The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants

Probing the Effect of Mutations on Light Harvesting in CP29 by Transient Absorption and First-Principles Simulations

Natural light harvesting is exceptionally efficient thanks to the local energy funnel created within light-harvesting complexes (LHCs). To understand the design principles underlying energy transport in LHCs, ultrafast spectroscopy is often complemented by mutational studies that introduce perturbations into the excitonic structure of the natural complexes. However, such studies may fall short of identifying all excitation energy transfer (EET) pathways and their changes upon mutation. Here, we show that a synergistic combination of first-principles calculations and ultrafast spectroscopy can give unprecedented insight into the EET pathways occurring within LHCs. We measured the transient absorption spectra of the minor CP29 complex of plants and of two mutants, systematically mapping the kinetic components seen in experiments to the simulated exciton dynamics. With our combined strategy, we show that EET in CP29 is surprisingly robust to the changes in the exciton states induced by mutations, explaining the versatility of plant LHCs.

Site-Directed Mutagenesis of the Chlorophyll-Binding Sites Modulates Excited-State Lifetime and Chlorophyll-Xanthophyll Energy Transfer in the Monomeric Light-Harvesting Complex CP29

We combine site-directed mutagenesis with picosecond time-resolved fluorescence and femtosecond transient absorption (TA) spectroscopies to identify excitation energy transfer (EET) processes between chlorophylls (Chls) and xanthophylls (Xant) in the minor antenna complex CP29 assembled inside nanodiscs, which result in quenching. When compared to WT CP29, a longer lifetime was observed in the A2 mutant, missing Chl a612, which closely interacts with Xant Lutein in site L1. Conversely, a shorter lifetime was obtained in the A5 mutant, in which the interaction between Chl a603 and Chl a609 is strengthened, shifting absorption to lower energy and enhancing Chl-Xant EET. Global analysis of TA data indicated that EET from Chl a Qy to a Car dark state S* is active in both the A2 and A5 mutants and that their rate constants are modulated by mutations. Our study provides experimental evidence that multiple Chl-Xant interactions are involved in the quenching activity of CP29.

Unravelling the fluorescence kinetics of light-harvesting proteins with simulated measurements

The plant light-harvesting pigment-protein complex LHCII is the major antenna sub-unit of PSII and is generally (though not universally) accepted to play a role in photoprotective energy dissipation under high light conditions, a process known Non-Photochemical Quenching (NPQ). The underlying mechanisms of energy trapping and dissipation within LHCII are still debated. Various models have been proposed for the underlying molecular detail of NPQ, but they are often based on different interpretations of very similar transient absorption measurements of isolated complexes. Here we present a simulated measurement of the fluorescence decay kinetics of quenched LHCII aggregates to determine whether this relatively simple measurement can discriminate between different potential NPQ mechanisms. We simulate not just the underlying physics (excitation, energy migration, quenching and singlet-singlet annihilation) but also the signal detection and typical experimental data analysis. Comparing this to a selection of published fluorescence decay kinetics we find that: (1) Different proposed quenching mechanisms produce noticeably different fluorescence kinetics even at low (annihilation free) excitation density, though the degree of difference is dependent on pulse width. (2) Measured decay kinetics are consistent with most LHCII trimers becoming relatively slow excitation quenchers. A small sub-population of very fast quenchers produces kinetics which do not resemble any observed measurement. (3) It is necessary to consider at least two distinct quenching mechanisms in order to accurately reproduce experimental kinetics, supporting the idea that NPQ is not a simple binary switch.

First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex

The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption (TA) spectroscopy is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra as the number of EET processes occurring at the same time is very large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here, we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems.

Kinetics of the xanthophyll cycle and its role in photoprotective memory and response

Efficiently balancing photochemistry and photoprotection is crucial for survival and productivity of photosynthetic organisms in the rapidly fluctuating light levels found in natural environments. The ability to respond quickly to sudden changes in light level is clearly advantageous. In the alga Nannochloropsis oceanica we observed an ability to respond rapidly to sudden increases in light level which occur soon after a previous high-light exposure. This ability implies a kind of memory. In this work, we explore the xanthophyll cycle in N. oceanica as a short-term photoprotective memory system. By combining snapshot fluorescence lifetime measurements with a biochemistry-based quantitative model, we show that short-term memory arises from the xanthophyll cycle. In addition, the model enables us to characterize the relative quenching abilities of the three xanthophyll cycle components. Given the ubiquity of the xanthophyll cycle in photosynthetic organisms the model described here will be of utility in improving our understanding of vascular plant and algal photoprotection with important implications for crop productivity.

Impact of Structure, Coupling Scheme, and State of Interest on the Energy Transfer in CP29

The Qy and Bx excitation energy transfer (EET) in the minor light-harvesting complex CP29 (LHCII B4.1) antenna complex of Pisum sativum was characterized using a computational approach. We applied Förster resonance energy transfer (FRET) and the transition density cube (TDC) method to estimate the Coulombic coupling, based on a combination of classical molecular dynamics and quantum mechanics/molecular mechanics calculations. Employing TDC instead of FRET mostly affects the EET between chlorophylls (Chls) and carotenoids (Crts), as expected due to the Crts being spatially more challenging for FRET. Only between Chls, effects are found to be small (about only 0.1 EET efficiency change when introducing TDC instead of FRET). Effects of structural sampling were found to be small, illustrated by a small average standard deviation for the Qy state coupling elements (FRET/TDC: 0.97/0.94 cm-1). Due to the higher flexibility of the Bx state, the corresponding deviations are larger (FRET/TDC between Chl-Chl pairs: 17.58/22.67 cm-1, between Crt-Chl pairs: 62.58/31.63 cm-1). In summary, it was found for the Q band that the coupling between Chls varies only slightly depending on FRET or TDC, resulting in a minute effect on EET acceptor preference. In contrast, the coupling in the B band spectral region is found to be more affected. Here, the S2 (1Bu) states of the spatially challenging Crts may act as acceptors in addition to the B states of the Chls. Depending on FRET or TDC, several Chls show different Chl-to-Crt couplings. Interestingly, the EET between Chls or Crts in the B band is found to often outcompete the corresponding decay processes. The individual efficiencies for B band EET to Crts vary however strongly with the chosen coupling scheme (e.g., up to 0.29/0.99 FRET/TDC efficiency for the Chl a604/neoxanthin pair). Thus, the choice of the coupling scheme must involve a consideration of the state of interest.

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.

The origin of pigment-binding differences in CP29 and LHCII: the role of protein structure and dynamics

The first step of photosynthesis in plants is performed by the light-harvesting complexes (LHC), a large family of pigment-binding proteins embedded in the photosynthetic membranes. These complexes are conserved across species, suggesting that each has a distinct role. However, they display a high degree of sequence homology and their static structures are almost identical. What are then the structural features that determine their different properties? In this work, we compared the two best-characterized LHCs of plants: LHCII and CP29. Using molecular dynamics simulations, we could rationalize the difference between them in terms of pigment-binding properties. The data also show that while the loops between the helices are very flexible, the structure of the transmembrane regions remains very similar in the crystal and the membranes. However, the small structural differences significantly affect the excitonic coupling between some pigment pairs. Finally, we analyzed in detail the structure of the long N-terminus of CP29, showing that it is structurally stable and it remains on top of the membrane even in the absence of other proteins. Although the structural changes upon phosphorylation are minor, they can explain the differences in the absorption properties of the pigments observed experimentally.

Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes

We propose a machine learning (ML)-based strategy for an inexpensive calculation of excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical molecular dynamics simulations of LHCs in their natural environment in combination with ML prediction of the excitonic Hamiltonian of the embedded aggregate of pigments. The proposed ML model can reproduce the effects of geometrical fluctuations together with those due to electrostatic and polarization interactions between the pigments and the protein. The training is performed on the chlorophylls of the major LHC of plants, but we demonstrate that the model is able to extrapolate well beyond the initial training set. Moreover, the accuracy in predicting the effects of the environment is tested on the simulation of the small changes observed in the absorption spectra of the wild-type and a mutant of a minor LHC.

A fast method for electronic couplings in embedded multichromophoric systems

Electronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories.

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.

Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy

Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, light-harvesting complex stress-related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work, we propose a structural model of LHCSR1 from the moss P. patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses.

The structure of the moss P. patens light-harvesting complex stress-related 1 (LHCSR1) is determined using a multi-scale computational approach for investigations of its photoprotective function.

Effect of protein matrix on CP29 spectra and energy transfer pathways

We investigate energy transfer pathways between strongly coupled chlorophylls (Chls) in the CP29 (LHCII B4.1) antenna complex of Pisum sativum, including the possibility of higher energy states. We test for the environmental effects caused by the protein, membrane and solvent using a hybrid QM/MM approach. Classical molecular dynamics simulations of the full CP29 complex embedded in a DOPC membrane have been performed, followed by calculations of the time dependent DFT spectra of all Chls at several timesteps. The relative orientations of transition dipole moments (TDMs) were specifically analyzed, including and excluding the point charge field (PCF) of the surrounding environment. The PCF is found to drastically shift the spectra of specific Chls, while the majority of Chls is mostly unaffected. The net effect on the sum spectrum is however found to be negligible: The few strong changes in Chl spectra cancel each other due to being opposite in sign. We further find that the spectra of the Chls coordinating to water show a blue shift upon introduction of the environment. Conversely, the spectra of the Chls coordinating to glutamine show a red shift upon activation of the PCF. As the main influence of the PCF for tuning the couplings, we identify the energetic position of the individual chromophores. The fine-tuning, especially for states energetically above the Q_y state, is however controlled by the changes in the TDM orientations. We also find an indication for the PCF to steer potentially harmful high energy excitations away from the PSII core complex.

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.

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.

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.