Constrained geometric dynamics of the Fenna–Matthews–Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer

The trimeric Fenna–Mathews–Olson (FMO) complex of green sulphur bacteria is a well-studied example of a photosynthetic pigment–protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient excitonic energy transfer from antenna complexes to the reaction centres. By a range of simulation methods, many of the electronic properties of the FMO complex can be extracted from knowledge of the static crystal structure. However, the recent observation and analysis of long-lasting quantum dynamics in the FMO complex point to protein dynamics as a key factor in protecting and generating quantum coherence under laboratory conditions. While fast inter- and intra-molecular vibrations have been investigated extensively, the slow, conformational dynamics which effectively determine the optical inhomogeneous broadening of experimental ensembles has received less attention. The following study employs constrained geometric dynamics to study the flexibility in the protein network by efficiently generating the accessible conformational states from the published crystal structure. Statistical and principle component analyses reveal highly correlated low frequency motions between functionally relevant elements, including strong correlations between pigments that are excitonically coupled. Our analysis reveals a hierarchy of structural interactions which enforce these correlated motions, from the level of monomer-monomer interfaces right down to the α-helices, β-sheets and pigments. In addition to inducing strong spatial correlations across the conformational ensemble, we find that the overall rigidity of the FMO complex is exceptionally high. We suggest that these observations support the idea of highly correlated inhomogeneous disorder of the electronic excited states, which is further supported by the remarkably low variance (typically <5 %) of the excitonic couplings of the conformational ensemble.     

Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium

The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna–Matthews–Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

Native electrospray mass spectrometry reveals the nature and stoichiometry of pigments in the FMO photosynthetic antenna protein

The nature and stoichiometry of pigments in the Fenna-Matthews-Olson (FMO) photosynthetic antenna protein complex were determined by native electrospray mass spectrometry. The FMO antenna complex was the first chlorophyll-containing protein that was crystallized. Previous results indicate that the FMO protein forms a trimer with seven bacteriochlorophyll a in each monomer. This model has long been a working basis to understand the molecular mechanism of energy transfer through pigment/pigment and pigment/protein coupling. Recent results have suggested, however, that an eighth bacteriochlorophyll is present in some subunits. In this report, a direct mass spectrometry measurement of the molecular weight of the intact FMO protein complex clearly indicates the existence of an eighth pigment, which is assigned as a bacteriochlorophyll a by mass analysis of the complex and HPLC analysis of the pigment. The eighth pigment is found to be easily lost during purification, which results in its partial occupancy in the mass spectra of the intact complex prepared by different procedures. The results are consistent with the recent X-ray structural models. The existence of the eighth bacteriochlorophyll a in this model antenna protein gives new insights into the functional role of the FMO protein and motivates the need for new theoretical and spectroscopic assignments of spectral features of the FMO protein.     

Coherent phenomena in photosynthetic light harvesting: part one—theory and spectroscopy

The role of non-trivial quantum mechanical effects in biology has been the subject of intense scrutiny over the past decade. Much of the focus on potential “quantum biology” has been on energy transfer processes in photosynthetic light harvesting systems. Ultrafast laser spectroscopy of several light harvesting proteins has uncovered coherent oscillations dubbed “quantum beats” that persist for hundreds of femtoseconds and are putative signatures for quantum transport phenomena. This review describes the language and basic quantum mechanical phenomena that underpin quantum transport in open systems such as light harvesting and photosynthetic proteins, including the photosystem reaction centre. Coherent effects are discussed in detail, separating various meanings of the term, from delocalized excitations, or excitons, to entangled states and coherent transport. In particular, we focus on the time, energy and length scales of energy transport processes, as these are critical in understanding whether or not coherent processes are important. The role played by the protein in maintaining chromophore systems is analysed. Finally, the spectroscopic techniques that are used to probe energy transfer dynamics and that have uncovered the quantum beats are described with reference to coherent phenomena in light harvesting.     

Ultrafast absorption difference spectra of the Fenna-Matthews-Olson protein at 19 K: experiment and simulations.

We describe simulations of absorption difference spectra in strongly coupled photosynthetic antennas. In the presence of large resonance couplings, distinctive features arise from excited-state absorption transitions between one- and two-exciton levels. We first outline the theory for the heterodimer and for the general N-pigment system, and we demonstrate the transition between the strong and weak coupling regimes. The theory is applied to Fenna-Matthews-Olson (FMO) bacteriochlorophyll a protein trimers from the green photosynthetic bacterium Prosthecochloris aestuarii and then compared with experimental low-temperature absorption difference spectra of FMO trimers from the green bacterium Chlorobium tepidum.     

The reaction center complex from the green sulfur bacterium Chlorobium tepidum: a structural analysis by scanning transmission electron microscopy.

The three-dimensional (3D) structure of the reaction center (RC) complex isolated from the green sulfur bacterium Chlorobium tepidum was determined from projections of negatively stained preparations by angular reconstitution. The purified complex contained the PscA, PscC, PscB, PscD subunits and the Fenna-Matthews-Olson (FMO) protein. Its mass was found to be 454 kDa by scanning transmission electron microscopy (STEM), indicating the presence of two copies of the PscA subunit, one copy of the PscB and PscD subunits, three FMO proteins and at least one copy of the PscC subunit. An additional mass peak at 183 kDa suggested that FMO trimers copurify with the RC complexes. Images of negatively stained RC complexes were recorded by STEM and aligned and classified by multivariate statistical analysis. Averages of the major classes indicated that different morphologies of the elongated particles (length=19 nm, width=8 nm) resulted from a rotation around the long axis. The 3D map reconstructed from these projections allowed visualization of the RC complex associated with one FMO trimer. A second FMO trimer could be correspondingly accommodated to yield a symmetric complex, a structure observed in a small number of side views and proposed to be the intact form of the RC complex.     

Unravelling coherent dynamics and energy dissipation in photosynthetic complexes by 2D spectroscopy

Spectroscopic studies of light harvesting and the subsequent energy conversion in photosynthesis can track quantum dynamics happening on the microscopic level. The Fenna-Matthews-Olson complex of the photosynthetic green sulfur bacteria Chlorobium tepidum is a prototype efficient light-harvesting antenna: it stores the captured photon energy in the form of excitons (collective excitations), which are subsequently converted to chemical energy with almost 100% efficiency. These excitons show an elaborate relaxation pattern involving coherent and incoherent pathways. We make use of the complex chirality and fundamental symmetries of multidimensional optical signals to design new sequences of ultrashort laser pulses that can distinguish between coherent quantum oscillations and incoherent energy dissipation during the exciton relaxation. The cooperative dynamical features, which reflect the coherent nature of excitations, are amplified. The extent of quantum oscillations and their timescales in photosynthesis can be readily extracted from the designed signals, showing that cooperativity is maintained during energy transport in the Fenna-Matthews-Olson complex. The proposed pulse sequences may also be applied to reveal information on the robustness of quantum states in the presence of fluctuating environments in other nanoscopic complexes and devices.     

Effects of exogenous phenolic acids on photosystem functions and photosynthetic electron transport rate in strawberry leaves

Our study investigated the physiological and biochemical basis for the effects of exogenous phenolic acids on the function of the photosynthetic apparatus and photosynthetic electron transport rate in strawberry seedlings. Potted seedlings of the strawberry (Fragaria × ananassa Duch.) were used. Syringic acid inhibited net photosynthetic rate and water-use efficiency decreased. Additionally, primary quinone electron acceptor of the PSII reaction centre, the PSII reaction centre and the oxygen evolving complex were also impaired. Both the maximum quantum yield of the PSII primary photochemistry and the performance index on absorption basis were depressed, resulting in reduced function of the photosynthetic electron transport chain. Otherwise, low phthalic acid concentrations enhanced photosynthetic capacity, while high concentrations showed opposite effects. Syringic acid exhibited a higher toxic effect than that of phthalic acid which was more evident at higher concentrations.     

Characterization of the FMO protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum

Candidatus Chloracidobacterium (Cab.) thermophilum is a recently discovered aerobic chlorophototroph belonging to the phylum Acidobacteria. From analyses of genomic sequence data, this organism was inferred to have type-1 homodimeric reaction centers, chlorosomes, and the bacteriochlorophyll (BChl) a-binding Fenna–Matthews–Olson protein (FMO). Here, we report the purification and characterization of Cab. thermophilum FMO. Absorption, fluorescence emission, and CD spectra of the FMO protein were measured at room temperature and at 77 K. The spectroscopic features of this FMO protein were different from those of the FMO protein of green sulfur bacteria (GSB) and suggested that exciton coupling of the BChls in the FMO protein is weaker than in FMO of GSB especially at room temperature. HPLC analysis of the pigments extracted from the FMO protein only revealed the presence of BChl a esterified with phytol. Despite the distinctive spectroscopic properties, the residues known to bind BChl a molecules in the FMO of GSB are well conserved in the primary structure of the Cab. thermophilum FMO protein. This suggests that the FMO of Cab. thermophilum probably also binds seven or possibly eight BChl a(P) molecules. The results imply that, without changing pigment composition or structure dramatically, the FMO protein has acquired properties that allow it to perform light harvesting efficiently under aerobic conditions.     

Brassinosteroids protect photosynthesis and antioxidant system of eggplant seedlings from high-temperature stress

The effects of 24-epibrassinolide under high temperature in eggplant (Solanum melongena L.) seedlings were studied by investigating the plant growth, chlorophyll content, photosynthesis and antioxidant systems. High temperature significantly inhibited the plant growth and markedly decreased the chlorophyll content, net photosynthetic rate, stomatal conductance and transpiration rate, while it increased intercellular CO₂ concentration. In a similar manner, high temperature also decreased significantly maximum quantum efficiency of PSII, potential photochemical efficiency, the quantum efficiency of PSII, photochemical quenching, the excitation capture efficiency of open centers, and increased non-photochemical quenching. Application of 0.05–0.2 μM EBR remarkably promoted the plant growth and alleviated high-temperature-induced inhibition of photosynthesis. Under high temperature, reactive oxygen species levels and lipid peroxidation were markedly increased, which were remarkably inhibited by application of 0.05–0.2 μM EBR. The activities of antioxidative enzymes such as superoxide dismutase, peroxidase, catalase and ascorbate peroxidase, and contents of ascorbic acid and reduced glutathione were significantly increased during high-temperature treatments, and these increases were more pronounced than those of EBR at 0.05–0.2 μM treatment. The EBR treatment also greatly enhanced contents of proline, soluble sugar and protein under high-temperature stress. Taken together, it can be concluded that 0.05–0.2 μM EBR could alleviate the detrimental effects of high temperatures on plant growth by increasing photosynthetic efficiency and enhancing antioxidant enzyme systems. Addition of 0.1 μM EBR had the best ameliorative effect against high temperature, while the addition of 0.4 μM EBR had no significant effects.     

Comparison of the photosynthetic characteristics in the pericarp and flag leaves during wheat (Triticum aestivum L.) caryopsis development

The pericarp of cereal crops is considered a photosynthetically active tissue. Although extensive studies have been performed on green leaves, the photosynthetic role of the pericarp in cereal caryopsis development has not been well investigated. In the present study, we investigated the anatomy, ultrastructure, chlorophyll (Chl) fluorescence, and oxygen evolution of the pericarp during caryopsis ontogenesis in field wheat (Triticum aestivum L.). The results showed that wheat pericarp cross-cells contained Chl; the grana stacks and thylakoid membranes in the cross-cells were more distinct in the pericarp than those in the flag leaves as shown by transmission electron microscopy. Chl fluorescence revealed that the photosynthetic efficiency, which was indicated by values of maximum efficiency of PSII photochemistry and effective PSII quantum yield, was lower in the pericarp compared to that of the flag leaf eight days after anthesis (DAA), whereas similar values were subsequently observed. The nonphotochemical quenching values were lower from 8–16 DAA but significantly increased in the pericarp from 24–32 DAA compared to the flag leaf. The oxygen evolution rate of the flag leaves was consistently higher than that of pericarp; notably, isolated pericarps released more oxygen than intact pericarps during caryopsis development. These results suggest that the pericarp plays a key role in caryopsis development by performing photosynthesis as well as by supplying oxygen to the endosperm and dissipating excessive energy during the grain-filling stages.     

Study of Diurnal Changes in Photosynthetic Rate and Quantum Efficiency of Grapevine Leaves and Their Utilization in Canopy Management

Photosynthetic rate and quatum efficiency of grapevine (Vitis vinifera L. cv. Sauvignon blanc) leaves were measured under the field with ample soil water supply, and in phytotron with ample supply of water and mineral nutrients, constant air humidity and CO2 concentration, and optimum air temperature, respectively. Under field conditions CO2 assimilation quantum efficiency of leaves reached its maximum in the morning, which was followed by continuous decrease and midday depression. The leaves intercepting more light energy in the morning showed a higher quantum efficiency. Those leaves subjected continuously to strong irradiance exhibited a more obvious and longer midday depression. Reduction of leaf light interception around midday could reduce midday depression. Shaded leaves had a higher quantum efficiency than leaves under direct sunlight. The diurnal changes in photosynthetic rate and quantum efficiency of leaves were shown to be closely related to the variations in mesophyll resistance to CO2. In phytotron experiments the photosynthetic quantum efficiency of leaves was reduced after a certain period of illumination not only at 1200 μmol · m-2 · s-1 PFD, higher than the saturating light of vine leaves (≈1000 μmol · m-2 · s-1), which was caused by "photoinhibition”, but also at 800 and 200μmol · m-2 · s-1, which was similar to "photoinhibition”. But photosynthetic quantum efficiency of leaves exposed continuously to a very weak PFD (100 μmol · m -2 · s-1) remained contant. The diurnal changes in mesophyll resistance to CO2 of vine leaves could be partly related to photoinhibition. It is considered that, under field conditions without soil water limitation, midday depression of vine leaf photosynthesis could be a result of an increase of the mesophyll resistance induced by multiple effects of strong light, high temperature and low humidity. A higher light interception by canopy plane in the morning may be advantageous to exploit higher photosynthetic potentiality of leaves, but a lower light interception in the middle of day may reduce midday depression. The north-south orientation plane can provide optimum light regime and improve photosynthetic environment in vineyards.     

Extracting the Excitonic Hamiltonian of the Fenna-Matthews-Olson Complex Using Three-Dimensional Third-Order Electronic Spectroscopy

We extend traditional two-dimensional (2D) electronic spectroscopy into a third Fourier dimension without the use of additional optical interactions. By acquiring a set of 2D spectra evenly spaced in waiting time and dividing the area of the spectra into voxels, we can eliminate population dynamics from the data and transform the waiting time dimension into frequency space. The resultant 3D spectrum resolves quantum beating signals arising from excitonic coherences along the waiting frequency dimension, thereby yielding up to 2n-fold redundancy in the set of frequencies necessary to construct a complete set of n excitonic transition energies. Using this technique, we have obtained, to our knowledge, the first fully experimental set of electronic eigenstates for the Fenna-Matthews-Olson (FMO) antenna complex, which can be used to improve theoretical simulations of energy transfer within this protein. Whereas the strong diagonal peaks in the 2D rephasing spectrum of the FMO complex obscure all but one of the crosspeaks at 77 K, extending into the third dimension resolves 19 individual peaks. Analysis of the independently collected nonrephasing data provides the same information, thereby verifying the calculated excitonic transition energies. These results enable one to calculate the Hamiltonian of the FMO complex in the site basis by fitting to the experimental linear absorption spectrum.     

Quantum Transport in Networks and Photosynthetic Complexes at the Steady State

Recently, several works have analysed the efficiency of photosynthetic complexes in a transient scenario and how that efficiency is affected by environmental noise. Here, following a quantum master equation approach, we study the energy and excitation transport in fully connected networks both in general and in the particular case of the Fenna–Matthew–Olson complex. The analysis is carried out for the steady state of the system where the excitation energy is constantly “flowing” through the system. Steady state transport scenarios are particularly relevant if the evolution of the quantum system is not conditioned on the arrival of individual excitations. By adding dephasing to the system, we analyse the possibility of noise-enhancement of the quantum transport.     

Leaf physiology of shade-grownCycas micronesica leaves following removal of shade

The photosynthetic characteristics ofCycas micronesica K.D. Hill were studied from August 1998 until February 1999 using chlorophyll fluorescence and gas-exchange techniques to determine the responses to long-term shade of 35% ambient light transmission, followed by the transfer of shade-grown leaves into full-sun conditions. The shade-grown leaves exhibited increased photosynthetic light use efficiency and effective quantum efficiency of photosystem II (PS II) and decreased photosynthetic light saturation point and dark respiration when compared with leaves grown in full sun. Shade was removed from shade-grownC. micronesica leaves during midday on December 14, 1998, when effective quantum efficiency of shaded leaves was 45% greater than that of sun leaves. Following one hour in full sun, effective quantum efficiency of the shade-grown leaves declined to below that of the sun-grown leaves. After receiving full sunlight for the rest of the photoperiod, maximum quantum efficiency of PS II photochemistry for shade-grown leaves was below that of sun-grown leaves throughout the night. The damage caused by excessive light to shade-grown leaves progressed for the first three days after shade removal. On day 3, effective quantum efficiency during midday was 30%, net photosynthesis was 47%, apparent quantum yield was 65%, and light compensation point was 136% of that for sun-grown leaves. After day 3, the relationship between full-sun leaves and the previously shaded leaves for these response variables was relatively stable. Two months following removal of shade, the previously shaded leaves continued to exhibit damage from high light. These results have application to transplanting cycad plants from a shaded nursery to a field site or, after tropical cyclones, where protective forest canopy cover has been destroyed and cycad plants in the forest subcanopy are abruptly exposed to full-sun conditions.     

Chemical oxidation of the FMO antenna protein from Chlorobaculum tepidum

Effect of chemical oxidation by ferricyanide on bacteriochlorophyll a (BChl a) in the Fenna–Matthews–Olson protein (FMO) was studied using absorbance and fluorescence spectroscopy at ambient and cryogenic temperatures. Partially selective oxidation of pigments bound to the antenna complex was achieved and the probable absorption wavelength corresponding to the recently discovered bacteriochlorophyll No. 8 of 806 nm was obtained by comparative analysis of the effect of chemical oxidation and the effect of different isolation procedures. Formation of a stable product identified as a chlorophyll a derivative occurred upon chemical oxidation. This new pigment remained bound within the pigment–protein complex, and exhibited an efficient energy transfer to BChl a. Furthermore, complex effects of the pigment oxidation upon the fluorescence yield of the FMO protein were observed. Utility of this approach based on chemical modifications for the investigation of the native regulatory mechanisms involved in the energy transfer in the FMO protein is discussed.     

Maximum photosynthetic efficiency: a problem to be resolved

The great disarray in the measurements of the maximum efficiency of conservation of light energy in photosynthesis is an outstanding problem in the development of photosynthetic biotechnology. The short-term measurements of the efficiency based on O(2) release by suspensions of cells or chloroplasts have given minimum quantum demands between 4 and 12 hv/O(2). The defect of the short term measurements is that the effects of growth conditions, which can alter the efficiency by a factor of 2, have been generally ignored. In contrast, the steady-state growth method, which depends on measurement of the maximum growth yield in photosynthesis, ensures that growth and photosynthesis are normally coupled. This growth method indicates that the minimum quantum demand lies in the relatively narrow range of 5.3 to 8.6 hv/O(2). The question of whether the minimum quantum demand is less or greater than 8 hv/O(2) is a crucial test for present theoretical concepts of the conversion of radiant energy to chemical energy in photosynthesis. To obtain the definitive maximum value more rigorously controlled measurements of photosynthetic efficiency in growing organisms are essential.     

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFIEs are usually analyzed in a matrix form called an IFIE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFIE matrix, a so-called IFIE map. We comprehensively examine what information the IFIE map contains concerning structures and stabilities of the protein-DNA complex.