Ultrafast excited-state dynamics of Luteins in the major light-harvesting complex LHCII

Carotenoid pigments are known to present a functional versatility when bound to light-harvesting complexes. This versatility originates from a strong correlation between a complex electronic structure and a flexible geometry that is easily tunable by the surrounding protein environment. Here, we investigated how the different L1 and L2 sites of the major trimeric light-harvesting complex (LHCII) of green plants tune the electronic structure of the two embedded luteins, and how this reflects on their ultrafast dynamics upon excitation. By combining molecular dynamics and quantum mechanics/molecular mechanics calculations, we found that the two luteins feature a different conformation around the second dihedral angle in the lumenal side. The s-cis preference of the lutein in site L2 allows for a more planar geometry of the π -conjugated backbone, which results in an increased degree of delocalization and a reduced excitation energy, explaining the experimentally observed red shift. Despite these remarkable differences, according to surface hopping simulations the two luteins present analogous ultrafast dynamics upon excitation: the bright S 2 state quickly decays (in ∼ 50 fs) to the dark intermediate S x , eventually ending up in the S 1 state. Furthermore, by employing two different theoretical approaches (i.e., Förster theory and an excitonic version of surface hopping), we investigated the experimentally debated energy transfer between the two luteins. With both approaches, no evident energy transfer was observed in the ultrafast timescale.

A perspective on the major light-harvesting complex dynamics under the effect of pH, salts, and the photoprotective PsbS protein

The photosynthetic apparatus is a highly modular assembly of large pigment-binding proteins. Complexes called antennae can capture the sunlight and direct it from the periphery of two Photosystems (I, II) to the core reaction centers, where it is converted into chemical energy. The apparatus must cope with the natural light fluctuations that can become detrimental to the viability of the photosynthetic organism. Here we present an atomic scale view of the photoprotective mechanism that is activated on this line of defense by several photosynthetic organisms to avoid overexcitation upon excess illumination. We provide a complete macroscopic to microscopic picture with specific details on the conformations of the major antenna of Photosystem II that could be associated with the switch from the light-harvesting to the photoprotective state. This is achieved by combining insight from both experiments and all-atom simulations from our group and the literature in a perspective article.

Towards the description of charge transfer states in solubilised LHCII using subsystem DFT

Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.

Revealing Intermolecular Electronic and Vibronic Coherence with Polarization-Dependent Two-Dimensional Beating Maps

Two-dimensional electronic spectroscopy (2DES) has been widely employed as an efficient tool to reveal the impact of intermolecular electronic and/or vibronic quantum coherence on excitation energy transfer in light-harvesting complexes. However, intramolecular vibrational coherence would also contribute to oscillating signals in 2D spectra, along with the intermolecular coherence signals that are directly related to energy transfer. In this work, the possibility of screening the vibrational coherence signals is explored through polarization-dependent 2DES. The all-parallel (AP) and double-crossed (DC) polarization-dependent two-dimensional rephasing spectra (2DRS) are simulated for a minimalist heterodimer model with vibrational coupling. By combining the DC-2DRS and the 2D beating maps, we demonstrate that the population and vibrational coherence signals can be largely suppressed, resulting in highlighted intermolecular electronic and vibronic coherence signals. Moreover, the AP- and DC-2DBMs show rather different patterns at the vibrational frequency, indicating a possible way to identify pure vibrational coherence.

Low-Lying Excited States of Natural Carotenoids Viewed by Ab Initio Methods

Low-lying excited states of carotenoids (the optically dark 2A_g^- and bright 1B_u⁺) are deeply involved in energy transfer processes in photosynthetic antennas, such as light harvesting and non-photochemical quenching. Though any ab initio modeling of these phenomena has to rely on precise energies of the carotenoid electronic states, the accurate evaluation of these states remains a challenging problem due to their different natures. The paper aims to study the accuracy of the excitation energies of the low-lying excited states of certain open- and closed-chain carotenoids obtained by a state-of-the-art multireference approach for electronic structure calculation. Here, density matrix renormalization group SCF (DMRGSCF) and a perturbative approach based on driven similarity renormalization group second-order multireference perturbation theory (DSRG-MRPT2) were used to treat the static and dynamic correlation, respectively. Nuclear geometries of the electronic states were optimized with DFT-based approaches. It is demonstrated that spin-flip TD-DFT can replace multiconfigurational methods for the geometry optimization of the 2A_g^- state but not for the calculation of the excitation energy. Adiabatic excitation energies to the 1B_u⁺ state were shown to be within a margin of 1000 cm^-1 with an appropriate flow parameter value. Adiabatic excitation energies to the 2A_g^- state for the open-chain carotenoids lie within a range of experimental values (taking into account the broad range of experimental estimates); for the closed-chain ones, the error does not exceed 2000 cm^-1. Ab initio stationary (1A_g^- → 1B_u⁺) and transient (2A_g^- → 1B_u⁺) absorption spectra were modeled for violaxanthin and lycopene, and these spectra showed good agreement with the experimental ones both in terms of the vibronic structure and the transition energies.

Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.

Q-Band relaxation in chlorophyll: new insights from multireference quantum dynamics

The ultrafast relaxation within the Q-bands of chlorophyll plays a crucial role in photosynthetic light-harvesting. We investigate this process via nuclear and electronic quantum dynamics on multireference potential energy surfaces.

A different perspective for nonphotochemical quenching in plant antenna complexes

Light-harvesting complexes of plants exert a dual function of light-harvesting (LH) and photoprotection through processes collectively called nonphotochemical quenching (NPQ). While LH processes are relatively well characterized, those involved in NPQ are less understood. Here, we characterize the quenching mechanisms of CP29, a minor LHC of plants, through the integration of two complementary enhanced-sampling techniques, dimensionality reduction schemes, electronic calculations and the analysis of cryo-EM data in the light of the predicted conformational ensemble. Our study reveals that the switch between LH and quenching state is more complex than previously thought. Several conformations of the lumenal side of the protein occur and differently affect the pigments' relative geometries and interactions. Moreover, we show that a quenching mechanism localized on a single chlorophyll-carotenoid pair is not sufficient but many chlorophylls are simultaneously involved. In such a diffuse mechanism, short-range interactions between each carotenoid and different chlorophylls combined with a protein-mediated tuning of the carotenoid excitation energies have to be considered in addition to the commonly suggested Coulomb interactions.

Time-dependent atomistic simulations of the CP29 light-harvesting complex

Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II, which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional-based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results, the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, time-dependent and time-independent excitonic Hamiltonians of the system have been constructed and applied to the determination of absorption spectra as well as exciton dynamics.

Toward an Accurate Ab Initio Description of Low-Lying Singlet Excited States of Polyenes

The low-lying excited states of carotenoids play a crucial role in many important biophysical processes such as photosynthesis. Most of these excited states are strongly correlated, which makes them both challenging for a qualitative ab initio description and an engaging model system for trying out emerging multireference methods. Among these methods, driven similarity renormalization group (DSRG) and its perturbative version (DSRG-MRPT2) are especially attractive in terms of both accuracy and moderate numerical complexity. In this paper, we applied density matrix renormalization group (DMRG) followed by DSRG-MRPT2 for the calculation of vertical and adiabatic excitation energies into the 2A_g^-, 1B_u^-, and 1B_u⁺ electronic states of polyenes containing from 8 to 13 conjugating double bonds acting as a model for natural carotenoids. It was shown that the DSRG flow parameter should be adjusted to ensure both the energy convergence with respect to it and the agreement with the experimental data. With the increased flow parameter, the proposed combination of methods provides a reasonable agreement with the experiment. The deviations of the adiabatic excitation energies are less than 1000 cm^-1 for the 2A_g^- and less than 3000 cm^-1 for the excited states of the B_u symmetry, which in terms of accuracy significantly outperforms the N-electron valence state perturbation theory. At the same time, DSRG-MRPT2 is shown to be robust with respect to variation of quality of the DMRG reference wave function such as the orbital optimization or the number of electronic states in the averaging.

Understanding photosynthesis in a spatial-temporal multiscale: The need for a systemic view

In October 2020, at the peak of the COVID-19 pandemic, a group of young Brazilian photosynthesis researchers organized the 1st Brazilian Symposium on Photosynthesis. The event was free and online, with the presence of important guest speakers from all over the world, who discussed their recent works on topics related to the future and perspectives of photosynthesis research. Summarizing the expectations of this symposium we highlighted the importance of adopting a systemic perspective for a better understanding of photosynthesis as a complex and dynamic process. Plants are modular and self-regulating presenting metabolic redundancy and functional degeneration. Among the various biological processes, photosynthesis plays a crucial role in promoting the direct conversion of light energy into carbon skeletons for support growth and productivity. In the past decades, significant advances have been made in photosynthesis at the biophysical, biochemical, and molecular levels. However, this myriad of knowledge has been insufficient to answer crucial questions, such as: how can we understand and eventually increase photosynthetic efficiency and yield in crops subjected to adverse environment related to climate-changing? We believe that a crucial limitation to the whole comprehension of photosynthesis is associated with a vastly widespread classic reductionist view. Moreover, this perspective is commonly accompanied by non-integrative, simplistic, and descriptive approaches to investigate a complex and dynamic process as photosynthesis. Herein, we propose the use of new approaches, mostly based on the Systems Theory, which certainly comes closer to the real world, such as the complex systems that the plants represent.

Model Lipid Membranes Assembled from Natural Plant Thylakoids into 2D Microarray Patterns as a Platform to Assess the Organization and Photophysics of Light-Harvesting Proteins

Natural photosynthetic "thylakoid" membranes found in green plants contain a large network of light-harvesting (LH) protein complexes. Rearrangement of this photosynthetic machinery, laterally within stacked membranes called "grana", alters protein-protein interactions leading to changes in the energy balance within the system. Preparation of an experimentally accessible model system that allows the detailed investigation of these complex interactions can be achieved by interfacing thylakoid membranes and synthetic lipids into a template comprised of polymerized lipids in a 2D microarray pattern on glass surfaces. This paper uses this system to interrogate the behavior of LH proteins at the micro- and nanoscale and assesses the efficacy of this model. A combination of fluorescence lifetime imaging and atomic force microscopy reveals the differences in photophysical state and lateral organization between native thylakoid and hybrid membranes, the mechanism of LH protein incorporation into the developing hybrid membranes, and the nanoscale structure of the system. The resulting model system within each corral is a high-quality supported lipid bilayer that incorporates laterally mobile LH proteins. Photosynthetic activity is assessed in the hybrid membranes versus proteoliposomes, revealing that commonly used photochemical assays to test the electron transfer activity of photosystem II may actually produce false-positive results.

Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.

Trivial Excitation Energy Transfer to Carotenoids Is an Unlikely Mechanism for Non-photochemical Quenching in LHCII

Higher plants defend themselves from bursts of intense light via the mechanism of Non-Photochemical Quenching (NPQ). It involves the Photosystem II (PSII) antenna protein (LHCII) adopting a conformation that favors excitation quenching. In recent years several structural models have suggested that quenching proceeds via energy transfer to the optically forbidden and short-lived S ₁ states of a carotenoid. It was proposed that this pathway was controlled by subtle changes in the relative orientation of a small number of pigments. However, quantum chemical calculations of S ₁ properties are not trivial and therefore its energy, oscillator strength and lifetime are treated as rather loose parameters. Moreover, the models were based either on a single LHCII crystal structure or Molecular Dynamics (MD) trajectories about a single minimum. Here we try and address these limitations by parameterizing the vibronic structure and relaxation dynamics of lutein in terms of observable quantities, namely its linear absorption (LA), transient absorption (TA) and two-photon excitation (TPE) spectra. We also analyze a number of minima taken from an exhaustive meta-dynamical search of the LHCII free energy surface. We show that trivial, Coulomb-mediated energy transfer to S ₁ is an unlikely quenching mechanism, with pigment movements insufficiently pronounced to switch the system between quenched and unquenched states. Modulation of S ₁ energy level as a quenching switch is similarly unlikely. Moreover, the quenching predicted by previous models is possibly an artifact of quantum chemical over-estimation of S ₁ oscillator strength and the real mechanism likely involves short-range interaction and/or non-trivial inter-molecular states.

Energy transfer pathways in the CAC light-harvesting complex of Rhodomonas salina

Photosynthetic organisms had to evolve diverse mechanisms of light-harvesting to supply photosynthetic apparatus with enough energy. Cryptophytes represent one of the groups of photosynthetic organisms combining external and internal antenna systems. They contain one type of immobile phycobiliprotein located at the lumenal side of the thylakoid membrane, together with membrane-bound chlorophyll a/c antenna (CAC). Here we employ femtosecond transient absorption spectroscopy to study energy transfer pathways in the CAC proteins of cryptophyte Rhodomonas salina. The major CAC carotenoid, alloxanthin, is a cryptophyte-specific carotenoid, and it is the only naturally-occurring carotenoid with two triple bonds in its structure. In order to explore the energy transfer pathways within the CAC complex, three excitation wavelengths (505, 590, and 640 nm) were chosen to excite pigments in the CAC antenna. The excitation of Chl c at either 590 or 640 nm proves efficient energy transfer between Chl c and Chl a. The excitation of alloxanthin at 505 nm shows an active pathway from the S₂ state with efficiency around 50%, feeding both Chl a and Chl c with approximately 1:1 branching ratio, yet, the S₁-route is rather inefficient. The 57 ps energy transfer time to Chl a gives ~25% efficiency of the S₁ channel. The low efficiency of the S₁ route renders the overall carotenoid-Chl energy transfer efficiency low, pointing to the regulatory role of alloxanthin in the CAC antenna.

Ab Initio Study of Low-Lying Excited States of Carotenoid-Derived Polyenes

Knowledge about excited states of carotenoids is essential for understanding photophysical processes underlying photosynthesis. However, due to the presence of a large number of optically dark states, experimental study of the excited-state manifold is limited to a significant extent. In this paper, we apply high-level ab initio quantum chemical methods to study the low-lying excited states of polyenes containing from 8 to 13 conjugated double bonds, which serve as a model for natural carotenoids. Vertical and adiabatic excitation energies from the ground 1A_g^- state to the excited 2A_g^-, 1B_u⁺, and 1B_u^- states were evaluated by means of density matrix renormalization group (DMRG) with NEVPT2 perturbative correction. The energies of all excited states are highly sensitive to nuclear geometry, especially the 2A_g^- state. Thus, the 2A_g^- and 1B_u⁺ states interchange their relative positions upon geometry relaxation, while the vertical excitation energy to the 2A_g^- state is rather high. At the same time, the 1B_u^- state energy is shown to be higher than other studied excited states at any geometry. With relaxed geometries of the excited states, absorption and transient absorption spectra were calculated within the Franck-Condon approximation bridging the gap between experimental spectroscopic data and computational results.

Electron-Vibrational Spectra and Dynamics of the Lutein Molecule

The carotenoid molecules such as lutein play an important role in the absorption of light and the following transfer of energy during photosynthesis. However, the study of these processes by the experimental methods only is quite difficult because some of the transitions between the electronic states of carotenoids are optically forbidden and the effect of vibrational states change also must be taken into account. In the present work, electronic-vibrational states of the lutein molecule in the LHCII complex of higher plants and in the diethyl ether solution were described using the ab initio methods. For lutein of LHCII, the electronic energy transfer processes were modeled. The role of the "hot" S₁ states of lutein was shown to be of great importance.

Exciton properties and optical spectra of light harvesting complex II from a fully atomistic description

We present a fully atomistic simulation of linear optical spectra (absorption, fluorescence and circular dichroism) of the Light Harvesting Complex II (LHCII) trimer using a hybrid approach, which couples a quantum chemical description of the chlorophylls with a classical model for the protein and the external environment (membrane and water). The classical model uses a polarizable Molecular Mechanics force field, thus allowing mutual polarization effects in the calculations of the excitonic properties. The investigation is performed both on the crystal structure and on structures generated by a μs long classical molecular dynamics simulation of the complex within a solvated membrane. The results show that this integrated approach not only provides a good description of the excitonic properties and optical spectra without the need for additional refinements of the excitonic parameters, but it also allows an atomistic investigation of the relative importance of electronic, structural and environment effects in determining the optical spectra.

Excitation quenching in chlorophyll-carotenoid antenna systems: 'coherent' or 'incoherent'

Plants possess an essential ability to rapidly down-regulate light-harvesting in response to high light. This photoprotective process involves the formation of energy-quenching interactions between the chlorophyll and carotenoid pigments within the antenna of Photosystem II (PSII). The nature of these interactions is currently debated, with, among others, 'incoherent' or 'coherent' quenching models (or a combination of the two) suggested by a range of time-resolved spectroscopic measurements. In 'incoherent quenching', energy is transferred from a chlorophyll to a carotenoid and is dissipated due to the intrinsically short excitation lifetime of the latter. 'Coherent quenching' would arise from the quantum mechanical mixing of chlorophyll and carotenoid excited state properties, leading to a reduction in chlorophyll excitation lifetime. The key parameters are the energy gap, [Formula: see text] and the resonance coupling, J, between the two excited states. Coherent quenching will be the dominant process when [Formula: see text] i.e., when the two molecules are resonant, while the quenching will be largely incoherent when [Formula: see text] One would expect quenching to be energetically unfavorable for [Formula: see text] The actual dynamics of quenching lie somewhere between these limiting regimes and have non-trivial dependencies of both J and [Formula: see text] Using the Hierarchical Equation of Motion (HEOM) formalism we present a detailed theoretical examination of these excitation dynamics and their dependence on slow variations in J and [Formula: see text] We first consider an isolated chlorophyll-carotenoid dimer before embedding it within a PSII antenna sub-unit (LHCII). We show that neither energy transfer, nor the mixing of excited state lifetimes represent unique or necessary pathways for quenching and in fact discussing them as distinct quenching mechanisms is misleading. However, we do show that quenching cannot be switched 'on' and 'off' by fine tuning of [Formula: see text] around the resonance point, [Formula: see text] Due to the large reorganization energy of the carotenoid excited state, we find that the presence (or absence) of coherent interactions have almost no impact of the dynamics of quenching. Counter-intuitively significant quenching is present even when the carotenoid excited state lies above that of the chlorophyll. We also show that, above a rather small threshold value of [Formula: see text]quenching becomes less and less sensitive to J (since in the window [Formula: see text] the overall lifetime is independent of it). The requirement for quenching appear to be only that [Formula: see text] Although the coherent/incoherent character of the quenching can vary, the overall kinetics are likely robust with respect to fluctuations in J and [Formula: see text] This may be the basis for previous observations of NPQ with both coherent and incoherent features.

Characterization of fluorescent chlorophyll charge-transfer states as intermediates in the excited state quenching of light-harvesting complex II

Light-harvesting complex II (LHCII) is the major antenna complex in higher plants and green algae. It has been suggested that a major part of the excited state energy dissipation in the so-called "non-photochemical quenching" (NPQ) is located in this antenna complex. We have performed an ultrafast kinetics study of the low-energy fluorescent states related to quenching in LHCII in both aggregated and the crystalline form. In both sample types the chlorophyll (Chl) excited states of LHCII are strongly quenched in a similar fashion. Quenching is accompanied by the appearance of new far-red (FR) fluorescence bands from energetically low-lying Chl excited states. The kinetics of quenching, its temperature dependence down to 4 K, and the properties of the FR-emitting states are very similar both in LHCII aggregates and in the crystal. No such FR-emitting states are found in unquenched trimeric LHCII. We conclude that these states represent weakly emitting Chl-Chl charge-transfer (CT) states, whose formation is part of the quenching process. Quantum chemical calculations of the lowest energy exciton and CT states, explicitly including the coupling to the specific protein environment, provide detailed insight into the chemical nature of the CT states and the mechanism of CT quenching. The experimental data combined with the results of the calculations strongly suggest that the quenching mechanism consists of a sequence of two proton-coupled electron transfer steps involving the three quenching center Chls 610/611/612. The FR-emitting CT states are reaction intermediates in this sequence. The polarity-controlled internal reprotonation of the E175/K179 aa pair is suggested as the switch controlling quenching. A unified model is proposed that is able to explain all known conditions of quenching or non-quenching of LHCII, depending on the environment without invoking any major conformational changes of the protein.

Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs

Plants prevent photodamage under high light by dissipating excess energy as heat. Conformational changes of the photosynthetic antenna complexes activate dissipation by leveraging the sensitivity of the photophysics to the protein structure. The mechanisms of dissipation remain debated, largely due to two challenges. First, because of the ultrafast timescales and large energy gaps involved, measurements lacked the temporal or spectral requirements. Second, experiments have been performed in detergent, which can induce non-native conformations, or in vivo, where contributions from homologous antenna complexes cannot be disentangled. Here, we overcome both challenges by applying ultrabroadband two-dimensional electronic spectroscopy to the principal antenna complex, LHCII, in a near-native membrane. Our data provide evidence that the membrane enhances two dissipative pathways, one of which is a previously uncharacterized chlorophyll-to-carotenoid energy transfer. Our results highlight the sensitivity of the photophysics to local environment, which may control the balance between light harvesting and dissipation in vivo.

Charge transfer from the carotenoid can quench chlorophyll excitation in antenna complexes of plants

The photosynthetic apparatus of higher plants can dissipate excess excitation energy during high light exposure, by deactivating excited chlorophylls through a mechanism called nonphotochemical quenching (NPQ). However, the precise molecular details of quenching and the mechanism regulating the quenching level are still not completely understood. Focusing on the major light-harvesting complex LHCII of Photosystem II, we show that a charge transfer state involving Lutein can efficiently quench chlorophyll excitation, and reduce the excitation lifetime of LHCII to the levels measured in the deeply quenched LHCII aggregates. Through a combination of molecular dynamics simulations, multiscale quantum chemical calculations, and kinetic modeling, we demonstrate that the quenching level can be finely tuned by the protein, by regulating the energy of the charge transfer state. Our results suggest that a limited conformational rearrangement of the protein scaffold could act as a molecular switch to activate or deactivate the quenching mechanism.

The conformational phase space of the photoprotective switch in the major light harvesting complex II

Extensive conformational sampling of the major light harvesting complex II defines the collective variables of the photoprotective switch.

How carotenoid distortions may determine optical properties: lessons from the Orange Carotenoid Protein

Carotenoids in photosynthetic proteins carry out the dual function of harvesting light and defending against photo-damage by quenching excess energy. The latter involves the low-lying, dark, excited state labelled S1. Here "dark" means optically-forbidden, a property that is often attributed to molecular symmetry, which leads to speculation that its optical properties may be strongly-perturbed by structural distortions. This has been both explicitly and implicitly proposed as an important feature of photo-protective energy quenching. Here we present a theoretical analysis of the relationship between structural distortions and S1 optical properties. We outline how S1 is dark not because of overall geometric symmetry but because of a topological symmetry related to bond length alternation in the conjugated backbone. Taking the carotenoid echinenone as an example and using a combination of molecular dynamics, quantum chemistry, and the theory of spectral lineshapes, we show that distortions that break this symmetry are extremely stiff. They are therefore absent in solution and only marginally present in even a very highly-distorted protein binding pocket such as in the Orange Carotenoid Protein (OCP). S1 remains resolutely optically-forbidden despite any breaking of bulk molecular symmetry by the protein environment. However, rotations of partially conjugated end-rings can result in fine tuning of the S1 transition density which may exert some influence on interactions with neighbouring chromophores.

What proteomics can reveal about plant-virus interactions? Photosynthesis-related proteins on the spotlight

Plant viruses are responsible for losses in worldwide production of numerous economically important food and fuel crops. As obligate cellular parasites with very small genomes, viruses rely on their hosts for replication, assembly, intra- and intercellular movement, and attraction of vectors for dispersal. Chloroplasts are photosynthesis and are the site of replication for several viruses. When viruses replicate in chloroplasts, photosynthesis, an essential process in plant physiology, is inhibited. The mechanisms underlying molecular and biochemical changes during compatible and incompatible plants-virus interactions, are only beginning to be elucidated, including changes in proteomic profiles induced by virus infections. In this review, we highlight the importance of proteomic studies to understand plant-virus interactions, especially emphasizing the changes in photosynthesis-related protein accumulation. We focus on: (a) chloroplast proteins that differentially accumulate during viral infection; (b) the significance with respect to chloroplast-virus interaction; and (c) alterations in plant's energetic metabolism and the subsequently the plant defense mechanisms to overcome viral infection.

Correlated fluorescence quenching and topographic mapping of Light-Harvesting Complex II within surface-assembled aggregates and lipid bilayers

Light-Harvesting Complex II (LHCII) is a chlorophyll-protein antenna complex that efficiently absorbs solar energy and transfers electronic excited states to photosystems I and II. Under excess light intensity LHCII can adopt a photoprotective state in which excitation energy is safely dissipated as heat, a process known as Non-Photochemical Quenching (NPQ). In vivo NPQ is triggered by combinatorial factors including transmembrane ΔpH, PsbS protein and LHCII-bound zeaxanthin, leading to dramatically shortened LHCII fluorescence lifetimes. In vitro, LHCII in detergent solution or in proteoliposomes can reversibly adopt an NPQ-like state, via manipulation of detergent/protein ratio, lipid/protein ratio, pH or pressure. Previous spectroscopic investigations revealed changes in exciton dynamics and protein conformation that accompany quenching, however, LHCII-LHCII interactions have not been extensively studied. Here, we correlated fluorescence lifetime imaging microscopy (FLIM) and atomic force microscopy (AFM) of trimeric LHCII adsorbed to mica substrates and manipulated the environment to cause varying degrees of quenching. AFM showed that LHCII self-assembled onto mica forming 2D-aggregates (25-150 nm width). FLIM determined that LHCII in these aggregates were in a quenched state, with much lower fluorescence lifetimes (~0.25 ns) compared to free LHCII in solution (2.2-3.9 ns). LHCII-LHCII interactions were disrupted by thylakoid lipids or phospholipids, leading to intermediate fluorescent lifetimes (0.6-0.9 ns). To our knowledge, this is the first in vitro correlation of nanoscale membrane imaging with LHCII quenching. Our findings suggest that lipids could play a key role in modulating the extent of LHCII-LHCII interactions within the thylakoid membrane and so the propensity for NPQ activation.

The peculiar NPQ regulation in the stramenopile Phaeomonas sp. challenges the xanthophyll cycle dogma

In changing light conditions, photosynthetic organisms develop different strategies to maintain a fine balance between light harvesting, photochemistry, and photoprotection. One of the most widespread photoprotective mechanisms consists in the dissipation of excess light energy in the form of heat in the photosystem II antenna, which participates to the Non Photochemical Quenching (NPQ) of chlorophyll fluorescence. It is tightly related to the reversible epoxidation of xanthophyll pigments, catalyzed by the two enzymes, the violaxanthin deepoxidase and the zeaxanthin epoxidase. In Phaeomonas sp. (Pinguiophyte, Stramenopiles), we show that the regulation of the heat dissipation process is different from that of the green lineage: the NPQ is strictly proportional to the amount of the xanthophyll pigment zeaxanthin and the xanthophyll cycle enzymes are differently regulated. The violaxanthin deepoxidase is already active in the dark, because of a low luminal pH, and the zeaxanthin epoxidase shows a maximal activity under moderate light conditions, being almost inactive in the dark and under high light. This light-dependency mirrors the one of NPQ: Phaeomonas sp. displays a large NPQ in the dark as well as under high light, which recovers under moderate light. Our results pinpoint zeaxanthin epoxidase activity as the prime regulator of NPQ in Phaeomonas sp. and therefore challenge the deepoxidase-regulated xanthophyll cycle dogma.

Can red-emitting state be responsible for fluorescence quenching in LHCII aggregates?

Non-photochemical quenching (NPQ) is responsible for protecting the light-harvesting apparatus of plants from damage at high light conditions. Although it is agreed that the major part of NPQ, an energy-dependent quenching (qE), originates in the light-harvesting antenna, its exact mechanism is still debated. In our earlier work (Chmeliov et al. in Nat Plants 2:16045, 2016), we have analyzed the time-resolved fluorescence (TRF) from the trimers and aggregates of the major light-harvesting complexes of plants (LHCII) over a broad temperature range and came to a conclusion that three distinct states are required to describe the experimental data: two of them correspond to the emission bands centered at ~680 and ~700 nm, and the third state is responsible for the excitation quenching. This was opposite to earlier suggestions of a two-state model, where the red-shifted fluorescence and excitation quenching were assumed to be related. To examine such possibility, in the current work we repeat our analysis of the TRF data in terms of the two-state model. We find that even though it can reasonably describe the aggregate fluorescence, it fails to do so for the LHCII trimers. We conclude that the red-emitting state cannot be responsible for fluorescence quenching in the LHCII aggregates and reaffirm that the three-state model is the simplest possible description of the experimental data.

Revisiting the Role of Xanthophylls in Nonphotochemical Quenching

Photoprotective nonphotochemical quenching (NPQ) of absorbed solar energy is vital for survival of photosynthetic organisms, and NPQ modifications significantly improve plant productivity. However, the exact NPQ quenching mechanism is obscured by discrepancies between reported mechanisms, involving xanthophyll-chlorophyll (Xan-Chl) and Chl-Chl interactions. We present evidence of an experimental artifact that may explain the discrepancies: strong laser pulses lead to the formation of a novel electronic species in the major plant light-harvesting complex (LHCII). This species evolves from a high excited state of Chl a and is absent with weak laser pulses. It resembles an excitonically coupled heterodimer of Chl a and lutein (or other Xans at site L1) and acts as a de-excitation channel. Laser powers, and consequently amounts of artifact, vary strongly between NPQ studies, thereby explaining contradicting spectral signatures attributed to NPQ. Our results offer pathways toward unveiling NPQ mechanisms and highlight the necessity of careful attention to laser-induced artifacts.

Fine control of chlorophyll-carotenoid interactions defines the functionality of light-harvesting proteins in plants

Photosynthetic antenna proteins can be thought of as "programmed solvents", which bind pigments at specific mutual orientations, thus tuning the overall energetic landscape and ensuring highly efficient light-harvesting. While positioning of chlorophyll cofactors is well understood and rationalized by the principle of an "energy funnel", the carotenoids still pose many open questions. Particularly, their short excited state lifetime (<25 ps) renders them potential energy sinks able to compete with the reaction centers and drastically undermine light-harvesting efficiency. Exploration of the orientational phase-space revealed that the placement of central carotenoids minimizes their interaction with the nearest chlorophylls in the plant antenna complexes LHCII, CP26, CP29 and LHCI. At the same time we show that this interaction is highly sensitive to structural perturbations, which has a profound effect on the overall lifetime of the complex. This links the protein dynamics to the light-harvesting regulation in plants by the carotenoids.

The carotenoid pathway: what is important for excitation quenching in plant antenna complexes?

Plant light-harvesting is regulated by the Non-Photochemical Quenching (NPQ) mechanism involving the slow trapping of excitation energy by carotenoids in the Photosystem II (PSII) antenna in response to high light.

Coulomb couplings in solubilised light harvesting complex II (LHCII): challenging the ideal dipole approximation from TDDFT calculations

We investigate the coulomb coupling interactions of natural chromophores in the solubilised light harvesting complex II (LHCII) using DFT quantum chemistry calculations.

Energizing the light harvesting antenna: Insight from CP29

How do plants cope with excess light energy? Crop health and stress tolerance are governed by molecular photoprotective mechanisms. Protective exciton quenching in plants is activated by membrane energization, via unclear conformational changes in proteins called antennas. Here we show that pH and salt gradients stimulate the response of such an antenna under low and high energization by all-atom Molecular Dynamics Simulations. Novel insight establishes that helix-5 (H5) conformation in CP29 from spinach is regulated by chemiosmotic factors. This is selectively correlated with the chl-614 macrocycle deformation and interactions with nearby pigments, that could suggest a role in plant photoprotection. Adding to the significance of our findings, H5 domain is conserved among five antennas (LHCB1-5). These results suggest that light harvesting complexes of Photosystem II, one of the most abundant proteins on earth, can sense chemiosmotic gradients via their H5 domains in an upgraded role from a solar detector to also a chemiosmotic sensor.

An In Vivo Quantitative Comparison of Photoprotection in Arabidopsis Xanthophyll Mutants

Contribution of different LHCII antenna carotenoids to protective NPQ (pNPQ) were tested using a range of xanthophyll biosynthesis mutants of Arabidopsis: plants were either devoid of lutein (lut2), violaxanthin (npq2), or synthesized a single xanthophyll species, namely violaxanthin (aba4npq1lut2), zeaxanthin (npq2lut2), or lutein (chy1chy2lut5). A novel pulse amplitude modulated (PAM) fluorescence analysis procedure, that used a gradually increasing actinic light intensity, allowed the efficiency of pNPQ to be tested using the photochemical quenching (qP) parameter measured in the dark (qPd). Furthermore, the yield of photosystem II (ΦPSII) was calculated, and the light intensity which induces photoinhibition in 50% of leaves for each mutant was ascertained. Photoprotective capacities of each xanthophyll were quantified, taking into account chlorophyll a/b ratios and excitation pressure. Here, light tolerance, pNPQ capacity, and ΦPSII were highest in wild type plants. Of the carotenoid mutants, lut2 (lutein-deficient) plants had the highest light tolerance, and the joint the highest ΦPSII with violaxanthin only plants. We conclude that all studied mutants possess pNPQ and a more complete composition of xanthophylls in their natural binding sites is the most important factor governing photoprotection, rather than any one specific xanthophyll suggesting a strong structural effect of the molecules upon the LHCII antenna organization and discuss the results significance for future crop development.

Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.

The nature of self-regulation in photosynthetic light-harvesting antenna

The photosynthetic apparatus of green plants is well known for its extremely high efficiency that allows them to operate under dim light conditions. On the other hand, intense sunlight may result in overexcitation of the light-harvesting antenna and the formation of reactive compounds capable of 'burning out' the whole photosynthetic unit. Non-photochemical quenching is a self-regulatory mechanism utilized by green plants on a molecular level that allows them to safely dissipate the detrimental excess excitation energy as heat. Although it is believed to take place in the plant's major light-harvesting complexes (LHC) II, there is still no consensus regarding its molecular nature. To get more insight into its physical origin, we performed high-resolution time-resolved fluorescence measurements of LHCII trimers and their aggregates across a wide temperature range. Based on simulations of the excitation energy transfer in the LHCII aggregate, we associate the red-emitting state, having fluorescence maximum at ∼700 nm, with the partial mixing of excitonic and chlorophyll-chlorophyll charge transfer states. On the other hand, the quenched state has a totally different nature and is related to the incoherent excitation transfer to the short-lived carotenoid excited states. Our results also show that the required level of photoprotection in vivo can be achieved by a very subtle change in the number of LHCIIs switched to the quenched state.

Mixing of exciton and charge-transfer states in light-harvesting complex Lhca4

Structure-based modeling of spectra of the wild-type Lhca4 and NH mutant enables us to build the exciton model of the complex that includes a charge-transfer state mixed with the excited-state manifold.

Dynamic quenching in single photosystem II supercomplexes

Time-resolved fluorescence measurements of single PSII supercomplexes to investigate blinking and dynamic quenching in the context of non-photochemical quenching (NPQ).