Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides

Signature of Quantum Coherence in the Exciton Energy Pathways of the LH2 Photosynthetic Complex

Unraveling the energy transfer pathways in photosynthetic complexes is an important step toward understanding their structure-function interplay. Here, we use an open quantum systems approach to investigate energy transfer within the LH2 photosynthetic apparatus and its dependence on environmental conditions. We find that energy transfer pathways strongly depend on the environment-induced dephasing time. A comparison between the computational results and experiments performed on similar systems demonstrates that quantum coherences are present in these systems under physiological conditions and have an important role in shaping the energy transfer pathways. Moreover, our calculations indicate that relatively simple spectroscopy experiments can be used to detect traces of quantum coherence. Finally, our results suggest that quantum coherence may play a role in photosynthesis, but not in enhancing the efficiency as was previously suggested.

Conversion of light into electricity in a semi-synthetic system based on photosynthetic bacterial chromatophores

Chromatophores (Chr) from photosynthetic nonsulfur purple bacterium Rhodobacter sphaeroides immobilized onto a Millipore membrane filter (MF) and sandwiched between two semiconductor indium tin oxide (ITO) electrodes (termed ITO|Chr - MF|ITO) have been used to measure voltage (ΔV) induced by continuous illumination. The maximum ΔV was detected in the presence of ascorbate / N,N,N'N'-tetramethyl-p-phenylenediamine couple, coenzyme UQ₀, disaccaride trehalose and antimycin A, an inhibitor of cytochrome bc₁ complex. In doing so, the light-induced electron transfer in the reaction centers was the major source of photovoltages. The stability of the voltage signal upon prolonged irradiation (>1 h) may be due to the maintenance of a conformation that is optimal for the functioning of integral protein complexes and stabilization of lipid bilayer membranes in the presence of trehalose. Retaining ∼70 % of the original photovoltage performance on the 30th day of storage at 23 °C in the dark under air was achieved after re-injection of fresh buffer (∼40 μL) containing redox mediators into the ITO|Chr - MF|ITO system. The approach we use is easy and can be extended to other biological intact systems (cells, thylakoid membranes) capable of converting energy of light.

Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides

Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.

Anionic Lipids Confine Cytochrome c2 to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners

Cytochrome c₂ (cyt. c₂) is a major element in electron transfer between redox proteins in bioenergetic membranes. While the interaction between cyt. c₂ and anionic lipids abundant in bioenergetic membranes has been reported, their effect on the shuttling activity of cyt. c₂ remains elusive. Here, the effect of anionic lipids on the interaction and binding of cyt. c₂ to the cytochrome bc₁ complex (bc₁) is investigated using a combination of molecular dynamics (MD) and Brownian dynamics (BD) simulations. MD is used to generate thermally accessible conformations of cyt. c₂ and membrane-embedded bc₁, which were subsequently used in multireplica BD simulations of diffusion of cyt. c₂ from solution to bc₁, in the presence of various lipids. We show that, counterintuitively, anionic lipids facilitate association of cyt. c₂ with bc₁ by localizing its diffusion to the membrane surface. The observed lipid-mediated bc₁ association is further enhanced by the oxidized state of cyt. c₂, in line with its physiological function. This lipid-mediated enhancement is salinity-dependent, and anionic lipids can disrupt cyt. c₂-bc₁ interaction at nonphysiological salt levels. Our data highlight the importance of the redox state of cyt. c₂, the lipid composition of the chromatophore membrane, and the salinity of the chromatophore in regulating the efficiency of the electron shuttling process mediated by cyt. c₂. The conclusions can be extrapolated to mitochondrial systems and processes, or any bioenergetic membrane, given the structural similarity between cyt. c₂ and bc₁ and their mitochondrial counterparts.

Do photosynthetic complexes use quantum coherence to increase their efficiency? Probably not

Answering the titular question has become a central motivation in the field of quantum biology, ever since the idea was raised following a series of experiments demonstrating wave-like behavior in photosynthetic complexes. Here, we report a direct evaluation of the effect of quantum coherence on the efficiency of three natural complexes. An open quantum systems approach allows us to simultaneously identify their level of "quantumness" and efficiency, under natural physiological conditions. We show that these systems reside in a mixed quantum-classical regime, characterized by dephasing-assisted transport. Yet, we find that the change in efficiency at this regime is minute at best, implying that the presence of quantum coherence does not play a substantial role in enhancing efficiency. However, in this regime, efficiency is independent of any structural parameters, suggesting that evolution may have driven natural complexes to their parameter regime to "design" their structure for other uses.

Photoautotrophic hydrogen production of Rhodobacter sphaeroides in a microbial electrosynthesis cell

Conventional photoheterotrophic H₂ production by purple sulfur bacteria requires additional organic substrates as the carbon and energy sources. This study examined the novel photoautotrophic H₂ production of Rhodobacter sphaeroides with concomitant CO₂ uptake in microbial electrosynthesis (MES). Under an applied potential of -0.9 V vs. Ag/AgCl to the cathode, Rhodobacter sphaeroides produced hydrogen with CO₂ as the sole carbon source under illumination. The initial planktonic cells decreased rapidly in suspension, whereas biomass formation on the cathode surface increased gradually during MES operation. The electron and carbon flow under photoautotrophic conditions in MES were estimated. Glutamate, as the nitrogen source, enhanced hydrogen production significantly (328 mL/L/day) compared to NH₄Cl (67 mL/L/day) during seven days of operation. The photoautotrophic condition with 6000 lx presented CO₂ consumption and simultaneous biomass formation on the cathode electrode. MES-driven electron and proton transfer enabled the simultaneous production of hydrogen and CO₂ uptake_.

Purple phototrophic bacteria for resource recovery: Challenges and opportunities

Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a "removal and disposal" approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g COD_biomass·g COD_removed^-1)), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9_, 0.3-2.2 and 0.1-0.3 $·kg_{dry biomass}^-1. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg^-1) appears as a promising valorisation route.

Tools for Low-Dimensional Chemistry

Many biological mechanisms can be considered to be low-dimensional systems: their function is determined by molecular objects of reduced dimensionality. Bacterial photosynthesis is a very good example: the photosynthetic pathway is contained within nano-objects (vesicles) whose function is determined by the numbers and nanoscale organization of membrane proteins and by the ratios of the different types of protein that they contain. Systems biology has provided computational models for studying these processes, but there is a need for experimental platforms with which to test their predictions. This Invited Feature Article reviews recent work on the development of tools for the reconstruction of membrane processes on solid surfaces. Photochemical methods provide a powerful, versatile means for the organization of molecules and membranes across length scales from the molecular to the macroscopic. Polymer brushes are highly effective supports for model membranes and versatile functional and structural components in low-dimensional systems. The incorporation of plasmonic elements facilitates enhanced measurement of spectroscopic properties and provides an additional design strategy via the exploitation of quantum optical phenomena. A low-dimensional system that incorporates functional transmembrane proteins and a mechanism for the in situ measurement of proton transport is described.

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to their redox partners and integral membrane proteins and exchanging electrons. Diffusive search, recognition, binding, and unbinding of these proteins often amount to kinetic bottlenecks in cellular energy conversion, but despite the availability of structures and intense study, the physical mechanisms controlling redox partner interactions remain largely unknown. The present molecular dynamics study provides an all-atom description of the cytochrome c2-docked bc1 complex in Rhodobacter sphaeroides in terms of an ensemble of favorable docking conformations and reveals an intricate series of conformational changes that allow cytochrome c2 to recognize the bc1 complex and bind or unbind in a redox state-dependent manner. In particular, the role of electron transfer in triggering a molecular switch and in altering water-mediated interface mobility, thereby strengthening and weakening complex formation, is described. The results resolve long-standing discrepancies between structural and functional data.

Photosynthetic Proteins in Supported Lipid Bilayers: Towards a Biokleptic Approach for Energy Capture

In nature, plants and some bacteria have evolved an ability to convert solar energy into chemical energy usable by the organism. This process involves several proteins and the creation of a chemical gradient across the cell membrane. To transfer this process to a laboratory environment, several conditions have to be met: i) proteins need to be reconstituted into a lipid membrane, ii) the proteins need to be correctly oriented and functional and, finally, iii) the lipid membrane should be capable of maintaining chemical and electrical gradients. Investigating the processes of photosynthesis and energy generation in vivo is a difficult task due to the complexity of the membrane and its associated proteins. Solid, supported lipid bilayers provide a good model system for the systematic investigation of the different components involved in the photosynthetic pathway. In this review, the progress made to date in the development of supported lipid bilayer systems suitable for the investigation of membrane proteins is described; in particular, there is a focus on those used for the reconstitution of proteins involved in light capture.

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.

Optimization of exciton currents in photosynthetic systems

In an approach analogous to that used to treat electronic currents in semiconductor quantum dots, we investigate the exciton current in a pigment network that is sandwiched between two exciton reservoirs, also known as the emitter and the acceptor. Employing the master equation for the reduced density matrix, the exciton current is obtained analytically for a two-site model, and numerically for an eight-site Fenna-Matthews-Olson (FMO) subunit model. It is found that, to maximize the exciton current with a specific network configuration, there exist optimal emitter temperatures and exciton transfer rates between the network and the reservoirs. The steady state current in the FMO model is consistent with the trapping time calculated by network optimization in the one-exciton picture. The current optimization with respect to various control parameters is discussed for the FMO model. At and below the biologically relevant transfer rate 1 ps(-1), the FMO network is more efficient for excitation energy transfer than the two-site model. Beyond this scale, the FMO network shows robustness with respect to the interplay with the reservoirs.

Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments

Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now straightforwardly be applied to other currently less well characterized but biologically more relevant systems.

Algal photosynthesis as the primary driver for a sustainable development in energy, feed, and food production

High oil prices and global warming that accompany the use of fossil fuels are an incentive to find alternative forms of energy supply. Photosynthetic biofuel production represents one of these since for this, one uses renewable resources. Sunlight is used for the conversion of water and CO₂ into biomass. Two strategies are used in parallel: plant-based production via sugar fermentation into ethanol and biodiesel production through transesterification. Both, however, exacerbate other problems, including regional nutrient balancing and the world's food supply, and suffer from the modest efficiency of photosynthesis. Maximizing the efficiency of natural and engineered photosynthesis is therefore of utmost importance. Algal photosynthesis is the system of choice for this particularly for energy applications. Complete conversion of CO₂ into biomass is not necessary for this. Innovative methods of synthetic biology allow one to combine photosynthetic and fermentative metabolism via the so-called Photanol approach to form biofuel directly from Calvin cycle intermediates through use of the naturally transformable cyanobacterium Synechocystis sp. PCC 6803. Beyond providing transport energy and chemical feedstocks, photosynthesis will continue to be used for food and feed applications. Also for this application, arguments of efficiency will become more and more important as the size of the world population continues to increase. Photosynthetic cells can be used for food applications in various innovative forms, e.g., as a substitute for the fish proteins in the diet supplied to carnivorous fish or perhaps--after acid hydrolysis--as a complex, animal-free serum for growth of mammalian cells in vitro.

Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles

The purple phototrophic bacteria synthesize an extensive system of intracytoplasmic membranes (ICM) in order to increase the surface area for absorbing and utilizing solar energy. Rhodobacter sphaeroides cells contain curved membrane invaginations. In order to study the biogenesis of ICM in this bacterium mature (ICM) and precursor (upper pigmented band - UPB) membranes were purified and compared at the single membrane level using electron, atomic force and fluorescence microscopy, revealing fundamental differences in their morphology, protein organization and function. Cryo-electron tomography demonstrates the complexity of the ICM of Rba. sphaeroides. Some ICM vesicles have no connection with other structures, others are found nearer to the cytoplasmic membrane (CM), often forming interconnected structures that retain a connection to the CM, and possibly having access to the periplasmic space. Near-spherical single invaginations are also observed, still attached to the CM by a 'neck'. Small indents of the CM are also seen, which are proposed to give rise to the UPB precursor membranes upon cell disruption. 'Free-living' ICM vesicles, which possess all the machinery for converting light energy into ATP, can be regarded as bacterial membrane organelles.

Light-harvesting mechanism of bacteria exploits a critical interplay between the dynamics of transport and trapping

Light-harvesting bacteria Rhodospirillum photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes exploit dissipation as a photoprotective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes efficiently process unused illumination intensity by channeling it to open reaction centers. More generally, our analysis elucidates and quantifies the trade-offs in natural network design for solar energy conversion.

Energy transfer in light-adapted photosynthetic membranes: from active to saturated photosynthesis

In bacterial photosynthesis light-harvesting complexes, LH2 and LH1 absorb sunlight energy and deliver it to reaction centers (RCs) with extraordinarily high efficiency. Submolecular resolution images have revealed that both the LH2:LH1 ratio, and the architecture of the photosynthetic membrane itself, adapt to light intensity. We investigate the functional implications of structural adaptations in the energy transfer performance in natural in vivo low- and high-light-adapted membrane architectures of Rhodospirillum photometricum. A model is presented to describe excitation migration across the full range of light intensities that cover states from active photosynthesis, where all RCs are available for charge separation, to saturated photosynthesis where all RCs are unavailable. Our study outlines three key findings. First, there is a critical light-energy density, below which the low-light adapted membrane is more efficient at absorbing photons and generating a charge separation at RCs, than the high-light-adapted membrane. Second, connectivity of core complexes is similar in both membranes, suggesting that, despite different growth conditions, a preferred transfer pathway is through core-core contacts. Third, there may be minimal subareas on the membrane which, containing the same LH2:LH1 ratio, behave as minimal functional units as far as excitation transfer efficiency is concerned.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX polypeptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rhodobacter sphaeroides and the circular BChl arrangement found in other purple bacteria.

Using F0F1-ATPase motors as micro-mixers accelerates thrombolysis

We have developed a novel micro-mixer using a biological molecular ATP motor. The micro-mixer was constructed from arrays of chromatophore-embedded delta-free F(0)F(1)-ATPases, where the delta-free F(1) part acted as a rotator to mix solutions, and the F(0) part was driven by light. Confocal microscope studies indicated that the micro-mixer did not touch directly on the fibrin labeled with FITC. The nanomechanical force generated by the motor induced drug movement in the solution and accelerated the fibrinolysis process. All results strongly suggest that the micro-mixers generated a nanomechanical force which accelerated the fibrinolysis process in the presence of lower concentrations of lumbrokinase.

Organisation and function of the Phaeospirillum molischianum photosynthetic apparatus

We have investigated the organisation of the photosynthetic apparatus in Phaeospirillum molischianum, using biochemical fractionation and functional kinetic measurements. We show that only a fraction of the ATP-synthase is present in the membrane regions which contain most of the photosynthetic apparatus and that, despite its complicated stacked structure, the intracytoplasmic membrane delimits a single connected space. We find that the diffusion time required for a quinol released by the reaction centre to reach a cytochrome bc1 complex is about 260 ms. On the other hand, the reduction of the cytochrome c chain by the cytochrome bc1 complex in the presence of a reduced quinone pool occurs with a time constant of about 5 ms. The overall turnover time of the cyclic electron transfer is about 25 ms in vivo under steady-state illumination. The sluggishness of the quinone shuttle appears to be compensated, at least in part, by the size of the quinone pool. Together, our results show that P. molischianum contains a photosynthetic system, with a very different organisation from that found in Rhodobacter sphaeroides, in which quinone/quinol diffusion between the RC and the cytochrome bc1 is likely to be the rate-limiting factor for cyclic electron transfer.

Intrinsic curvature properties of photosynthetic proteins in chromatophores

In purple bacteria, photosynthesis is carried out on large indentations of the bacterial plasma membrane termed chromatophores. Acting as primitive organelles, chromatophores are densely packed with the membrane proteins necessary for photosynthesis, including light harvesting complexes LH1 and LH2, reaction center (RC), and cytochrome bc(1). The shape of chromatophores is primarily dependent on species, and is typically spherical or flat. How these shapes arise from the protein-protein and protein-membrane interactions is still unknown. Now, using molecular dynamics simulations, we have observed the dynamic curvature of membranes caused by proteins in the chromatophore. A membrane-embedded array of LH2s was found to relax to a curved state, both for LH2 from Rps. acidophila and a homology-modeled LH2 from Rb. sphaeroides. A modeled LH1-RC-PufX dimer was found to develop a bend at the dimerizing interface resulting in a curved shape as well. In contrast, the bc(1) complex, which has not been imaged yet in native chromatophores, did not induce a preferred membrane curvature in simulation. Based on these results, a model for how the different photosynthetic proteins influence chromatophore shape is presented.

Modeling the electron transport chain of purple non-sulfur bacteria

Purple non-sulfur bacteria (Rhodospirillaceae) have been extensively employed for studying principles of photosynthetic and respiratory electron transport phosphorylation and for investigating the regulation of gene expression in response to redox signals. Here, we use mathematical modeling to evaluate the steady-state behavior of the electron transport chain (ETC) in these bacteria under different environmental conditions. Elementary-modes analysis of a stoichiometric ETC model reveals nine operational modes. Most of them represent well-known functional states, however, two modes constitute reverse electron flow under respiratory conditions, which has been barely considered so far. We further present and analyze a kinetic model of the ETC in which rate laws of electron transfer steps are based on redox potential differences. Our model reproduces well-known phenomena of respiratory and photosynthetic operation of the ETC and also provides non-intuitive predictions. As one key result, model simulations demonstrate a stronger reduction of ubiquinone when switching from high-light to low-light conditions. This result is parameter insensitive and supports the hypothesis that the redox state of ubiquinone is a suitable signal for controlling photosynthetic gene expression.

Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle

The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

On the effects of PufX on the absorption properties of the light-harvesting complexes of Rhodobacter sphaeroides

Some species of purple bacteria as, e.g., Rhodobacter sphaeroides contain the protein PufX. Concurrently, the light harvesting complexes 1 (LH1) form dimers of open rings. In mutants without PufX, the LH1s are closed rings and photosynthesis breaks down, because the ubiquinone exchange at the reaction center is blocked. However, the main purpose of the LH1 is light harvesting. We therefore investigate the effects that the PufX-induced dimerization has on the absorption properties of the core complexes. Calculations with a dipole model, which compare the photosynthetic efficiency of various configurations of monomeric and dimeric core complexes, show that the dimer can absorb photons directly into the reaction centers more efficiently, but that the performance of the more sophisticated dimeric LH1 antenna degrades faster with structural perturbations. The calculations predict an optimal orientation of the reaction centers relative to the LH1 dimer, which agrees well with the experimentally found configuration. Based on experimental observations indicating that the dimeric core complexes are indeed rather rigid, we hypothesize that in PufX(+) species the association between the LH1 and the reaction centers is enhanced. This mechanical stabilization of the core complexes would lead to the observed quinone blockage, when PufX is missing.

Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: identification of new proteins

The Rhodobacter sphaeroides intracytoplasmic membrane (ICM) is an inducible membrane that is dedicated to the major events of bacterial photosynthesis, including harvesting light energy, separating primary charges, and transporting electrons. In this study, multichromatographic methods coupled with Fourier transform ion cyclotron resonance mass spectrometry, combined with subcellular fractionation, was used to test the hypothesis that the photosynthetic membrane of R. sphaeroides 2.4.1 contains a significant number of heretofore unidentified proteins in addition to the integral membrane pigment-protein complexes, including light-harvesting complexes 1 and 2, the photochemical reaction center, and the cytochrome bc(1) complex described previously. Purified ICM vesicles are shown to be enriched in several abundant, newly identified membrane proteins, including a protein of unknown function (AffyChip designation RSP1760) and a possible alkane hydroxylase (RSP1467). When the genes encoding these proteins are mutated, specific photosynthetic phenotypes are noted, illustrating the potential new insights into solar energy utilization to be gained by this proteomic blueprint of the ICM. In addition, proteins necessary for other cellular functions, such as ATP synthesis, respiration, solute transport, protein translocation, and other physiological processes, were also identified to be in association with the ICM. This study is the first to provide a more global view of the protein composition of a photosynthetic membrane from any source. This protein blueprint also provides insights into potential mechanisms for the assembly of the pigment-protein complexes of the photosynthetic apparatus, the formation of the lipid bilayer that houses these integral membrane proteins, and the possible functional interactions of ICM proteins with activities that reside in domains outside this specialized bioenergetic membrane.

Bridging from molecular simulation to biochemical networks

How can we make the connection between the three-dimensional structures of individual proteins and understanding how complex biological systems involving many proteins work? The modelling and simulation of protein structures can help to answer this question for systems ranging from multimacromolecular complexes to organelles and cells. On one hand, multiscale modelling and simulation techniques are advancing to permit the spatial and temporal properties of large systems to be simulated using atomic-detail structures. On the other hand, the estimation of kinetic parameters for the mathematical modelling of biochemical pathways using protein structure information provides a basis for iterative manipulation of biochemical pathways guided by protein structure. Recent advances include the structural modelling of protein complexes on the genomic level, novel coarse-graining strategies to increase the size of the system and the time span that can be simulated, and comparative molecular field analyses to estimate enzyme kinetic parameters.

Molecular stochastic simulations of chromatophore vesicles from Rhodobacter sphaeroides

A kinetic model is presented for photosynthetic processes under varying illumination based on the recently introduced steady state model of the photosynthetic chromatophore vesicles of the purple bacterium Rhodobacter sphaeroides. A stochastic simulation system is built up from independent copies of the different transmembrane proteins, each encapsulating its own set of binding sites and internal states. The proteins are then connected through pools for each of the metabolites. A number of steady state and time-dependent scenarios are presented showing that even under steady state conditions the stochastic model exhibits a different behavior than a continuous description. We find that the electronic coupling between the light harvesting complexes increases the efficiency of the core complexes which eventually allows the bacteria to bridge short illumination outages at already lower light intensities. Some new experiments are proposed by which the DeltapH dependent characteristic of the bc(1) complex or the proton buffering capacity of the vesicle could be determined.

A spatial model of the chromatophore vesicles of Rhodobacter sphaeroides and the position of the Cytochrome bc1 complex

The photosynthetic apparatus of purple bacteria is generally considered a well-studied and understood system. However, recent atomic force microscopy images of flattened chromatophore vesicles from Rhodobacter sphaeroides restarted a debate about the stoichiometry and positions of the membrane proteins, with the interpretations of the observed images only partly being in agreement with earlier models. The most puzzling observation from the recent images is that the Cytochrome bc(1) complex, which is a central part of the photosynthetic apparatus, seems to be missing on the chromatophore vesicles, even when these were extracted from photosynthetically grown bacteria. From the available information on the geometry of the vesicle and of the proteins we reconstructed here a three-dimensional model vesicle at molecular resolution. Its central feature, also determining its diameter of approximately 45 nm, is an equatorial array of LH1 dimers, lined by a region of LH2 rings. This naturally puts the Cytochrome bc(1) complexes and the ATPase at the vesicle's poles. This spatial model may explain why the vesicle's endcaps with the bc(1) complexes are lost during the preparatory steps of the imaging process together with the ATPase and are therefore absent from the available images.