Photosynthetic vesicle architecture and constraints on efficient energy harvesting

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

Molecular and Supramolecular Materials: From Light-Harvesting to Quantum Information Science and Technology

The past two decades have witnessed immense advances in quantum information technology (QIT), benefited by advances in physics, chemistry, biology, and materials science and engineering. It is intriguing to consider whether these diverse molecular and supramolecular structures and materials, partially inspired by quantum effects as observed in sophisticated biological systems such as light-harvesting complexes in photosynthesis and the magnetic compass of migratory birds, might play a role in future QIT. If so, how? Herein, we review materials and specify the relationship between structures and quantum properties, and we identify the challenges and limitations that have restricted the intersection of QIT and chemical materials. Examples are broken down into two categories: materials for quantum sensing where nonclassical function is observed on the molecular scale and systems where nonclassical phenomena are present due to intermolecular interactions. We discuss challenges for materials chemistry and make comparisons to related systems found in nature. We conclude that if chemical materials become relevant for QIT, they will enable quite new kinds of properties and functions.

Excitation energy transfer in proteoliposomes reconstituted with LH2 and RC-LH1 complexes from Rhodobacter sphaeroides

Light-harvesting 2 (LH2) and reaction-centre light-harvesting 1 (RC-LH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were reconstituted into proteoliposomes either separately, or together at three different LH2:RC-LH1 ratios, for excitation energy transfer studies. Atomic force microscopy (AFM) was used to investigate the distribution and association of the complexes within the proteoliposome membranes. Absorption and fluorescence emission spectra were similar for LH2 complexes in detergent and liposomes, indicating that reconstitution retains the structural and optical properties of the LH2 complexes. Analysis of fluorescence emission shows that when LH2 forms an extensive series of contacts with other such complexes, fluorescence is quenched by 52.6 ± 1.4%. In mixed proteoliposomes, specific excitation of carotenoids in LH2 donor complexes resulted in emission of fluorescence from acceptor RC-LH1 complexes engineered to assemble with no carotenoids. Extents of energy transfer were measured by fluorescence lifetime microscopy; the 0.72 ± 0.08 ns lifetime in LH2-only membranes decreases to 0.43 ± 0.04 ns with a ratio of 2:1 LH2 to RC-LH1, and to 0.35 ± 0.05 ns for a 1:1 ratio, corresponding to energy transfer efficiencies of 40 ± 14% and 51 ± 18%, respectively. No further improvement is seen with a 0.5:1 LH2 to RC-LH1 ratio. Thus, LH2 and RC-LH1 complexes perform their light harvesting and energy transfer roles when reconstituted into proteoliposomes, providing a way to integrate native, non-native, engineered and de novo designed light-harvesting complexes into functional photosynthetic systems.

Light energy transduction in liposome-based artificial cells

In this work we review the latest strategies for the bottom-up assembly of energetically autonomous artificial cells capable of transducing light energy into chemical energy and support internalized metabolic pathways. Such entities are built by taking inspiration from the photosynthetic machineries found in nature which are purified and reconstituted directly in the membrane of artificial compartments or encapsulated in form of organelle-like structures. Specifically, we report and discuss recent examples based on liposome-technology and multi-compartment (nested) architectures pointing out the importance of this matter for the artificial cell synthesis research field and some limitations and perspectives of the bottom-up approach.

Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.

Spatial Patterns of Light-Harvesting Antenna Complex Arrangements Tune the Transfer-to-Trap Efficiency of Excitons in Purple Bacteria

In photosynthesis, the efficiency with which a photogenerated exciton reaches the reaction center is dictated by chromophore energies and the arrangement of chromophores in the supercomplex. Here, we explore the interplay between the arrangement of light-harvesting antennae and the efficiency of exciton transport in purple bacterial photosynthesis. Using a Miller-Abrahams-based exciton hopping model, we compare different arrangements of light-harvesting proteins on the intracytoplasmic membrane. We find that arrangements with aggregated LH1s have a higher efficiency than arrangements with randomly distributed LH1s in a wide range of physiological light fluences. This effect is robust to the introduction of defects on the intracytoplasmic membrane. Our result explains the absence of species with aggregated LH1 arrangements in low-light niches and the large increase seen in the expression of LH1 dimer complexes in high fluences. We suggest that the effect seen in our study is an adaptive strategy toward solar light fluence across different purple bacterial species.

Chromatophores efficiently promote light-driven ATP synthesis and DNA transcription inside hybrid multicompartment artificial cells

The construction of energetically autonomous artificial protocells is one of the most ambitious goals in bottom-up synthetic biology. Here, we show an efficient manner to build adenosine 5'-triphosphate (ATP) synthesizing hybrid multicompartment protocells. Bacterial chromatophores from Rhodobacter sphaeroides accomplish the photophosphorylation of adenosine 5'-diphosphate (ADP) to ATP, functioning as nanosized photosynthetic organellae when encapsulated inside artificial giant phospholipid vesicles (ATP production rate up to ∼100 ATP∙s^-1 per ATP synthase). The chromatophore morphology and the orientation of the photophosphorylation proteins were characterized by cryo-electron microscopy (cryo-EM) and time-resolved spectroscopy. The freshly synthesized ATP has been employed for sustaining the transcription of a DNA gene, following the RNA biosynthesis inside individual vesicles by confocal microscopy. The hybrid multicompartment approach here proposed is very promising for the construction of full-fledged artificial protocells because it relies on easy-to-obtain and ready-to-use chromatophores, paving the way for artificial simplified-autotroph protocells (ASAPs).

Excitation energy transfer between monomolecular layers of light harvesting LH2 and LH1-reaction centre complexes printed on a glass substrate

Light-harvesting 2 (LH2) and light-harvesting 1 - reaction centre (RCLH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were cross-patterned on glass surfaces for energy transfer studies. Atomic force microscopy (AFM) images of the RCLH1 and LH2 patterns show the deposition of monomolecular layers of complexes on the glass substrate. Spectral imaging and fluorescence life-time imaging microscopy (FLIM) revealed that RCLH1 and LH2 complexes, sealed under physiological conditions, retained their native light-harvesting and energy transfer functions. Measurements of the amplitude and lifetime decay of fluorescence emission from LH2 complexes, the energy transfer donors, and gain of fluorescence emission from acceptor RCLH1 complexes, provide evidence for excitation energy transfer from LH2 to RCLH1. Directional energy transfer on the glass substrate was unequivocally established by using LH2-carotenoid complexes and RCLH1 complexes with genetically removed carotenoids. Specific excitation of carotenoids in donor LH2 complexes elicited fluorescence emission from RCLH1 acceptors. To explore the longevity of this novel nanoprinted photosynthetic unit, RCLH1 and LH2 complexes were cross-patterned on a glass surface and sealed under a protective argon atmosphere. The results show that both complexes retained their individual and collective functions and are capable of directional excitation energy transfer for at least 60 days.

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay audience, including children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. Software advancements necessitated by this project have led to significant performance and feature advances, including hardware-accelerated cinematic ray tracing and instanced visualizations for efficient cell-scale modeling. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories-the interplay between light and life.

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.

Slow polymer diffusion on brush-patterned surfaces in aqueous solution

A model system for the investigation of diffusional transport in compartmentalized nanosystems is described. Arrays of "corrals" enclosed within poly[oligo(ethylene glycol)methyl ether methacrylate] (POEGMA) "walls" were fabricated using double-exposure interferometric lithography to deprotect aminosilane films protected by a nitrophenyl group. In exposed regions, removal of the nitrophenyl group enabled attachment of an initiator for the atom-transfer radical polymerization of end-grafted POEGMA (brushes). Diffusion coefficients for poly(ethylene glycol) in these corrals were obtained by fluorescence correlation spectroscopy. Two modes of surface diffusion were observed: one which is similar to diffusion on the unpatterned surface and a very slow mode of surface diffusion that becomes increasingly important as confinement increases. Diffusion within the POEGMA brushes does not significantly contribute to the results.

Impact of the lipid bilayer on energy transfer kinetics in the photosynthetic protein LH2

Photosynthetic purple bacteria convert solar energy to chemical energy with near unity quantum efficiency. The light-harvesting process begins with absorption of solar energy by an antenna protein called Light-Harvesting Complex 2 (LH2). Energy is subsequently transferred within LH2 and then through a network of additional light-harvesting proteins to a central location, termed the reaction center, where charge separation occurs. The energy transfer dynamics of LH2 are highly sensitive to intermolecular distances and relative organizations. As a result, minor structural perturbations can cause significant changes in these dynamics. Previous experiments have primarily been performed in two ways. One uses non-native samples where LH2 is solubilized in detergent, which can alter protein structure. The other uses complex membranes that contain multiple proteins within a large lipid area, which make it difficult to identify and distinguish perturbations caused by protein-protein interactions and lipid-protein interactions. Here, we introduce the use of the biochemical platform of model membrane discs to study the energy transfer dynamics of photosynthetic light-harvesting complexes in a near-native environment. We incorporate a single LH2 from Rhodobacter sphaeroides into membrane discs that provide a spectroscopically amenable sample in an environment more physiological than detergent but less complex than traditional membranes. This provides a simplified system to understand an individual protein and how the lipid-protein interaction affects energy transfer dynamics. We compare the energy transfer rates of detergent-solubilized LH2 with those of LH2 in membrane discs using transient absorption spectroscopy and transient absorption anisotropy. For one key energy transfer step in LH2, we observe a 30% enhancement of the rate for LH2 in membrane discs compared to that in detergent. Based on experimental results and theoretical modeling, we attribute this difference to tilting of the peripheral bacteriochlorophyll in the B800 band. These results highlight the importance of well-defined systems with near-native membrane conditions for physiologically-relevant measurements.

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.

Determination of Controlled Self-Assembly of a Paracrystalline Material by Homology Modelling with Hybrid NMR and TEM

Controlling complexity, flexibility, and functionality of synthetic and biomimetic materials requires insight into how molecular functionalities can be exploited for steering their packing. A fused NDI‐salphen (NDI=naphthalene diimide) prototypic artificial photosynthesis material, DATZnS, is shown to be comprised of a phenazine motif, in which the alignment of electric dipole moments in a P2/c supramolecular scaffold can be modulated with bulky substituents. They can also be switched between parallel stacks of dipoles running antiparallel in the DATZnS‐H compared with parallel stacks of dipoles in polar layers running in opposite directions in the DATZnS(3′‐NMe) parent compound. Spatial correlations obtained from HETCOR spectra, collected with a long cross polarization contact time of 2 ms, reveal an antiparallel stacking for the DATZnS‐H homologue. These constraints and limited data from TEM are used to construct a structural model within the P2/c space group determined by the molecular C₂ symmetry. By using homology modelling, a pseudo octahedral coordination of the Zn is shown to follow the packing‐induced chirality with enantiomeric pairs of the Λ and Δ forms alternating along antiparallel stacks. The model helps to understand how the steric hindrance modulates the self‐assembly in this novel class of fused materials by steric hindrance at the molecular level.

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.

Geometry, Supertransfer, and Optimality in the Light Harvesting of Purple Bacteria

The remarkable rotational symmetry of the photosynthetic antenna complexes of purple bacteria has long been thought to enhance their light harvesting and excitation energy transport. We study the role of symmetry by modeling hypothetical antennas whose symmetry is broken by altering the orientations of the bacteriochlorophyll pigments. We find that in both LH2 and LH1 complexes, symmetry increases energy transfer rates by enabling the cooperative, coherent process of supertransfer. The enhancement is particularly pronounced in the LH1 complex, whose natural geometry outperforms the average randomized geometry by 5.5 standard deviations, the most significant coherence-related enhancement found in a photosynthetic complex.

Biosynthesis of Chlorophyll a in a Purple Bacterial Phototroph and Assembly into a Plant Chlorophyll-Protein Complex

Improvements to photosynthetic efficiency could be achieved by manipulating pigment biosynthetic pathways of photosynthetic organisms in order to increase the spectral coverage for light absorption. The development of organisms that can produce both bacteriochlorophylls and chlorophylls is one way to achieve this aim, and accordingly we have engineered the bacteriochlorophyll-utilizing anoxygenic phototroph Rhodobacter sphaeroides to make chlorophyll a. Bacteriochlorophyll and chlorophyll share a common biosynthetic pathway up to the precursor chlorophyllide. Deletion of genes responsible for the bacteriochlorophyll-specific modifications of chlorophyllide and replacement of the native bacteriochlorophyll synthase with a cyanobacterial chlorophyll synthase resulted in the production of chlorophyll a. This pigment could be assembled in vivo into the plant water-soluble chlorophyll protein, heterologously produced in Rhodobacter sphaeroides, which represents a proof-of-principle for the engineering of novel antenna complexes that enhance the spectral range of photosynthesis.

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

Spectral and kinetic effects accompanying the assembly of core complexes of Rhodobacter sphaeroides

In the present work, spectral and kinetic changes accompanying the assembly of the light-harvesting 1 (LH1) complex with the reaction center (RC) complex into monomeric RC-LH1 and dimeric RC-LH1-PufX core complexes of the photosynthetic purple bacterium Rhodobacter sphaeroides are systematically studied over the temperature range of 4.5-300K. The samples were interrogated with a combination of optical absorption, hole burning, fluorescence excitation, steady state and picosecond time resolved fluorescence spectroscopy. Fair additivity of the LH1 and RC absorption spectra suggests rather weak electronic coupling between them. A low-energy tail revealed at cryogenic temperatures in the absorption spectra of both monomeric and dimeric core complexes is proved to be due to the special pair of the RC. At selected excitation intensity and temperature, the fluorescence decay time of core complexes is shown to be a function of multiple factors, most importantly of the presence/absence of RCs, the supramolecular architecture (monomeric or dimeric) of the complexes, and whether the complexes were studied in a native membrane environment or in a detergent - purified state.

Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation

A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.

Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms

The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing molecules (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solutions for light harvesting. In this review, we describe the underlying photophysical principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment molecules. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.

Distinguishing the roles of energy funnelling and delocalization in photosynthetic light harvesting

Photosynthetic complexes improve the transfer of excitation energy from peripheral antennas to reaction centers in several ways. In particular, a downward energy funnel can direct excitons in the right direction, while coherent excitonic delocalization can enhance transfer rates through the cooperative phenomenon of supertransfer. However, isolating the role of purely coherent effects is difficult because any change to the delocalization also changes the energy landscape. Here, we show that the relative importance of the two processes can be determined by comparing the natural light-harvesting apparatus with counterfactual models in which the delocalization and the energy landscape are altered. Applied to the example of purple bacteria, our approach shows that although supertransfer does enhance the rates somewhat, the energetic funnelling plays the decisive role. Because delocalization has a minor role (and is sometimes detrimental), it is most likely not adaptive, being a side-effect of the dense chlorophyll packing that evolved to increase light absorption per reaction center.

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and β-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain. Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.

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.

All-atom molecular dynamics simulation of a photosystem i/detergent complex

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

Engineered biosynthesis of bacteriochlorophyll b in Rhodobacter sphaeroides

Bacteriochlorophyll b has the most red-shifted absorbance maximum of all naturally occurring photopigments. It has a characteristic ethylidene group at the C8 position in place of the more common ethyl group, the product of a C8-vinyl reductase, which is carried by the majority of chlorophylls and bacteriochlorophylls used in photosynthesis. The subsequent and first step exclusive to bacteriochlorophyll biosynthesis, the reduction of the C7 = C8 bond, is catalyzed by chlorophyllide oxidoreductase. It has been demonstrated that the enzyme from bacteriochlorophyll a-utilizing bacteria can catalyze the formation of compounds carrying an ethyl group at C8 from both ethyl- and vinyl-carrying substrates, indicating a surprising additional C8-vinyl reductase function, while the enzyme from organisms producing BChl b could only catalyze C7 = C8 reduction with a vinyl substrate, but this product carried an ethylidene group at the C8 position. We have replaced the native chlorophyllide oxidoreductase-encoding genes of Rhodobacter sphaeroides with those from Blastochloris viridis, but the switch from bacteriochlorophyll a to b biosynthesis is only detected when the native conventional C8-vinyl reductase is absent. We propose a non-enzymatic mechanism for ethylidene group formation based on the absence of cellular C8-vinyl reductase activity.

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We engineer the production of a foreign photopigment in Rhodobacter sphaeroides.

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Native COR-encoding genes are replaced with those from Blastochloris viridis.

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Bacteriochlorophyll b is produced upon additional deletion of conventional 8VR.

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We propose that loss of 8VR activity by COR leads to ethylidene bond formation.

Organization in photosynthetic membranes of purple bacteria in vivo: the role of carotenoids

Photosynthesis in purple bacteria is performed by pigment-protein complexes that are closely packed within specialized intracytoplasmic membranes. Here we report on the influence of carotenoid composition on the organization of RC-LH1 pigment-protein complexes in intact membranes and cells of Rhodobacter sphaeroides. Mostly dimeric RC-LH1 complexes could be isolated from strains expressing native brown carotenoids when grown under illuminated/anaerobic conditions, or from strains expressing green carotenoids when grown under either illuminated/anaerobic or dark/semiaerobic conditions. However, mostly monomeric RC-LH1 complexes were isolated from strains expressing the native photoprotective red carotenoid spheroidenone, which is synthesized during phototrophic growth in the presence of oxygen. Despite this marked difference, linear dichroism (LD) and light-minus-dark LD spectra of oriented intact intracytoplasmic membranes indicated that RC-LH1 complexes are always assembled in ordered arrays, irrespective of variations in the relative amounts of isolated dimeric and monomeric RC-LH1 complexes. We propose that part of the photoprotective response to the presence of oxygen mediated by synthesis of spheroidenone may be a switch of the structure of the RC-LH1 complex from dimers to monomers, but that these monomers are still organized into the photosynthetic membrane in ordered arrays. When levels of the dimeric RC-LH1 complex were very high, and in the absence of LH2, LD and ∆LD spectra from intact cells indicated an ordered arrangement of RC-LH1 complexes. Such a degree of ordering implies the presence of highly elongated, tubular membranes with dimensions requiring orientation along the length of the cell and in a proportion larger than previously observed.

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.

Structure-based model for light-harvesting properties of nucleic acid nanostructures

Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.

Excitons in intact cells of photosynthetic bacteria

Live cells and regular crystals seem fundamentally incompatible. Still, effects characteristic to ideal crystals, such as coherent sharing of excitation, have been recently used in many studies to explain the behavior of several photosynthetic complexes, especially the inner workings of the light-harvesting apparatus of the oldest known photosynthetic organisms, the purple bacteria. To this date, there has been no concrete evidence that the same effects are instrumental in real living cells, leaving a possibility that this is an artifact of unnatural study conditions, not a real effect relevant to the biological operation of bacteria. Hereby, we demonstrate survival of collective coherent excitations (excitons) in intact cells of photosynthetic purple bacteria. This is done by using excitation anisotropy spectroscopy for tracking the temperature-dependent evolution of exciton bands in light-harvesting systems of increasing structural complexity. The temperature was gradually raised from 4.5 K to ambient temperature, and the complexity of the systems ranged from detergent-isolated complexes to complete bacterial cells. The results provide conclusive evidence that excitons are indeed one of the key elements contributing to the energetic and dynamic properties of photosynthetic organisms.

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.

Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers

Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.

Adaptation of intracytoplasmic membranes to altered light intensity in Rhodobacter sphaeroides

The model photosynthetic bacterium Rhodobacter sphaeroides uses a network of bacteriochlorophyll (BChl)-protein complexes embedded in spherical intracytoplasmic membranes (ICM) to collect and utilise solar energy. We studied the effects of high- and low-light growth conditions, where BChl levels increased approximately four-fold from 1.6×10(6) to 6.5×10(6) molecules per cell. Most of this extra pigment is accommodated in the proliferating ICM system, which increases from approximately 274 to 1468 vesicles per cell. Thus, 16×10(6)nm(2) of specialised membrane surface area is made available for harvesting and utilising solar energy compared to 3×10(6)nm(2) under high-light conditions. Membrane mapping using atomic force microscopy revealed closely packed dimeric and monomeric reaction centre-light harvesting 1-PufX (RC-LH1-PufX) complexes in high-light ICM with room only for small clusters of LH2, whereas extensive LH2-only domains form during adaptation to low light, with the LH2/RC ratio increasing three-fold. The number of upper pigmented band (UPB) sites where membrane invagination is initiated hardly varied; 704 (5.8×10(5) BChls/cell) and 829 (4.9×10(5) BChls/cell) UPB sites per cell were estimated under high- and low-light conditions, respectively. Thus, the lower ICM content in high-light cells is a consequence of fewer ICM invaginations reaching maturity. Taking into account the relatively poor LH2-to-LH1 energy transfer in UPB membranes it is likely that high-light cells are relatively inefficient at energy trapping, but can grow well enough without the need to fully develop their photosynthetic membranes from the relatively inefficient UPB to highly efficient mature ICM.

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.

Carotenoids are essential for normal levels of dimerisation of the RC-LH1-PufX core complex of Rhodobacter sphaeroides: characterisation of R-26 as a crtB (phytoene synthase) mutant

Carotenoids play important roles in photosynthesis where they are involved in light-harvesting, in photo-protection and in the assembly and structural stability of light-harvesting and reaction centre complexes. In order to examine the effects of carotenoids on the oligomeric state of the reaction centre-light-harvesting 1 -PufX (RC-LH1-PufX) core complex of Rhodobacter sphaeroides two carotenoid-less mutants, TC70 and R-26, were studied. Detergent fractionation showed that in the absence of carotenoids LH2 complexes do not assemble, as expected, but also that core complexes are predominantly found as monomers, although levels of the PufX polypeptide appeared to be unaffected. Analysis of R-26 membranes by electron microscopy and atomic force microscopy reveals arrays of hexagonally packed monomeric RC-LH1-PufX complexes. Transfer of the crtB gene encoding phytoene synthase to TC70 and R-26 restores the normal synthesis of carotenoids demonstrating that the R-26 mutant of Rba. sphaeroides harbours a mutation in crtB, among its other defects. The transconjugant TC70 and R-26 strains containing crtB had regained their ability to assemble wild-type levels of dimeric RC-LH1-PufX core complexes and normal energy transfer pathways were restored, demonstrating that carotenoids are essential for the normal assembly and function of both the LH2 and RC-LH1-PufX complexes in this bacterial photosystem.

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

Förster’s theory of resonant energy transfer underlies a fundamental process in nature, namely the harvesting of sunlight by photosynthetic life forms. The theoretical framework developed by Förster and others describes how electronic excitation migrates in the photosynthetic apparatus of plants, algae, and bacteria from light absorbing pigments to reaction centers where light energy is utilized for the eventual conversion into chemical energy. The demand for highest possible efficiency of light harvesting appears to have shaped the evolution of photosynthetic species from bacteria to plants which, despite a great variation in architecture, display common structural themes founded on the quantum physics of energy transfer as described first by Förster. Herein, Förster’s theory of excitation transfer is summarized, including recent extensions, and the relevance of the theory to photosynthetic systems as evolved in purple bacteria, cyanobacteria, and plants is demonstrated. Förster’s energy transfer formula, as used widely today in many fields of science, is also derived.

Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation.

The effect of correlated bath fluctuations on exciton transfer

Excitation dynamics of various light harvesting systems have been investigated with many theoretical methods including various non-Markovian descriptions of dissipative quantum dynamics. It is typically assumed that each excited state is coupled to an independent thermal environment, i.e., that fluctuations in different environments are uncorrelated. Here the assumption is dropped and the effect of correlated bath fluctuations on excitation transfer is investigated. Using the hierarchy equations of motion for dissipative quantum dynamics it is shown for models of the B850 bacteriochlorophylls of LH2 that correlated bath fluctuations have a significant effect on the LH2→LH2 excitation transfer rate. It is also demonstrated that inclusion of static disorder is crucial for an accurate description of transfer dynamics.

Davydov splitting of excitons in cyclic bacteriochlorophyll a nanoaggregates of bacterial light-harvesting complexes between 4.5 and 263 K

The nature of electronic excitations created by photon absorption in the cyclic B850 aggregates of 18 bacteriochlorophyll molecules of LH2 antenna complexes of photosynthetic bacteria is studied over a broad temperature range using absorption, fluorescence, and fluorescence anisotropy spectra. The latter technique has been proved to be suitable for revealing the hidden structure of excitons in inhomogeneously broadened spectra of cyclic aggregates. A theoretical model that accounts for differences of absorbing excitons in undeformed and emitting exciton polarons in deformed antenna lattices is also developed. Only a slight decrease of the exciton bandwidth and exciton coupling energy with temperature is observed. Survival of excitons in the whole temperature span from cryogenic to nearly ambient temperatures strongly suggests that collective, coherent electronic excitations might play a role in the functional light-harvesting process taking place at physiological temperatures.

Time-dependent atomistic view on the electronic relaxation in light-harvesting system II

Aiming at a better understanding of the molecular details in light absorption during photosynthesis, spatial and temporal correlation functions as well as spectral densities have been determined. At the focus of the present study are the light-harvesting II complexes of the purple bacterium Rhodospirillum molischianum. The calculations are based on a time-dependent combination of molecular dynamics simulations and quantum chemistry methods. Using a 12 ps long trajectory, different quantum chemical methods have been compared to each other. Furthermore, several approaches to determine the couplings between the individual chromophores have been tested. Correlations between energy gap fluctuations of different individual pigments are analyzed but found to be negligible. From the energy gap fluctuations, spectral densities are extracted which serve as input for calculations of optical properties and exciton dynamics. To this end, the spectral densities are tested by determining the linear absorption of the complete two-ring system. One important difference from earlier studies is given by the severely extended length of the trajectory along which the quantum chemical calculations have been performed. Due to this extension, more accurate and reliable data have been obtained in the low frequency regime which is important in the dynamics of electronic relaxation.

Quest for spatially correlated fluctuations in the FMO light-harvesting complex

The light absorption in light-harvesting complexes is performed by molecules such as chlorophyll, carotenoid, or bilin. Recent experimental findings in some of these complexes suggest the existence of long-lived coherences between the individual pigments at low temperatures. In this context, the question arises if the bath-induced fluctuations at different chromophores are spatially correlated or not. Here we investigate this question for the Fenna-Matthews-Olson (FMO) complex of Chlorobaculum tepidum by a combination of atomistic theories, i.e., classical molecular dynamics simulations and semiempirical quantum chemistry calculations. In these investigations at ambient temperatures, only weak correlations between the movements of the chromophores can be detected at the atomic level and none at the more coarse-grained level of site energies. The often-employed uncorrelated bath approximations indeed seem to be valid. Nevertheless, correlations between fluctuations in the electronic couplings between the pigments can be found. Depending on the level of theory employed, also correlations between the fluctuations of site energies and the fluctuations in electronic couplings are discernible.