Toward understanding molecular mechanisms of light harvesting and charge separation in photosystem II

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from the antenna complex to the reaction center is still not fully understood. A central element is the accurate evaluation of the individual chlorophyll excitation energies (site energies). Such an evaluation must include a detailed treatment of site specific environmental influences on structural and electrostatic properties, but also their evolution in the temporal domain, because of the dynamic nature of the energy transfer process. In this work, we calculate the site energies of all 96 chlorophylls in a membrane-embedded model of PSI. The employed hybrid QM/MM approach using the multireference DFT/MRCI method in the QM region allows to obtain accurate site energies under explicit consideration of the natural environment. We identify energy traps and barriers in the antenna complex and discuss their implications for energy transfer to the reaction center. Going beyond previous studies, our model also accounts for the molecular dynamics of the full trimeric PSI complex. Via statistical analysis we show that the thermal fluctuations of single chlorophylls prevent the formation of a single prominent energy funnel within the antenna complex. These findings are also supported by a dipole exciton model. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers. The set of site energies provided in this work sets the stage for theoretical and experimental studies on the highly efficient energy transfer mechanisms in PSI.

Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.

The roles of photochemical and non-photochemical quenching in regulating photosynthesis depend on the phases of fluctuating light conditions

The induction and relaxation of photochemistry and non-photochemical quenching (NPQ) are not instantaneous and require time to respond to fluctuating environments. There is a lack of integrated understanding on how photochemistry and NPQ influence photosynthesis in fluctuating environments. We measured the induction and relaxation of chlorophyll a fluorescence and gas exchange in poplar and cotton at varying temperatures under saturating and fluctuating lights. When the light shifted from dark to high, the fraction of open reaction centers in photosystem II (qL) gradually increased while NPQ increased suddenly and then remained stable. Temperature significantly changed the response of qL but not that of NPQ during the dark to high light transition. Increased qL led to higher photosynthesis but their precise relationship was affected by NPQ and temperature. qL was significantly related to biochemical capacity. Thus, qL appears to be a strong indicator of the activation of carboxylase, leading to the similar dynamics between qL and photosynthesis. When the light shifted from high to low intensity, NPQ is still engaged at a high level, causing a stronger decline in photosynthesis. Our finding suggests that the dynamic effects of photochemistry and NPQ on photosynthesis depend on the phases of environmental fluctuations and interactive effects of light and temperature. Across the full spectra of light fluctuation, the slow induction of qL is a more important limiting factor than the slow relaxation of NPQ for photosynthesis in typical ranges of temperature for photosynthesis. The findings provided a new perspective to improve photosynthetic productivity with molecular biology under natural fluctuating environments.

Hybrid Fluorescent Poly(silsesquioxanes) with Amide- and Triazole-Containing Side Groups for Light Harvesting and Cation Sensing

Hybrid polymers containing pyrene (Py) units bound to linear poly(silsesquioxane) (LPSQ) chains through flexible linkers containing heteroatoms (S, N, O) (LPSQ-triazole-Py and LPSQ-amide-Py) exhibit intense fluorescence emission, both in very diluted solutions (c = 10-8 mol/L) and in the solid state. The materials are thermally stable and exhibit good thin film forming abilities. Their optical and physicochemical properties were found to be strongly dependent on the structure of the side chains. Comparative studies with octahedral silsesquioxane (POSS) analogues (POSS-triazole-Py and POSS-amide-Py) emphasized the role of the specific double-strand architecture of the LPSQ backbone and distribution of side Py groups for their photo-luminescent properties. The new hybrid materials were tested as fluorescence energy donors to red-emitting dyes (Nile Red and Coumarine 6). All the silsesquioxanes studied were found to be able to transfer FL emission energy to Coumarin 6, irrespectively of their spatial structure. However, due to the differences in the wavelength range of FL emission, only LPSQ-triazole-Py were able to act as energy donors to Nile Red. The Py-grafted LPSQ may be also applied for development of soluble and highly emissive chemosensors. Their fluorescent nature was explored for the detection of Cu(II), Fe(III), Co(II), Ag(I), Hg(II), Mg(II), Ca(II), Pb(II) and Zn(II). The morphology of the side chains and hydrogen-bonding interactions influenced the sensing capacity of all the studied materials.

Structural Characterization and Photochemical Properties of Mono- and Bimetallic Cu-Mabiq Complexes

We present a series of monometallic ([Cu(Mabiq)OTf] (1) and [Cu(Mabiq)] (2)) and bimetallic copper-Mabiq complexes ([Cu₂(Mabiq)(PPh₃)₂(OTf)₂] (3) and [Cu₂(Mabiq)(PPh₃)₂]PF₆ (4)). The latter compounds contain an additional Cu^I center that binds in a tetrahedral fashion to the external bipyrimidine nitrogens of the macrocyclic ligand. Compounds 3 and 4 represent the first examples of bimetallic transition metal Mabiq complexes, stable both in solution and in the solid state. The structural and electronic properties of compounds 1-4 were analyzed by means of X-ray crystallography, cyclic voltammetry, and spectroscopic methods. One-electron reduced 2 and 4 consist of a Cu^II ion coordinated by a Mabiq ligand radical, [Cu^II(Mabiq^•)]. Thus, both bimetallic compounds are mixed-valent with respect to the copper oxidation states. Complexes 2 and 4 can be generated photochemically, upon irradiation of 1 or 3 with visible light in the presence of a sacrificial electron donor.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

Circularly polarized luminescence spectroscopy reveals low-energy excited states and dynamic localization of vibronic transitions in CP43

Circularly polarized luminescence (CPL) spectroscopy is an established but relatively little-used technique that monitors the chirality of an emission. When applied to photosynthetic pigment assemblies, we find that CPL provides sensitive and detailed information on low-energy exciton states, reflecting the interactions, site energies and geometries of interacting pigments. CPL is the emission analog of circular dichroism (CD) and thus spectra explore the optical activity only of fluorescent states of the pigment-protein complex and consequently the nature of the lowest-energy excited states (trap states), whose study is a critical area of photosynthesis research. In this work, we develop the new approach of temperature-dependent CPL spectroscopy, over the 2-120 K temperature range, and apply it to the CP43 proximal antenna protein of photosystem II. Our results confirm strong excitonic interactions for at least one of the two well-established emitting states of CP43 named "A" and "B". Previous structure-based models of CP43 spectra are evaluated in the light of the new CPL data. Our analysis supports the assignments of Shibata et al. [Shibata et al. J. Am. Chem. Soc. 135 (2013) 6903-6914], particularly for the highly-delocalized B-state. This state dominates CPL spectra and is attributed predominantly to chlorophyll a's labeled Chl 634 and Chl 636 (alternatively labeled Chl 43 and 45 by Shibata et al.). The absence of any CPL intensity in intramolecular vibrational sidebands associated with the delocalized "B" excited state is attributed to the dynamic localization of intramolecular vibronic transitions.

Linking chlorophyll a fluorescence to photosynthesis for remote sensing applications: mechanisms and challenges

Chlorophyll a fluorescence (ChlF) has been used for decades to study the organization, functioning, and physiology of photosynthesis at the leaf and subcellular levels. ChlF is now measurable from remote sensing platforms. This provides a new optical means to track photosynthesis and gross primary productivity of terrestrial ecosystems. Importantly, the spatiotemporal and methodological context of the new applications is dramatically different compared with most of the available ChlF literature, which raises a number of important considerations. Although we have a good mechanistic understanding of the processes that control the ChlF signal over the short term, the seasonal link between ChlF and photosynthesis remains obscure. Additionally, while the current understanding of in vivo ChlF is based on pulse amplitude-modulated (PAM) measurements, remote sensing applications are based on the measurement of the passive solar-induced chlorophyll fluorescence (SIF), which entails important differences and new challenges that remain to be solved. In this review we introduce and revisit the physical, physiological, and methodological factors that control the leaf-level ChlF signal in the context of the new remote sensing applications. Specifically, we present the basis of photosynthetic acclimation and its optical signals, we introduce the physical and physiological basis of ChlF from the molecular to the leaf level and beyond, and we introduce and compare PAM and SIF methodology. Finally, we evaluate and identify the challenges that still remain to be answered in order to consolidate our mechanistic understanding of the remotely sensed SIF signal.

A robust and effective time-independent route to the calculation of Resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects

We present an effective time-independent implementation to model vibrational resonance Raman (RR) spectra of medium-large molecular systems with the inclusion of Franck-Condon (FC) and Herzberg-Teller (HT) effects and a full account of the possible differences between the harmonic potential energy surfaces of the ground and resonant electronic states. Thanks to a number of algorithmic improvements and very effective parallelization, the full computations of fundamentals, overtones, and combination bands can be routinely performed for large systems possibly involving more than two electronic states. In order to improve the accuracy of the results, an effective inclusion of the leading anharmonic effects is also possible, together with environmental contributions under different solvation regimes. Reduced-dimensionality approaches can further enlarge the range of applications of this new tool. Applications to imidazole, pyrene, and chlorophyll a1 in solution are reported, as well as comparisons with available experimental data.

Light harvesting in photosystem II

Water oxidation in photosynthesis takes place in photosystem II (PSII). This photosystem is built around a reaction center (RC) where sunlight-induced charge separation occurs. This RC consists of various polypeptides that bind only a few chromophores or pigments, next to several other cofactors. It can handle far more photons than the ones absorbed by its own pigments and therefore, additional excitations are provided by the surrounding light-harvesting complexes or antennae. The RC is located in the PSII core that also contains the inner light-harvesting complexes CP43 and CP47, harboring 13 and 16 chlorophyll pigments, respectively. The core is surrounded by outer light-harvesting complexes (Lhcs), together forming the so-called supercomplexes, at least in plants. These PSII supercomplexes are complemented by some "extra" Lhcs, but their exact location in the thylakoid membrane is unknown. The whole system consists of many subunits and appears to be modular, i.e., both its composition and organization depend on environmental conditions, especially on the quality and intensity of the light. In this review, we will provide a short overview of the relation between the structure and organization of pigment-protein complexes in PSII, ranging from individual complexes to entire membranes and experimental and theoretical results on excitation energy transfer and charge separation. It will become clear that time-resolved fluorescence data can provide invaluable information about the organization and functioning of thylakoid membranes. At the end, an overview will be given of unanswered questions that should be addressed in the near future.

Diminished photoinhibition is involved in high photosynthetic capacities in spring ephemeral Berteroa incana under strong light conditions

Berteroa incana (B. incana), a spring ephemeral species of Brassicaceae, possesses very high photosynthetic capacities at high irradiances. Exploring the mechanism of the high light use efficiency of B. incana under strong light conditions may help to explore mechanisms of plants' survival strategies. Therefore, the photosynthetic characteristics of B. incana grown under three different light intensities (field conditions (field): 200-1500μmolphotonsm(-2)s(-1); greenhouse high light (HL) conditons: 600μmolphotonsm(-2)s(-1); and greenhouse low light (LL) conditions: 100μmolphotonsm(-2)s(-1)) were investigated and compared with those of the model plant Arabidopsis thaliana (A. thaliana). Our results revealed that B. incana behaved differently in adjusting its photosynthetic activities under both HL and LL conditions compared with what A. thaliana did under the same conditions, suggesting that the potential of photosynthetic capacity of B. incana might be enhanced under strong light conditions. Under LL conditions, B. incana reached its maximum photosynthetic activity at a much higher light intensity than A. thaliana did, although their maximum photochemical efficiency of photosystem II (PSII) (F(v)/F(m)) was almost the same. When grown under HL conditions, B. incana showed much higher photosynthetic capacity than A. thaliana. A detailed analysis of the OJIP transient kinetics of B. incana under HL and LL conditions revealed that HL-grown B. incana possessed not only a high ability in regulating photosystem stoichiometry that ensured high linear electron transport, but also an enhanced availability of oxidized plastoquinone (PQ) pool which reduced non-photochemical quenching (NPQ), especially its slow components qT and qI, and increased the photochemical efficiency, which in turn, increased the electron transport. We suggest that the high ability in regulating photosystem stoichiometry and the high level of the availability of oxidized PQ pool in B. incana under strong light conditions play important roles in its ability to retain higher photosynthetic capacity under extreme environmental conditions.

Modeling of a violaxanthin-chlorophyll b chromophore pair in its LHCII environment using CAM-B3LYP

Collecting energy for photosystem II is facilitated by several pigments, xanthophylls and chlorophylls, embedded in the light harvesting complex II (LHCII). One xanthophyll, violaxanthin (Vio), is loosely bound at a site close to a chlorophyll b (Chl). No final answer has yet been found for the role of this specific xanthophyll. We study the electronic structure of Vio in the presence of Chl and under the influence of the LHCII environment, represented by a point charge field (PCF). We compare the capability of the long range corrected density functional theory (DFT) functional CAM-B3LYP to B3LYP for the modeling of the UV/vis spectrum of the Vio+Chl pair. CAM-B3LYP was reported to allow for a very realistic reproduction of bond length alternation of linear polyenes, which has considerable impact on the carotenoid structure and spectrum. To account for the influence of the LHCII environment, the chromophore geometries are optimized using an ONIOM(DFT/6-31G(d):PM6) scheme. Our calculations show that the energies of the locally excited states are almost unaffected by the presence of the partner chromophore or the PCF. There are, however, indications for excitonic coupling of the Chl Soret band and Vio. We propose that Vio may accept energy from blue-light excited Chl.

Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems

The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.

Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes

The absorption and energy transfer properties of photosynthetic pigments are strongly influenced by their local environment or "site." Local electrostatic fields vary in time with protein and chromophore molecular movement and thus transiently influence the excited state transition properties of individual chromophores. Site-specific information is experimentally inaccessible in many light-harvesting pigment-proteins due to multiple chromophores with overlapping spectra. Full quantum mechanical calculations of each chromophores excited state properties are too computationally demanding to efficiently calculate the changing excitation energies along a molecular dynamics trajectory in a pigment-protein complex. A simplified calculation of electrostatic interactions with each chromophores ground to excited state transition, the so-called charge density coupling (CDC) for site energy, CDC, has previously been developed to address this problem. We compared CDC to more rigorous quantum chemical calculations to determine its accuracy in computing excited state energy shifts and their fluctuations within a molecular dynamics simulation of the bacteriochlorophyll containing light-harvesting Fenna-Mathews-Olson (FMO) protein. In most cases CDC calculations differed from quantum mechanical (QM) calculations in predicting both excited state energy and its fluctuations. The discrepancies arose from the inability of CDC to account for the differing effects of charge on ground and excited state electron orbitals. Results of our study show that QM calculations are indispensible for site energy computations and the quantification of contributions from different parts of the system to the overall site energy shift. We suggest an extension of QM/MM methodology of site energy shift calculations capable of accounting for long-range electrostatic potential contributions from the whole system, including solvent and ions.

Charge separation is virtually irreversible in photosystem II core complexes with oxidized primary quinone acceptor

X-ray structures of the Photosystem II (PSII) core revealed relatively large interpigment distances between the CP43 and CP47 antenna complexes and the reaction center (RC) with respect to the interpigment distances in a single unit. This finding questions the possibility of fast energy equilibration among the antenna and the RC, which has been the basic explanation for the measured PSII fluorescence kinetics for more than two decades. In this study, we present time-resolved fluorescence measurements obtained with a streak-camera setup on PSII core complexes from Thermosynechococcus elongatus at room temperature (RT) and at 77 K. Kinetic modeling of the RT data obtained with oxidized quinone acceptor Q(A), reveals that the kinetics are best described by fast primary charge separation at a time scale of 1.5 ps and slow energy transfer from the antenna into the RC, which results in an energy equilibration time between the antenna and the RC of about 44 ps. This model is consistent with structure-based computations. Primary radical pair formation was found to be a virtually irreversible process. Energy equilibration within the CP43 and CP47 complexes is shown to occur at a time scale of 8 ps. Kinetic modeling of the 77 K data reveals similar energy transfer time scales in the antenna units and among the antenna and the RC as at RT, respectively, 7 and 37 ps. We conclude that the energy transfer from the CP43/CP47 antenna to the RC is the dominant factor in the total charge separation kinetics in intact PSII cores.

Dynamics of light harvesting in photosynthesis

We review recent theoretical and experimental advances in the elucidation of the dynamics of light harvesting in photosynthesis, focusing on recent theoretical developments in structure-based modeling of electronic excitations in photosynthetic complexes and critically examining theoretical models for excitation energy transfer. We then briefly describe two-dimensional electronic spectroscopy and its application to the study of photosynthetic complexes, in particular the Fenna-Matthews-Olson complex from green sulfur bacteria. This review emphasizes recent experimental observations of long-lasting quantum coherence in photosynthetic systems and the implications of quantum coherence in natural photosynthesis.

Protein quality control in chloroplasts: a current model of D1 protein degradation in the photosystem II repair cycle

The chloroplast originated from endosymbiosis of photosynthetic bacteria. Thus, mechanisms essential for chloroplast biogenesis/homeostasis (protein synthesis, import from cytosol, assembly, and degradation) are predominantly governed by prokaryotic systems. Among these, the quality control system is crucial, because light energy constantly damages photosynthetic proteins and excessive light often limits plant growth by irreversibly inactivating the photosynthetic apparatuses. Here, we overview prokaryotic proteases (FtsH and Deg) which are two enzymes that play critical roles in this system. We particularly focus on Photosystem II (PSII) in thylakoid membranes, which is composed of more than 20 subunits. Among the subunits is one of the intrinsic reaction centre proteins (D1) which is considered to be the target of photodamage. Its rapid and specific turnover suggests that photodamaged D1 is degraded by these proteases and replaced with a de novo synthesized one in a system which is termed the PSII repair cycle. We discuss a current model of D1 degradation which is executed by a concerted action of particular FtsH and Deg isoforms.

Molecular dynamics simulations of porphyrin-dendrimer systems: toward modeling electron transfer in solution

We have performed computational simulations of porphyrin-dendrimer systems--a cationic porphyrin electrostatically associated to a negatively charged dendrimer--using the method of classical molecular dynamics (MD) with an atomistic force field. Previous experimental studies have shown a strong quenching effect of the porphyrin fluorescence that was assigned to electron transfer (ET) from the dendrimer's tertiary amines (Paulo, P. M. R.; Costa, S. M. B. J. Phys. Chem. B 2005, 109, 13928). In the present contribution, we evaluate computationally the role of the porphyrin-dendrimer conformation in the development of a statistical distribution of ET rates through its dependence on the donor-acceptor distance. We started from simulations without explicit solvent to obtain trajectories of the donor-acceptor distance and the respective time-averaged distributions for two dendrimer sizes and different initial configurations of the porphyrin-dendrimer pair. By introducing explicit solvent (water) in our simulations, we were able to estimate the reorganization energy of the medium for the systems with the dendrimer of smaller size. The values obtained are in the range 0.6-1.5 eV and show a linear dependence with the inverse of the donor-acceptor distance, which can be explained by a two-phase dielectric continuum model taking into account the medium heterogeneity provided by the dendrimer organic core. Dielectric relaxation accompanying ET was evaluated from the simulations with explicit solvent showing fast decay times of some tens of femtoseconds and slow decay times in the range of hundreds of femtoseconds to a few picoseconds. The variations of the slow relaxation times reflect the heterogeneity of the dendrimer donor sites which add to the complexity of ET kinetics as inferred from the experimental fluorescence decays.

Fully Integrated Approach to Compute Vibrationally Resolved Optical Spectra: From Small Molecules to Macrosystems

A general and effective time-independent approach to compute vibrationally resolved electronic spectra from first principles has been integrated into the Gaussian computational chemistry package. This computational tool offers a simple and easy-to-use way to compute theoretical spectra starting from geometry optimization and frequency calculations for each electronic state. It is shown that in such a way it is straightforward to combine calculation of Franck-Condon integrals with any electronic computational model. The given examples illustrate the calculation of absorption and emission spectra, all in the UV-vis region, of various systems from small molecules to large ones, in gas as well as in condensed phases. The computational models applied range from fully quantum mechanical descriptions to discrete/continuum quantum mechanical/molecular mechanical/polarizable continuum models.

D1-arginine257 mutants (R257E, K, and Q) of Chlamydomonas reinhardtii have a lowered QB redox potential: analysis of thermoluminescence and fluorescence measurements

Arginine257 (R257), in the de-helix that caps the Q(B) site of the D1 protein, has been shown by mutational studies to play a key role in the sensitivity of Photosystem II (PS II) to bicarbonate-reversible binding of the formate anion. In this article, the role of this residue has been further investigated through D1 mutations (R257E, R257Q, and R257K) in Chlamydomonas reinhardtii. We have investigated the activity of the Q(B) site by studying differences from wild type on the steady-state turnover of PS II, as assayed through chlorophyll (Chl) a fluorescence yield decay after flash excitation. The effects of p-benzoquinone (BQ, which oxidizes reduced Q(B), Q(B)(-) ) and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU, which blocks electron flow from Q(A)(-) to Q(B)) were measured. The equilibrium constants of the two-electron gate were obtained through thermoluminescence measurements. The thermoluminescence properties were changed in the mutants, especially when observed after pretreatment with 100 microM BQ. A theoretical analysis of the thermoluminescence data, based mainly on the recombination pathways model of Rappaport et al. (2005), led to the conclusion that the free-energy difference for the recombination of Q(B)(-) with S(2) was reduced by 20-40 mV in the three mutants (D1-R257K, D1-R257Q, and D1-R257E); this was interpreted to be due to a lowering of the redox potential of Q(B)/Q(B)(-). Further, since the recombination of Q(A)(-) with S(2) was unaffected, we suggest that no significant change in redox potential of Q(A)/Q(A)(-) occurred in these three mutants. The maximum variable Chl a fluorescence yield is lowered in the mutants, in the order R257K > R257Q > R257E, compared to wild type. Our analysis of the binary oscillations in Chl a fluorescence following pretreatment of cells with BQ showed that turnover of the Q(B) site was relatively unaffected in the three mutants. The mutant D1-R257E had the lowest growth rate and steady-state activity and showed the weakest binary oscillations. We conclude that the size and the charge of the amino acid at the position D1-257 play a role in PS II function by modulating the effective redox potential of the Q(B)/Q(B)(-) pair. We discuss an indirect mechanism mediated through electrostatic and/or surface charge effects and the possibility of more pleiotropic effects arising from decreased stability of the D1/D2 and D1/CP47 interfaces.

Computational analysis of photosynthetic systems

The use of various computational techniques for the study of photosynthetic systems is described ranging from genome analysis to density functional simulations of the oxygen evolving complex of PSII. The use of simulations for analyzing protein structures can aid in clarifying ambiguous and incomplete experimental results to identifying underlying rules to create efficient light-initiated charge separation at high efficiency.