partially disordered bay substituents. The two molecules in a unit cell form a butterfly-type arrangement. The hybrid methodology that has been developed is robust and widely applicable for critical structural underpinning of self-assembling structures of large organic molecules.

Connectivity of centermost chromatophores in Rhodobacter sphaeroides bacteria

The size of whole Rhodobacter sphaeroides prevents 3D visualization of centermost chromatophores in their native environment. This study combines cryo-focused ion beam milling with cryo-electron tomography to probe vesicle architecture both in situ and in 3D. Developing chromatophores are membrane-bound buds that remain in topological continuity with the cytoplasmic membrane and detach into vesicles when mature. Mature chromatophores closest to the cell wall are typically isolated vesicles, whereas centermost chromatophores are either linked to neighboring chromatophores or contain smaller, budding structures. Isolated chromatophores comprised a minority of centermost chromatophores. Connections between vesicles in growing bacteria are through ~10 nm-long, ~5 nm-wide linkers, and are thus physical rather than functional in terms of converting photons to ATP. In cells in the stationary phase, chromatophores fuse with neighboring vesicles, lose their spherical structure, and greatly increase in volume. The fusion and morphological changes seen in older bacteria are likely a consequence of the aging process, and are not representative of connectivity in healthy R. sphaeroides. Our results suggest that chromatophores can adopt either isolated or connected morphologies within a single bacterium. Revealing the organization of chromatophore vesicles throughout the cell is an important step in understanding the photosynthetic mechanisms in R. sphaeroides.

Misconceptions in electronic energy transfer: bridging the gap between chemistry and physics

Many treatments of energy transfer (ET) phenomena in current literature employ incorrect arguments and formulae and are not quantitative enough. This is unfortunate because we witness important breakthroughs from ET experiments in nanoscience. This review aims to clarify basic principles by focusing upon Förster-Dexter electric dipole-electric dipole (ED-ED) ET. The roles of ET in upconversion, downconversion and the antenna effect are described and the clichés and simple formulae to be avoided in ET studies are highlighted with alternative treatments provided.

The Role of Quantum Decoherence in FRET

Resonance energy transfer has become an indispensable experimental tool for single-molecule and single-cell biophysics. Its physical underpinnings, however, are subtle: it involves a discrete jump of excitation from one molecule to another, and so we regard it as a strongly quantum-mechanical process. And yet its kinetics differ from what many of us were taught about two-state quantum systems, quantum superpositions of the states do not seem to arise, and so on. Although J. R. Oppenheimer and T. Förster navigated these subtleties successfully, it remains hard to find an elementary derivation in modern language. The key step involves acknowledging quantum decoherence. Appreciating that aspect can be helpful when we attempt to extend our understanding to situations in which Förster's original analysis is not applicable.

A synthetic biological quantum optical system

In strong plasmon-exciton coupling, a surface plasmon mode is coupled to an array of localized emitters to yield new hybrid light-matter states (plexcitons), whose properties may in principle be controlled via modification of the arrangement of emitters. We show that plasmon modes are strongly coupled to synthetic light-harvesting maquette proteins, and that the coupling can be controlled via alteration of the protein structure. For maquettes with a single chlorin binding site, the exciton energy (2.06 ± 0.07 eV) is close to the expected energy of the Qy transition. However, for maquettes containing two chlorin binding sites that are collinear in the field direction, an exciton energy of 2.20 ± 0.01 eV is obtained, intermediate between the energies of the Qx and Qy transitions of the chlorin. This observation is attributed to strong coupling of the LSPR to an H-dimer state not observed under weak coupling.

Communication: Broad manifold of excitonic states in light-harvesting complex 1 promotes efficient unidirectional energy transfer in vivo

In photosynthetic organisms, the pigment-protein complexes that comprise the light-harvesting antenna exhibit complex electronic structures and ultrafast dynamics due to the coupling among the chromophores. Here, we present absorptive two-dimensional (2D) electronic spectra from living cultures of the purple bacterium, Rhodobacter sphaeroides, acquired using gradient assisted photon echo spectroscopy. Diagonal slices through the 2D lineshape of the LH1 stimulated emission/ground state bleach feature reveal a resolvable higher energy population within the B875 manifold. The waiting time evolution of diagonal, horizontal, and vertical slices through the 2D lineshape shows a sub-100 fs intra-complex relaxation as this higher energy population red shifts. The absorption (855 nm) of this higher lying sub-population of B875 before it has red shifted optimizes spectral overlap between the LH1 B875 band and the B850 band of LH2. Access to an energetically broad distribution of excitonic states within B875 offers a mechanism for efficient energy transfer from LH2 to LH1 during photosynthesis while limiting back transfer. Two-dimensional lineshapes reveal a rapid decay in the ground-state bleach/stimulated emission of B875. This signal, identified as a decrease in the dipole strength of a strong transition in LH1 on the red side of the B875 band, is assigned to the rapid localization of an initially delocalized exciton state, a dephasing process that frustrates back transfer from LH1 to LH2.

Controlling resonance energy transfer in nanostructure emitters by positioning near a mirror

The ability to control light-matter interactions in quantum objects opens up many avenues for new applications. We look at this issue within a fully quantized framework using a fundamental theory to describe mirror-assisted resonance energy transfer (RET) in nanostructures. The process of RET communicates electronic excitation between suitably disposed donor and acceptor particles in close proximity, activated by the initial excitation of the donor. Here, we demonstrate that the energy transfer rate can be significantly controlled by careful positioning of the RET emitters near a mirror. The results deliver equations that elicit new insights into the associated modification of virtual photon behavior, based on the quantum nature of light. In particular, our results indicate that energy transfer efficiency in nanostructures can be explicitly expedited or suppressed by a suitably positioned neighboring mirror, depending on the relative spacing and the dimensionality of the nanostructure. Interestingly, the resonance energy transfer between emitters is observed to "switch off" abruptly under suitable conditions of the RET system. This allows one to quantitatively control RET systems in a new way.

Applicability of transfer tensor method for open quantum system dynamics

Accurate simulations of open quantum system dynamics is a long standing issue in the field of chemical physics. Exact methods exist, but are costly, while perturbative methods are limited in their applicability. Recently a new black-box type method, called transfer tensor method (TTM), was proposed [J. Cerrillo and J. Cao, Phys. Rev. Lett. 112, 110401 (2014)]. It allows one to accurately simulate long time dynamics with a numerical cost of solving a time-convolution master equation, provided many initial system evolution trajectories are obtained from some exact method beforehand. The possible time-savings thus strongly depend on the ratio of total versus initial evolution lengths. In this work, we investigate the parameter regimes where an application of TTM would be most beneficial in terms of computational time. We identify several promising parameter regimes. Although some of them correspond to cases when perturbative theories could be expected to perform well, we find that the accuracy of such approaches depends on system parameters in a more complex way than it is commonly thought. We propose that the TTM should be applied whenever system evolution is expected to be long and accuracy of perturbative methods cannot be ensured or in cases when the system under consideration does not correspond to any single perturbative regime.

Quantum Coherent Excitation Energy Transfer by Carotenoids in Photosynthetic Light Harvesting

It remains an open question whether quantum coherence and molecular excitons created by delocalization of electronic excited states are essential features of the mechanisms that enable efficient light capture and excitation energy transfer to reaction centers in photosynthetic organisms. The peridinin-chlorophyll a protein from marine dinoflagellates is an example of a light-harvesting system with tightly clustered antenna chromophores in which quantum coherence has long been suspected, but unusually it features the carotenoid peridinin as the principal light absorber for mid-visible photons. We report that broad-band two-dimensional electronic spectroscopy indeed reveals the initial presence of exciton relaxation pathways that enable transfer of excitation from peridinin to chlorophyll a in <20 fs, but the quantum coherence that permits this is very short-lived. Strongly coupled excited-state vibrational distortions of the peridinins trigger a dynamic transition of the electronic structure of the system and a rapid conversion to incoherent energy transfer mechanisms.

Mapping the ultrafast flow of harvested solar energy in living photosynthetic cells

Photosynthesis transfers energy efficiently through a series of antenna complexes to the reaction center where charge separation occurs. Energy transfer in vivo is primarily monitored by measuring fluorescence signals from the small fraction of excitations that fail to result in charge separation. Here, we use two-dimensional electronic spectroscopy to follow the entire energy transfer process in a thriving culture of the purple bacteria, Rhodobacter sphaeroides. By removing contributions from scattered light, we extract the dynamics of energy transfer through the dense network of antenna complexes and into the reaction center. Simulations demonstrate that these dynamics constrain the membrane organization into small pools of core antenna complexes that rapidly trap energy absorbed by surrounding peripheral antenna complexes. The rapid trapping and limited back transfer of these excitations lead to transfer efficiencies of 83% and a small functional light-harvesting unit.

During photosynthesis, energy is transferred from photosynthetic antenna to reaction centers via ultrafast energy transfer. Here the authors track energy transfer in photosynthetic bacteria using two-dimensional electronic spectroscopy and show that these transfer dynamics constrain antenna complex organization.

Perspectives on dendritic architectures and their biological applications: From core to cell

The challenges of medicine today include the increasing stipulation for sensitive and effective systems that can improve the pathological responses with a simultaneous reduction in accumulation and drug side effects. The demand can be fulfilled through the advancements in nanomedicine that includes nanostructures and nanodevices for diagnosing, treating, and prevention of various diseases. In this respect, the nanoscience provides various novel techniques with carriers such as micelles, dendrimers, particles and vesicles for the transportation of active moieties. Further, an efficient way to improve these systems is through stimuli a responsive system that utilizes supramolecular hyperbranched structures to meet the above criteria. The stimuli-responsive dendritic architectures exhibit spatial, temporal, convenient, effective, safety and controlled drug release in response to specific trigger through electrostatic interactions plus π stacking. The stimuli-responsive systems are capable of sequestering the drug molecules underneath a predefined set of conditions and discharge them in a different environment through either exogenous or endogenous stimulus. The incorporation of photoresponsive moieties at various components of dendrimer such as core, branches or at the peripheral end exaggerates its significance in various allied fields of nanotechnology which includes sensors, photoswitch, electronic widgets and in drug delivery systems. This is due to the light instigated geometrical modifications at the core or at the surface molecules which generates huge conformational changes throughout the hyperbranched structure. Further, numerous synthetic methodologies have been investigated for utilization of dendrimers in therapeutic drug delivery and its applicability towards stimuli responsive systems such as photo-instigated, thermal-instigated, and pH-instigated hyperbranched structures and their advancement in the field of nanomedicine. This paper highlights the fascinating theoretical advances and principal mechanisms of dendrimer synthesis and their ability to capture light that strengthens its applicability from radiant energy to medical photonics.

Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models

Cell doubling times of the purple bacterium Rhodobacter sphaeroides during photosynthetic growth are determined experimentally and computationally as a function of illumination. For this purpose, energy conversion processes in an intracytoplasmic membrane vesicle, the chromatophore, are described based on an atomic detail structural model. The cell doubling time and its illumination dependence are computed in terms of the return-on-investment (ROI) time of the chromatophore, determined computationally from the ATP production rate, and the mass ratio of chromatophores in the cell, determined experimentally from whole cell absorbance spectra. The ROI time is defined as the time it takes to produce enough ATP to pay for the construction of another chromatophore. The ROI time of the low light-growth chromatophore is 4.5-2.6 h for a typical illumination range of 10-100 μmol photons m^-2 s^-1, respectively, with corresponding cell doubling times of 8.2-3.9 h. When energy expenditure is considered as a currency, the benefit-to-cost ratio computed for the chromatophore as an energy harvesting device is 2-8 times greater than for photovoltaic and fossil fuel-based energy solutions and the corresponding ROI times are approximately 3-4 orders of magnitude shorter for the chromatophore than for synthetic systems.

Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy

The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip-sample interaction in both lateral and vertical directions. Here, long-range tip-sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic "organelles", chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles.

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

We present GPU-accelerated ab initio molecular dynamics simulations of nonadiabatic dynamics in the LH2 complex in full atomistic detail.

Strong Coupling of Localized Surface Plasmons to Excitons in Light-Harvesting Complexes

Gold nanostructure arrays exhibit surface plasmon resonances that split after attaching light harvesting complexes 1 and 2 (LH1 and LH2) from purple bacteria. The splitting is attributed to strong coupling between the localized surface plasmon resonances and excitons in the light-harvesting complexes. Wild-type and mutant LH1 and LH2 from Rhodobacter sphaeroides containing different carotenoids yield different splitting energies, demonstrating that the coupling mechanism is sensitive to the electronic states in the light harvesting complexes. Plasmon-exciton coupling models reveal different coupling strengths depending on the molecular organization and the protein coverage, consistent with strong coupling. Strong coupling was also observed for self-assembling polypeptide maquettes that contain only chlorins. However, it is not observed for monolayers of bacteriochlorophyll, indicating that strong plasmon-exciton coupling is sensitive to the specific presentation of the pigment molecules.

Overall energy conversion efficiency of a photosynthetic vesicle

The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytb⁢c1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12–0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination.

DOI:http://dx.doi.org/10.7554/eLife.09541.001

Photosynthesis, or the conversion of light energy into chemical energy, is a process that powers almost all life on Earth. Plants and certain bacteria share similar processes to perform photosynthesis, though the purple bacterium Rhodobacter sphaeroides uses a photosynthetic system that is much less complex than that in plants. Light harvesting inside the bacterium takes place in up to hundreds of compartments called chromatophores. Each chromatophore in turn contains hundreds of cooperating proteins that together absorb the energy of sunlight and convert and store it in molecules of ATP, the universal energy currency of all cells.

The chromatophore of primitive purple bacteria provides a model for more complex photosynthetic systems in plants. Though researchers had characterized its individual components over the years, less was known about the overall architecture of the chromatophore and how its many components work together to harvest light energy efficiently and robustly. This knowledge would provide insight into the evolutionary pressures that shaped the chromatophore and its ability to work efficiently at different light intensities.

Sener et al. now present a highly detailed structural model of the chromatophore of purple bacteria based on the findings of earlier studies. The model features the position of every atom of the constituent proteins and is used to examine how energy is transferred and converted. Sener et al. describe the sequence of energy conversion steps and calculate the overall energy conversion efficiency, namely how much of the light energy arriving at the microorganism is stored as ATP.

These calculations show that the chromatophore is optimized to produce chemical energy at low light levels typical of purple bacterial habitats, and dissipate excess energy to avoid being damaged under brighter light. The chromatophore’s architecture also displays robustness against perturbations of its components. In the future, the approach used by Sener et al. to describe light harvesting in this bacterial compartment can be applied to more complex systems, such as those in plants.

DOI:http://dx.doi.org/10.7554/eLife.09541.002

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.

Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing

The cellular process responsible for providing energy for most life on Earth, namely photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers.

Contribution of bacteriochlorophyll conformation to the distribution of site-energies in the FMO protein

The structural data for the Fenna-Matthews-Olson (FMO) protein indicate that the bacteriochlorophylls (BChls) display a significant degree of conformational heterogeneity of their peripheral substituents and the protein-induced nonplanar skeletal deformations of the tetrapyrrole macrocycle. As electronic properties of chromophores are altered by such differences, a conformational effect may influence the site-energies of specific pigments and thus play a role in mediating the excitation energy transfer dynamics, but this has not yet been established. The difficulty of assessing this question is shown to be partly the result of the inability of the sequential truncation approach usually employed to account for interactions between the conformations of the macrocycle and its substituents and an alternative approach is suggested. By assigning the BChl atoms to meaningful atom groups and performing all possible permutations of partial optimizations in a full-factorial design, where each group is either frozen in the crystal geometry or optimized in vacuo, followed by excited state calculations on each resulting structure (PM6//ZIndo/S), the specific effects of the conformations of each BChl component as well as mutual interactions between the molecular fragments on the site-energy can be delineated. This factorial relaxation procedure gives different estimates of the macrocycle conformational perturbation than the approach of sequentially truncating the BChl periphery. The results were evaluated in the context of published site-energies for the FMO pigments from three species to identify how conformational effects contribute to their distribution and instances of cross-species conservation and functional divergence of the BChl nonplanarity conformational contribution are described.

Quantifying highly efficient incoherent energy transfer in perylene-based multichromophore arrays

Multichromophore perylene arrays were designed and synthesized to have extremely efficient resonance energy transfer, as confirmed by ultrafast spectroscopy.

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.

Vibrational and coherence dynamics of molecules

The relaxation of coherence in vibrational energy transport in molecules is investigated.

An ‘all pigment’ model of excitation quenching in LHCII

This work presents the first all-pigment microscopic model of a major light-harvesting complex of plants and the first attempt to capture the dissipative character of the known structure.

Photosynthesis at the forefront of a sustainable life

The development of a sustainable bio-based economy has drawn much attention in recent years, and research to find smart solutions to the many inherent challenges has intensified. In nature, perhaps the best example of an authentic sustainable system is oxygenic photosynthesis. The biochemistry of this intricate process is empowered by solar radiation influx and performed by hierarchically organized complexes composed by photoreceptors, inorganic catalysts, and enzymes which define specific niches for optimizing light-to-energy conversion. The success of this process relies on its capability to exploit the almost inexhaustible reservoirs of sunlight, water, and carbon dioxide to transform photonic energy into chemical energy such as stored in adenosine triphosphate. Oxygenic photosynthesis is responsible for most of the oxygen, fossil fuels, and biomass on our planet. So, even after a few billion years of evolution, this process unceasingly supports life on earth, and probably soon also in outer-space, and inspires the development of enabling technologies for a sustainable global economy and ecosystem. The following review covers some of the major milestones reached in photosynthesis research, each reflecting lasting routes of innovation in agriculture, environmental protection, and clean energy production.

Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides

Photosynthesis converts absorbed solar energy to a protonmotive force, which drives ATP synthesis. The membrane network of chlorophyll-protein complexes responsible for light absorption, photochemistry and quinol (QH2) production has been mapped in the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides using atomic force microscopy (AFM), but the membrane location of the cytochrome bc1 (cytbc1) complexes that oxidise QH2 to quinone (Q) to generate a protonmotive force is unknown. We labelled cytbc1 complexes with gold nanobeads, each attached by a Histidine10 (His10)-tag to the C-terminus of cytc1. Electron microscopy (EM) of negatively stained chromatophore vesicles showed that the majority of the cytbc1 complexes occur as dimers in the membrane. The cytbc1 complexes appeared to be adjacent to reaction centre light-harvesting 1-PufX (RC-LH1-PufX) complexes, consistent with AFM topographs of a gold-labelled membrane. His-tagged cytbc1 complexes were retrieved from chromatophores partially solubilised by detergent; RC-LH1-PufX complexes tended to co-purify with cytbc1 whereas LH2 complexes became detached, consistent with clusters of cytbc1 complexes close to RC-LH1-PufX arrays, but not with a fixed, stoichiometric cytbc1-RC-LH1-PufX supercomplex. This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1-RC-PufX dimers & 2 RC-LH1-PufX monomers, 4 cytbc1 dimers and 2 ATP synthases. Simulation of the interconnected energy, electron and proton transfer processes showed a half-maximal ATP turnover rate for a light intensity equivalent to only 1% of bright sunlight. Thus, the photosystem architecture of the chromatophore is optimised for growth at low light intensities.

Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette

The successful use of man-made proteins to advance synthetic biology requires both the fabrication of functional artificial proteins in a living environment, and the ability of these proteins to interact productively with other proteins and substrates in that environment. Proteins made by the maquette method integrate sophisticated oxidoreductase function into evolutionarily naive, non-computationally designed protein constructs with sequences that are entirely unrelated to any natural protein. Nevertheless, we show here that we can efficiently interface with the natural cellular machinery that covalently incorporates heme into natural cytochromes c to produce in vivo an artificial c-type cytochrome maquette. Furthermore, this c-type cytochrome maquette is designed with a displaceable histidine heme ligand that opens to allow functional oxygen binding, the primary event in more sophisticated functions ranging from oxygen storage and transport to catalytic hydroxylation. To exploit the range of functions that comes from the freedom to bind a variety of redox cofactors within a single maquette framework, this c-type cytochrome maquette is designed with a second, non-heme C, tetrapyrrole binding site, enabling the construction of an elementary electron transport chain, and when the heme C iron is replaced with zinc to create a Zn porphyrin, a light-activatable artificial redox protein. The work we describe here represents a major advance in de novo protein design, offering a robust platform for new c-type heme based oxidoreductase designs and an equally important proof-of-principle that cofactor-equipped man-made proteins can be expressed in living cells, paving the way for constructing functionally useful man-made proteins in vivo.

Combined topographic, spectroscopic, and model analyses of inhomogeneous energetic coupling of linear light harvesting complex II aggregates in native photosynthetic membranes

Light harvesting by LH1 and LH2 antenna proteins in the photosynthetic membranes of purple bacteria has been extensively studied in recent years for the fundamental understanding of the energy transfer dynamics and mechanism. Here we report the inhomogeneous structural organization of the LH2 complexes in photosynthetic membranes, giving evidence for the existence of energetically coupled linear LH2 aggregates in the native photosynthetic membranes of purple bacteria. Focusing on systematic model analyses, we combined AFM imaging and spectroscopic analysis with energetic coupling model analysis to characterize the inhomogeneous linear aggregation of LH2. Our AFM imaging results reveal that the LH2 complexes form linear aggregates with the monomer number varying from one to eight and each monomer tilted along the aggregated structure in photosynthetic membranes. The spectroscopic results support the attribution of aggregated LH2 complexes in the photosynthetic membranes, and the model calculation values for the absorption, emission and lifetime are consistent with the experimentally determined spectroscopic values, further proving a molecular-level understanding of the energetic coupling and energy transfer among the LH2 complexes in the photosynthetic membranes.

Extending the range of FRET--the Monte Carlo study of the antenna effect

The problem of extending the utilizable range of Förster resonance energy transfer (FRET) is of great current interest, due to the demand of conformation studies of larger biological structures at distances exceeding typical limiting distance of 100 Å. One of the ways to address this issue is the use of so-called antenna effect. In the present work, the influence of the antenna effect on the FRET efficiency is investigated by the Monte Carlo analysis. The previously published results Bojarski et al. (J Phys Chem B 115:10120–10125, 2011) indicate that using a simple model of donor linked with a protein labeled with multiple acceptors, significantly increases the transfer efficiency in comparison with donor–single acceptor system. The effect is stronger if the transition moments of acceptors are mutually parallel. In this work, to extend the scope of possible biological systems to be analyzed, different distributions of donor–acceptors distance are analyzed, as well as the size and shape of the attached molecule.

A mechanistic model for the light response of photosynthetic electron transport rate based on light harvesting properties of photosynthetic pigment molecules

Models describing the light response of photosynthetic electron transport rate (ETR) are routinely used to determine how light absorption influences energy, reducing power and yields of primary productivity; however, no single model is currently able to provide insight into the fundamental processes that implicitly govern the variability of light absorption. Here we present development and application of a new mechanistic model of ETR for photosystem II based on the light harvesting (absorption and transfer to the core 'reaction centres') characteristics of photosynthetic pigment molecules. Within this model a series of equations are used to describe novel biophysical and biochemical characteristics of photosynthetic pigment molecules and in turn light harvesting; specifically, the eigen-absorption cross-section and the minimum average lifetime of photosynthetic pigment molecules in the excited state, which describe the ability of light absorption of photosynthetic pigment molecules and retention time of excitons in the excited state but are difficult to be measured directly. We applied this model to a series of previously collected fluorescence data and demonstrated that our model described well the light response curves of ETR, regardless of whether dynamic down-regulation of PSII occurs, for a range of photosynthetic organisms (Abies alba, Picea abies, Pinus mugo and Emiliania huxleyi). Inherent estimated parameters (e.g. maximum ETR and the saturation irradiance) by our model are in very close agreement with the measured data. Overall, our mechanistic model potentially provides novel insights into the regulation of ETR by light harvesting properties as well as dynamical down-regulation of PSII.

Does Coherence Enhance Transport in Photosynthesis?

Recent observations of coherence in photosynthetic complexes have led to the question of whether quantum effects can occur in vivo, not under femtosecond laser pulses but in incoherent sunlight and at steady state, and, if so, whether the coherence explains the high exciton transfer efficiency. We introduce the distinction between state coherence and process coherence and show that although some photosynthetic pathways are partially coherent processes, photosynthesis in nature proceeds through stationary states. This distinction allows us to rule out several mechanisms of transport enhancement in sunlight. In particular, although they are crucial for understanding exciton transport, neither wavelike motion nor microscopic coherence, on their own, enhance the efficiency. By contrast, two partially coherent mechanisms-ENAQT and supertransfer-can enhance transport even in sunlight and thus constitute motifs for the optimization of artificial sunlight harvesting. Finally, we clarify the importance of ultrafast spectroscopy in understanding incoherent processes.

Excited state dynamics in photosynthetic reaction center and light harvesting complex 1

Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.

Powering the future of molecular artificial photosynthesis with light-harvesting metallosupramolecular dye assemblies

Chemical ingenuity will play a significant role in solving the greatest challenge currently facing society: providing clean and carbon neutral energy for all of humanity. Molecular artificial photosynthesis is an emerging technology based on principles learned from Nature where individual components perform the essential light-harvesting, charge-separation, and water splitting functions to store solar energy in the form of chemical bonds. This tutorial review focuses specifically on the application of metallosupramolecular self-assembly strategies to interface solar fuel catalysts with photosensitizers and construct light-harvesting antennae capable of achieving panchromatic absorption and directional energy concentration.

How Quantum Coherence Assists Photosynthetic Light Harvesting

This perspective examines how hundreds of pigment molecules in purple bacteria cooperate through quantum coherence to achieve remarkable light harvesting efficiency. Quantum coherent sharing of excitation, which modifies excited state energy levels and combines transition dipole moments, enables rapid transfer of excitation over large distances. Purple bacteria exploit the resulting excitation transfer to engage many antenna proteins in light harvesting, thereby increasing the rate of photon absorption and energy conversion. We highlight here how quantum coherence comes about and plays a key role in the photosynthetic apparatus of purple bacteria.