Excitation energy transfer and charge separation in photosystem II membranes revisited

Optimizing photosynthetic light-harvesting under stars: simple and general antenna models

In the next 10-20 years, several observatories will aim to detect the signatures of oxygenic photosynthesis on exoplanets, though targets must be carefully selected. Most known potentially habitable exo-planets orbit cool M-dwarf stars, which have limited emission in the photosynthetically active region of the spectrum (PAR, 400 < λ < 700 nm) used by Earth's oxygenic photoautotrophs. Still, recent experiments have shown that model cyanobacteria, algae, and non-vascular plants grow comfortably under simulated M-dwarf light, though vascular plants struggle. Here, we hypothesize that this is partly due to the different ways they harvest light, reflecting some general rule that determines how photosynthetic antenna structures may evolve under different stars. We construct a simple thermodynamic model of an oxygenic antenna-reaction centre supercomplex and determine the optimum structure, size and absorption spectrum under light from several star types. For the hotter G (e.g. the Sun) and K-stars, a small modular antenna is optimal and qualitatively resembles the PSII-LHCII supercomplex of higher plants. For the cooler M-dwarfs, a very large antenna with a steep 'energy funnel' is required, resembling the cyanobacterial phycobilisome. For the coolest M-dwarfs an upper limit is reached, where increasing antenna size further is subject to steep diminishing returns in photosynthetic output. We conclude that G- and K-stars could support a range of niches for oxygenic photo-autotrophs, including high-light adapted canopy vegetation that may generate detectable bio-signatures. M-dwarfs may only be able to support low light-adapted organisms that have to invest considerable resources in maintaining a large antenna. This may negatively impact global coverage and therefore detectability.

Bidirectional Energy Flow in the Photosystem II Supercomplex

The water-splitting capability of Photosystem II (PSII) of plants and green algae requires the system to balance efficient light harvesting along with effective photoprotection against excitation in excess of the photosynthetic capacity, particularly under the naturally fluctuating sunlight intensity. The comparatively flat energy landscape of the multicomponent structure, inferred from the spectra of the individual pigment-protein complexes and the rather narrow and featureless absorption spectrum, is well known. However, how the combination of the required functions emerges from the interactions among the multiple components of the PSII supercomplex (PSII-SC) cannot be inferred from the individual pigment-protein complexes. In this work, we investigate the energy transfer dynamics of the C2S2-type PSII-SC with a combined spectroscopic and modeling approach. Specifically, two-dimensional electronic-vibrational (2DEV) spectroscopy provides enhanced spectral resolution and the ability to map energy evolution in real space, while the quantum dynamical simulation allows complete kinetic modeling of the 210 chromophores. We demonstrate that additional pathways emerge within the supercomplex. In particular, we show that excitation energy can leave the vicinity of the charge separation components, the reaction center (RC), faster than it can transfer to it. This enables activatable quenching centers in the periphery of the PSII-SC to be effective in removing excessive energy in cases of overexcitation. Overall, we provide a quantitative description of how the seemingly contradictory functions of PSII-SC arise from the combination of its individual components. This provides a fundamental understanding that will allow further improvement of artificial solar energy devices and bioengineering processes for increasing crop yield.

Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Photosystem II (PSII), the principal enzyme of oxygenic photosynthesis, contains two integral light harvesting proteins (CP43 and CP47) that bind chlorophylls and carotenoids. The two intrinsic antennae play crucial roles in excitation energy transfer and photoprotection. CP43 interacts most closely with the reaction center of PSII, specifically with the branch of the reaction center (D1) that is responsible for primary charge separation and electron transfer. Deciphering the function of CP43 requires detailed atomic-level insights into the properties of the embedded pigments. To advance this goal, we employ a range of multiscale computational approaches to determine the site energies and excitonic profile of CP43 chlorophylls, using large all-atom models of a membrane-bound PSII monomer. In addition to time-dependent density functional theory (TD-DFT) used in the context of a quantum-mechanics/molecular-mechanics setup (QM/MM), we present a thorough analysis using the perturbed matrix method (PMM), which enables us to utilize information from long-timescale molecular dynamics simulations of native PSII-complexed CP43. The excited state energetics and excitonic couplings have both similarities and differences compared with previous experimental fits and theoretical calculations. Both static TD-DFT and dynamic PMM results indicate a layered distribution of site energies and reveal specific groups of chlorophylls that have shared contributions to low-energy excitations. Importantly, the contribution to the lowest energy exciton does not arise from the same chlorophylls at each system configuration, but rather changes as a function of conformational dynamics. An unexpected finding is the identification of a low-energy charge-transfer excited state within CP43 that involves a lumenal (C2) and the central (C10) chlorophyll of the complex. The results provide a refined basis for structure-based interpretation of spectroscopic observations and for further deciphering excitation energy transfer in oxygenic photosynthesis.

Inter-subunit energy transfer processes in a minimal plant photosystem II supercomplex

Photosystem II (PSII) is an integral part of the photosynthesis machinery, in which several light-harvesting complexes rely on inter-complex excitonic energy transfer (EET) processes to channel energy to the reaction center. In this paper, we report on a direct observation of the inter-complex EET in a minimal PSII supercomplex from plants, containing the trimeric light-harvesting complex II (LHCII), the monomeric light-harvesting complex CP26, and the monomeric PSII core complex. Using two-dimensional (2D) electronic spectroscopy, we measure an inter-complex EET timescale of 50 picoseconds for excitations from the LHCII-CP26 peripheral antenna to the PSII core. The 2D electronic spectra also reveal that the transfer timescale is nearly constant over the pump spectrum of 600 to 700 nanometers. Structure-based calculations reveal the contribution of each antenna complex to the measured inter-complex EET time. These results provide a step in elucidating the full inter-complex energy transfer network of the PSII machinery.

Excitation Energy Transfer between Higher Excited States of Photosynthetic Pigments: 2. Chlorophyll b is a B Band Excitation Trap

Chlorophylls (Chls) are known for fast, subpicosecond internal conversion (IC) from ultraviolet/blue absorbing ("B" or "Soret" states) to the energetically lower, red light-absorbing Q states. Consequently, excitation energy transfer (EET) in photosynthetic pigment-protein complexes involving the B states has so far not been considered. We present, for the first time, a theoretical framework for the existence of B-B EET in tightly coupled Chl aggregates such as photosynthetic pigment-protein complexes. We show that according to a Förster resonance energy transport (FRET) scheme, unmodulated B-B EET has an unexpectedly high range. Unsuppressed, it could pose an existential threat-the damage potential of blue light for photochemical reaction centers (RCs) is well-known. This insight reveals so-far undescribed roles for carotenoids (Crts, cf. previous article in this series) and Chl b (this article) of possibly vital importance. Our model system is the photosynthetic antenna pigment-protein complex (CP29). The focus of the study is on the role of Chl b for EET in the Q and B bands. Further, the initial excited pigment distribution in the B band is computed for relevant solar irradiation and wavelength-centered laser pulses. It is found that both accessory pigment classes compete efficiently with Chl a absorption in the B band, leaving only 40% of B band excitations for Chl a. B state population is preferentially relocated to Chl b after excitation of any Chls, due to a near-perfect match of Chl b B band absorption with Chl a B state emission spectra. This results in an efficient depletion of the Chl a population (0.66 per IC/EET step, as compared to 0.21 in a Chl a-only system). Since Chl b only occurs in the peripheral antenna complexes of plants and algae, and RCs contain only Chl a, this would automatically trap potentially dangerous B state population in the antennae, preventing forwarding to the RCs.

From antenna to reaction center: Pathways of ultrafast energy and charge transfer in photosystem II

The photosystem II core complex (PSII-CC) is a photosynthetic complex that contains antenna proteins, which collect energy from sunlight, and a reaction center, which converts the collected energy to redox potential. Understanding the interplay between the antenna proteins and the reaction center will facilitate the development of more efficient solar energy conversion technologies. Here, we study the sub-100-ps dynamics of PSII-CC with two-dimensional electronic-vibrational spectroscopy, which connects energy flows with physical space, allowing a direct mapping of energy transfer pathways. Our results reveal a complex dynamical scheme which includes a specific pathway that connects CP43 to the reaction center. Resolving this pathway experimentally provides insights into the energy conversion processes in natural photosynthesis.

The photosystem II core complex (PSII-CC) is the smallest subunit of the oxygenic photosynthetic apparatus that contains core antennas and a reaction center, which together allow for rapid energy transfer and charge separation, ultimately leading to efficient solar energy conversion. However, there is a lack of consensus on the interplay between the energy transfer and charge separation dynamics of the core complex. Here, we report the application of two-dimensional electronic-vibrational (2DEV) spectroscopy to the spinach PSII-CC at 77 K. The simultaneous temporal and spectral resolution afforded by 2DEV spectroscopy facilitates the separation and direct assignment of coexisting dynamical processes. Our results show that the dominant dynamics of the PSII-CC are distinct in different excitation energy regions. By separating the excitation regions, we are able to distinguish the intraprotein dynamics and interprotein energy transfer. Additionally, with the improved resolution, we are able to identify the key pigments involved in the pathways, allowing for a direct connection between dynamical and structural information. Specifically, we show that C505 in CP43 and the peripheral chlorophyll Chlz_D1 in the reaction center are most likely responsible for energy transfer from CP43 to the reaction center.

Ultrafast excitation quenching by the oxidized photosystem II reaction center

Photosystem II (PSII) is the pigment–protein complex driving the photoinduced oxidation of water and reduction of plastoquinone in all oxygenic photosynthetic organisms. Excitations in the antenna chlorophylls are photochemically trapped in the reaction center (RC) producing the chlorophyll–pheophytin radical ion pair P+ Pheo−. When electron donation from water is inhibited, the oxidized RC chlorophyll P+ acts as an excitation quencher, but knowledge on the kinetics of quenching is limited. Here, we used femtosecond transient absorption spectroscopy to compare the excitation dynamics of PSII with neutral and oxidized RC (P+). We find that equilibration in the core antenna has a major lifetime of about 300 fs, irrespective of the RC redox state. Two-dimensional electronic spectroscopy revealed additional slower energy equilibration occurring on timescales of 3–5 ps, concurrent with excitation trapping. The kinetics of PSII with open RC can be described well with previously proposed models according to which the radical pair P+ Pheo− is populated with a main lifetime of about 40 ps, which is primarily determined by energy transfer between the core antenna and the RC chlorophylls. Yet, in PSII with oxidized RC (P+), fast excitation quenching was observed with decay lifetimes as short as 3 ps and an average decay lifetime of about 90 ps, which is shorter than the excited-state lifetime of PSII with open RC. The underlying mechanism of this extremely fast quenching prompts further investigation.

The role of light-harvesting complex I in excitation energy transfer from LHCII to photosystem I in Arabidopsis

Photosynthesis powers nearly all life on Earth. Light absorbed by photosystems drives the conversion of water and carbon dioxide into sugars. In plants, photosystem I (PSI) and photosystem II (PSII) work in series to drive the electron transport from water to NADP+. As both photosystems largely work in series, a balanced excitation pressure is required for optimal photosynthetic performance. Both photosystems are composed of a core and light-harvesting complexes (LHCI) for PSI and LHCII for PSII. When the light conditions favor the excitation of one photosystem over the other, a mobile pool of trimeric LHCII moves between both photosystems thus tuning their antenna cross-section in a process called state transitions. When PSII is overexcited multiple LHCIIs can associate with PSI. A trimeric LHCII binds to PSI at the PsaH/L/O site to form a well-characterized PSI-LHCI-LHCII supercomplex. The binding site(s) of the "additional" LHCII is still unclear, although a mediating role for LHCI has been proposed. In this work, we measured the PSI antenna size and trapping kinetics of photosynthetic membranes from Arabidopsis (Arabidopsis thaliana) plants. Membranes from wild-type (WT) plants were compared to those of the ΔLhca mutant that completely lacks the LHCI antenna. The results showed that "additional" LHCII complexes can transfer energy directly to the PSI core in the absence of LHCI. However, the transfer is about two times faster and therefore more efficient, when LHCI is present. This suggests LHCI mediates excitation energy transfer from loosely bound LHCII to PSI in WT plants.

Water-Induced Tuning of the Emission of Polyaniline LEDs within the NIR to Vis Range

Tuning of the emission within the near-infrared to visible range is observed in p-toluenesulfonic acid-doped polyaniline light emitting diodes (PANI/PTSA), when water molecules are absorbed by the active material (wet PANI/PTSA). This is a hybrid material that combines a conjugated π-electron system and a proton system, both strongly interacting in close contact with each other. The proton system successfully competes with the electron system in excitation energy consumption (when electrically powered), thanks to the inductive resonance energy transfer from electrons to protons in wet PANI/PTSA at the energy levels of combination of vibrations and overtones in water, with subsequent light emission. Wet PANI/PTSA, in which electrons and protons can be excited parallelly owing to fast energy transfer, may emit light in different ranges (on a competitive basis). This results in intense light emission with a maximum at 750 nm (and the spectrum very similar to that of an excited protonic system in water), which is blue-shifted compared to the initial one at ∼850 nm that is generated by the PANI/PTSA dry sample, when electrically powered.

Time- and reduction-dependent rise of photosystem II fluorescence during microseconds-long inductions in leaves

Lettuce (Lactuca sativa) and benth (Nicotiana benthamiana) leaves were illuminated with 720 nm background light to mix S-states and oxidize electron carriers. Green-filtered xenon flashes of different photon dose were applied and O2 evolution induced by a flash was measured. After light intensity gradient across the leaf was mathematically considered, the flash-induced PSII electron transport (= 4·O2 evolution) exponentially increased with the flash photon dose in any differential layer of the leaf optical density. This proved the absence of excitonic connectivity between PSII units. Time courses of flash light intensity and 680 nm chlorophyll fluorescence emission were recorded. While with connected PSII the sigmoidal fluorescence rise has been explained by quenching of excitation in closed PSII by its open neighbors, in the absence of connectivity the sigmoidicity indicates gradual rise of the fluorescence yield of an individual closed PSII during the induction. Two phases were discerned: the specific fluorescence yield immediately increased from Fo to 1.8Fo in a PSII, whose reaction center became closed; fluorescence yield of the closed PSII was keeping time-dependent rise from 1.8Fo to about 3Fo, approaching the flash fluorescence yield Ff = 0.6Fm during 40 μs. The time-dependent fluorescence rise was resolved from the quenching by 3Car triplets and related to protein conformational change. We suggest that QA reduction induces a conformational change, which by energetic or structural means closes the gate for excitation entrance into the central radical pair trap-efficiently when QB cannot accept the electron, but less efficiently when it can.

Structural basis of light-harvesting in the photosystem II core complex

Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.

β-Carotene Probes the Energy Transfer Pathway in the Photosystem II Core Complex

The dynamics of the intact photosystem II core complex (PSII-CC) has been investigated extensively to elucidate its excellent photofunction. However, it is significantly difficult to observe the primary photosynthetic processes in PSII-CC because a vast number of chlorophylls (Chl) in the core complex show similar spectral features. In the present work, the dynamics of the energy transfer (ET) from β-carotene (Bcr) in intact PSII-CC followed by charge separation (CS) at the reaction center (RC) with different excitation wavelengths were compared. Upon excitation at 510 nm, which selectively excites Bcr (Bcr651) inside of the D1-D2 RC, the pheophytin anion absorption band appeared within 9.6 ps. On the other hand, upon excitation at 490 nm, mainly exciting unspecified Bcr in the antenna complex, the anion band appeared after 20 ps. These excitation wavelength dependence experiments revealed a new ET pathway of PSII-CC, which indicates that the initial CS of PSII-CC is limited by ET to the RC.

A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways

Here we present our theoretical investigations into the light reaction in the dimeric photosystem II (PSII) core complex. An effective model for excitation energy transfer (EET) and primary charge separation (CS) in the PSII core complex was developed, with model parameters constructed based on molecular dynamics (MD) simulation data. Compared to experimental results, we demonstrated that this model faithfully reproduces the absorption spectra of the RC and core light-harvesting complexes (CP43 and CP47) as well as the full EET dynamics among the chromophores in the PSII core complex. We then applied master equation simulations and network analysis to investigate detailed EET plus CS dynamics in the system, allowing us to identify key EET pathways and produce a coarse-grained cluster model for the light reaction in the dimeric PSII core complex. We show that non-equilibrium energy transfer channels play important roles in the efficient light harvesting process and that multiple EET pathways exist between subunits of PSII to ensure the robustness of light harvesting in the system. Furthermore, we revealed that inter-monomer energy transfer dominated by the coupling between the two CLA625 molecules enables efficient energy exchange between two CP47s in the dimeric PSII core complex, which leads to significant energy pooling in the CP47 domain during the light reaction. Our study provides a blueprint for the design of light harvesting in the PSII core and show that a structure-based approach using molecular dynamics simulations and quantum chemistry calculations can be effectively utilized to elucidate the dynamics of light harvesting in complex photosynthetic systems.

Excitation and emission wavelength dependence of fluorescence spectra in whole cells of the cyanobacterium Synechocystis sp. PPC6803: Influence on the estimation of Photosystem II maximal quantum efficiency

The fluorescence emission spectrum of Synechocystis sp. PPC6803 cells, at room temperature, displays: i) significant bandshape variations when collected under open (F₀) and closed (F_M) Photosystem II reaction centre conditions; ii) a marked dependence on the excitation wavelength both under F₀ and F_M conditions, due to the enhancement of phycobilisomes (PBS) emission upon their direct excitation. As a consequence: iii) the ratio of the variable and maximal fluorescence (F_V/F_M), that is a commonly employed indicator of the maximal photochemical quantum efficiency of PSII (Φ_{pc, PSII}), displays a significant dependency on both the excitation and the emission (detection) wavelength; iv) the F_V/F_M excitation/emission wavelength dependency is due, primarily, to the overlap of PSII emission with that of supercomplexes showing negligible changes in quantum yield upon trap closure, i.e. PSI and a PBS fraction which is incapable to transfer the excitation energy efficiently to core complexes. v) The contribution to the cellular emission and the relative absorption-cross section of PSII, PSI and uncoupled PBS are extracted using a spectral decomposition strategy. It is concluded that vi) Φ_{pc, PSII} is generally underestimated from the F_V/F_M measurements in this organism and, the degree of the estimation bias, which can exceed 50%, depends on the measurement conditions. Spectral modelling based on the decomposed emission/cross-section profiles were extended to other processes typically monitored from steady-state fluorescence measurements, in the presence of an actinic illumination, in particular non-photochemical quenching. It is suggested that vii) the quenching extent is generally underestimated in analogy to F_V/F_M but that viii) the location of quenching sites can be discriminated based on the combined excitation/emission spectral analysis.

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.

Ultrafast energy transfer within the photosystem II core complex

We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

Blue Native/SDS-PAGE and iTRAQ-Based Chloroplasts Proteomics Analysis of Nicotiana tabacum Leaves Infected with M Strain of Cucumber Mosaic Virus Reveals Several Proteins Involved in Chlorosis Symptoms

Virus infection in plants involves necrosis, chlorosis, and mosaic. The M strain of cucumber mosaic virus (M-CMV) has six distinct symptoms: vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery, and secondary mosaic. Chlorosis indicates the loss of chlorophyll which is highly abundant in plant leaves and plays essential roles in photosynthesis. Blue native/SDS-PAGE combined with mass spectrum was performed to detect the location of virus, and proteomic analysis of chloroplast isolated from virus-infected plants was performed to quantify the changes of individual proteins in order to gain a global view of the total chloroplast protein dynamics during the virus infection. Among the 438 proteins quantified, 33 showed a more than twofold change in abundance, of which 22 are involved in the light-dependent reactions and five in the Calvin cycle. The dynamic change of these proteins indicates that light-dependent reactions are down-accumulated, and the Calvin cycle was up-accumulated during virus infection. In addition to the proteins involved in photosynthesis, tubulin was up-accumulated in virus-infected plant, which might contribute to the autophagic process during plant infection. In conclusion, this extensive proteomic investigation on intact chloroplasts of virus-infected tobacco leaves provided some important novel information on chlorosis mechanisms induced by virus infection.

Resolving ultrafast exciton migration in organic solids at the nanoscale

Effectiveness of molecular-based light harvesting relies on transport of excitons to charge-transfer sites. Measuring exciton migration, however, has been challenging because of the mismatch between nanoscale migration lengths and the diffraction limit. Instead of using bulk substrate quenching methods, here we define quenching boundaries all-optically with sub-diffraction resolution, thus characterizing spatiotemporal exciton migration on its native nanometre and picosecond scales. By transforming stimulated emission depletion microscopy into a time-resolved ultrafast approach, we measure a 16-nm migration length in poly(2,5-di(hexyloxy)cyanoterephthalylidene) conjugated polymer films. Combined with Monte Carlo exciton hopping simulations, we show that migration in these films is essentially diffusive because intrinsic chromophore energetic disorder is comparable to chromophore inhomogeneous broadening. Our approach will enable previously unattainable correlation of local material structure to exciton migration character, applicable not only to photovoltaic or display-destined organic semiconductors but also to explaining the quintessential exciton migration exhibited in photosynthesis.

Long-range energy transport in photosystem II

We simulate the long-range inter-complex electronic energy transfer in photosystem II-from the antenna complex, via a core complex, to the reaction center-using a non-Markovian (ZOFE) quantum master equation description that allows the electronic coherence involved in the energy transfer to be explicitly included at all length scales. This allows us to identify all locations where coherence is manifested and to further identify the pathways of the energy transfer in the full network of coupled chromophores using a description based on excitation probability currents. We investigate how the energy transfer depends on the initial excitation-localized, coherent initial excitation versus delocalized, incoherent initial excitation-and find that the overall energy transfer is remarkably robust with respect to such strong variations of the initial condition. To explore the importance of vibrationally enhanced transfer and to address the question of optimization in the system parameters, we systematically vary the strength of the coupling between the electronic and the vibrational degrees of freedom. We find that the natural parameters lie in a (broad) region that enables optimal transfer efficiency and that the overall long-range energy transfer on a ns time scale appears to be very robust with respect to variations in the vibronic coupling of up to an order of magnitude. Nevertheless, vibrationally enhanced transfer appears to be crucial to obtain a high transfer efficiency, with the latter falling sharply for couplings outside the optimal range. Comparison of our full quantum simulations to results obtained with a "classical" rate equation based on a modified-Redfield/generalized-Förster description previously used to simulate energy transfer dynamics in the entire photosystem II complex shows good agreement for the overall time scales of excitation energy transport.

Chlorophyll fluorescence lifetime imaging provides new insight into the chlorosis induced by plant virus infection

KEY MESSAGE

Leaf chlorosis induced by plant virus infection has a short fluorescence lifetime, which reflects damaged photosynthetic complexes and degraded chloroplasts. Plant viruses often induce chlorosis and necrosis, which are intimately related to photosynthetic functions. Chlorophyll fluorescence lifetime measurement is a valuable noninvasive tool for analyzing photosynthetic processes and is a sensitive indicator of the environment surrounding the fluorescent molecules. In this study, our central goal was to explore the effect of viral infection on photosynthesis by employing chlorophyll fluorescence lifetime imaging (FLIM), steady-state fluorescence, non-photochemical quenching (NPQ), transmission electron microscopy (TEM), and pigment analysis. The data indicated that the chlorophyll fluorescence lifetime of chlorotic leaves was significantly shorter than that of healthy control leaves, and the fitted short lifetime component of chlorophyll fluorescence of chlorotic leaves was dominant. This dominant short lifetime component may result from damage to the structure of thylakoid, which was confirmed by TEM. The NPQ value of chlorotic leaves was slightly higher than that of healthy green leaves, which can be explained by increased neoxanthin, lutein and violaxanthin content relative to chlorophyll a. The difference in NPQ is slight, but FLIM can provide simple and direct characterization of PSII structure and photosynthetic function. Therefore, this technique shows great potential as a simple and rapid method for studying mechanisms of plant virus infection.

Efficiency of energy funneling in the photosystem II supercomplex of higher plants

The investigation of energy transfer properties in photosynthetic multi-protein networks gives insight into their underlying design principles. Here, we discuss the excitonic energy transfer mechanisms of the photosystem II (PS-II) C2S2M2 supercomplex, which is the largest isolated functional unit of the photosynthetic apparatus of higher plants. Despite the lack of a definite energy gradient in C2S2M2, we show that the energy transfer is directed by relaxation to low energy states. C2S2M2 is not organized to form pathways with strict energetically downhill transfer, which has direct consequences for the transfer efficiency, transfer pathways and transfer limiting steps. The exciton dynamics is sensitive to small changes in the energetic layout which, for instance, are induced by the reorganization of vibrational coordinates. In order to incorporate the reorganization process in our numerical simulations, we go beyond rate equations and use the hierarchically coupled equation of motion approach (HEOM). While transfer from the peripheral antenna to the proteins in proximity to the reaction center occurs on a faster time scale, the final step of the energy transfer to the RC core is rather slow, and thus the limiting step in the transfer chain. Our findings suggest that the structure of the PS-II supercomplex guarantees photoprotection rather than optimized efficiency.

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.

Is There Excitation Energy Transfer between Different Layers of Stacked Photosystem-II-Containing Thylakoid Membranes?

We have compared picosecond fluorescence decay kinetics for stacked and unstacked photosystem II membranes in order to evaluate the efficiency of excitation energy transfer between the neighboring layers. The measured kinetics were analyzed in terms of a recently developed fluctuating antenna model that provides information about the dimensionality of the studied system. Independently of the stacking state, all preparations exhibited virtually the same value of the apparent dimensionality, d = 1.6. Thus, we conclude that membrane stacking does not affect the efficiency of the delivery of excitation energy toward the reaction centers but ensures a more compact organization of the thylakoid membranes within the chloroplast and separation of photosystems I and II.

Multiscale model of light harvesting by photosystem II in plants

The first step of photosynthesis in plants is the absorption of sunlight by pigments in the antenna complexes of photosystem II (PSII), followed by transfer of the nascent excitation energy to the reaction centers, where long-term storage as chemical energy is initiated. Quantum mechanical mechanisms must be invoked to explain the transport of excitation within individual antenna. However, it is unclear how these mechanisms influence transfer across assemblies of antenna and thus the photochemical yield at reaction centers in the functional thylakoid membrane. Here, we model light harvesting at the several-hundred-nanometer scale of the PSII membrane, while preserving the dominant quantum effects previously observed in individual complexes. We show that excitation moves diffusively through the antenna with a diffusion length of 50 nm until it reaches a reaction center, where charge separation serves as an energetic trap. The diffusion length is a single parameter that incorporates the enhancing effect of excited state delocalization on individual rates of energy transfer as well as the complex kinetics that arise due to energy transfer and loss by decay to the ground state. The diffusion length determines PSII's high quantum efficiency in ideal conditions, as well as how it is altered by the membrane morphology and the closure of reaction centers. We anticipate that the model will be useful in resolving the nonphotochemical quenching mechanisms that PSII employs in conditions of high light stress.

Excitation migration in fluctuating light-harvesting antenna systems

Complex multi-exponential fluorescence decay kinetics observed in various photosynthetic systems like photosystem II (PSII) have often been explained by the reversible quenching mechanism of the charge separation taking place in the reaction center (RC) of PSII. However, this description does not account for the intrinsic dynamic disorder of the light-harvesting proteins as well as their fluctuating dislocations within the antenna, which also facilitate the repair of RCs, state transitions, and the process of non-photochemical quenching. Since dynamic fluctuations result in varying connectivity between pigment-protein complexes, they can also lead to non-exponential excitation decay kinetics. Based on this presumption, we have recently proposed a simple conceptual model describing excitation diffusion in a continuous medium and accounting for possible variations of the excitation transfer pathways. In the current work, this model is further developed and then applied to describe fluorescence kinetics originating from very diverse antenna systems, ranging from PSII of various sizes to LHCII aggregates and even the entire thylakoid membrane. In all cases, complex multi-exponential fluorescence kinetics are perfectly reproduced on the entire relevant time scale without assuming any radical pair equilibration at the side of the excitation quencher, but using just a few parameters reflecting the mean excitation energy transfer rate as well as the overall average organization of the photosynthetic antenna.

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).

Insights into colour-tuning of chlorophyll optical response in green plants

First-principles calculations within the framework of real-space time-dependent density functional theory have been performed for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex.

Optimal Energy Transfer in Light-Harvesting Systems

Photosynthesis is one of the most essential biological processes in which specialized pigment-protein complexes absorb solar photons, and with a remarkably high efficiency, guide the photo-induced excitation energy toward the reaction center to subsequently trigger its conversion to chemical energy. In this work, we review the principles of optimal energy transfer in various natural and artificial light harvesting systems. We begin by presenting the guiding principles for optimizing the energy transfer efficiency in systems connected to dissipative environments, with particular attention paid to the potential role of quantum coherence in light harvesting systems. We will comment briefly on photo-protective mechanisms in natural systems that ensure optimal functionality under varying ambient conditions. For completeness, we will also present an overview of the charge separation and electron transfer pathways in reaction centers. Finally, recent theoretical and experimental progress on excitation energy transfer, charge separation, and charge transport in artificial light harvesting systems is delineated, with organic solar cells taken as prime examples.

A comparison between plant photosystem I and photosystem II architecture and functioning

Oxygenic photosynthesis is indispensable both for the development and maintenance of life on earth by converting light energy into chemical energy and by producing molecular oxygen and consuming carbon dioxide. This latter process has been responsible for reducing the CO2 from its very high levels in the primitive atmosphere to the present low levels and thus reducing global temperatures to levels conducive to the development of life. Photosystem I and photosystem II are the two multi-protein complexes that contain the pigments necessary to harvest photons and use light energy to catalyse the primary photosynthetic endergonic reactions producing high energy compounds. Both photosystems are highly organised membrane supercomplexes composed of a core complex, containing the reaction centre where electron transport is initiated, and of a peripheral antenna system, which is important for light harvesting and photosynthetic activity regulation. If on the one hand both the chemical reactions catalysed by the two photosystems and their detailed structure are different, on the other hand they share many similarities. In this review we discuss and compare various aspects of the organisation, functioning and regulation of plant photosystems by comparing them for similarities and differences as obtained by structural, biochemical and spectroscopic investigations.

Light harvesting in a fluctuating antenna

One of the major players in oxygenic photosynthesis, photosystem II (PSII), exhibits complex multiexponential fluorescence decay kinetics that for decades has been ascribed to reversible charge separation taking place in the reaction center (RC). However, in this description the protein dynamics is not taken into consideration. The intrinsic dynamic disorder of the light-harvesting proteins along with their fluctuating dislocations within the antenna inevitably result in varying connectivity between pigment-protein complexes and therefore can also lead to nonexponential excitation decay kinetics. On the basis of this presumption, we propose a simple conceptual model describing excitation diffusion in a continuous medium and accounting for possible variations of the excitation transfer rates. Recently observed fluorescence kinetics of PSII of different sizes are perfectly reproduced with only two adjustable parameters instead of the many decay times and amplitudes required in standard analysis procedures; no charge recombination in the RC is required. The model is also able to provide valuable information about the structural and functional organization of the photosynthetic antenna and in a straightforward way solves various contradictions currently existing in the literature.

Modulation of the fluorescence yield in heliobacterial cells by induction of charge recombination in the photosynthetic reaction center

Heliobacteria contain a very simple photosynthetic apparatus, consisting of a homodimeric type I reaction center (RC) without a peripheral antenna system and using the unique pigment bacteriochlorophyll (BChl) g. They are thought to use a light-driven cyclic electron transport pathway to pump protons, and thereby phosphorylate ADP, although some of the details of this cycle are yet to be worked out. We previously reported that the fluorescence emission from the heliobacterial RC in vivo was increased by exposure to actinic light, although this variable fluorescence phenomenon exhibited very different characteristics to that in oxygenic phototrophs (Collins et al. 2010). Here, we describe the underlying mechanism behind the variable fluorescence in heliobacterial cells. We find that the ability to stably photobleach P800, the primary donor of the RC, using brief flashes is inversely correlated to the variable fluorescence. Using pump-probe spectroscopy in the nanosecond timescale, we found that illumination of cells with bright light for a few seconds put them in a state in which a significant fraction of the RCs underwent charge recombination from P800 (+)A0 (-) with a time constant of ~20 ns. The fraction of RCs in the rapidly back-reacting state correlated very well with the variable fluorescence, indicating that nearly all of the increase in fluorescence could be explained by charge recombination of P800 (+)A0 (-), some of which regenerated the singlet excited state. This hypothesis was tested directly by time-resolved fluorescence studies in the ps and ns timescales. The major decay component in whole cells had a 20-ps decay time, representing trapping by the RC. Treatment of cells with dithionite resulted in the appearance of a ~18-ns decay component, which accounted for ~0.6 % of the decay, but was almost undetectable in the untreated cells. We conclude that strong illumination of heliobacterial cells can result in saturation of the electron acceptor pool, leading to reduction of the acceptor side of the RC and the creation of a back-reacting RC state that gives rise to delayed fluorescence.

Disentangling two non-photochemical quenching processes in Cyclotella meneghiniana by spectrally-resolved picosecond fluorescence at 77K

Diatoms, which are primary producers in the oceans, can rapidly switch on/off efficient photoprotection to respond to fast light-intensity changes in moving waters. The corresponding thermal dissipation of excess-absorbed-light energy can be observed as non-photochemical quenching (NPQ) of chlorophyll a fluorescence. Fluorescence-induction measurements on Cyclotella meneghiniana diatoms show two NPQ processes: qE1 relaxes rapidly in the dark while qE2 remains present upon switching to darkness and is related to the presence of the xanthophyll-cycle pigment diatoxanthin (Dtx). We performed picosecond fluorescence measurements on cells locked in different (quenching) states, revealing the following sequence of events during full development of NPQ. At first, trimers of light-harvesting complexes (fucoxanthin-chlorophyll a/c proteins), or FCPa, become quenched, while being part of photosystem II (PSII), due to the induced pH gradient across the thylakoid membrane. This is followed by (partial) detachment of FCPa from PSII after which quenching persists. The pH gradient also causes the formation of Dtx which leads to further quenching of isolated PSII cores and some aggregated FCPa. In subsequent darkness, the pH gradient disappears but Dtx remains present and quenching partly pertains. Only in the presence of some light the system completely recovers to the unquenched state.

Wavelength dependence of the fluorescence emission under conditions of open and closed Photosystem II reaction centres in the green alga Chlorella sorokiniana

The fluorescence emission characteristics of the photosynthetic apparatus under conditions of open (F0) and closed (FM) Photosystem II reaction centres have been investigated under steady state conditions and by monitoring the decay lifetimes of the excited state, in vivo, in the green alga Chlorella sorokiniana. The results indicate a marked wavelength dependence of the ratio of the variable fluorescence, FV=FM-F0, over FM, a parameter that is often employed to estimate the maximal quantum efficiency of Photosystem II. The maximal value of the FV/FM ratio is observed between 660 and 680nm and the minimal in the 690-730nm region. It is possible to attribute the spectral variation of FV/FM principally to the contribution of Photosystem I fluorescence emission at room temperature. Moreover, the analysis of the excited state lifetime at F0 and FM indicates only a small wavelength dependence of Photosystem II trapping efficiency in vivo.

State transitions in Chlamydomonas reinhardtii strongly modulate the functional size of photosystem II but not of photosystem I

Plants and green algae optimize photosynthesis in changing light conditions by balancing the amount of light absorbed by photosystems I and II. These photosystems work in series to extract electrons from water and reduce NADP(+) to NADPH. Light-harvesting complexes (LHCs) are held responsible for maintaining the balance by moving from one photosystem to the other in a process called state transitions. In the green alga Chlamydomonas reinhardtii, a photosynthetic model organism, state transitions are thought to involve 80% of the LHCs. Here, we demonstrate with picosecond-fluorescence spectroscopy on C. reinhardtii cells that, although LHCs indeed detach from photosystem II in state 2 conditions, only a fraction attaches to photosystem I. The detached antenna complexes become protected against photodamage via shortening of the excited-state lifetime. It is discussed how the transition from state 1 to state 2 can protect C. reinhardtii in high-light conditions and how this differs from the situation in plants.

Thermal phase and excitonic connectivity in fluorescence induction

Chl fluorescence induction (FI) was recorded in sunflower leaves pre-adapted to darkness or low preferentially PSI light, or inhibited by DCMU. For analysis the FI curves were plotted against the cumulative number of excitations quenched by PSII, n q, calculated as the cumulative complementary area above the FI curve. In the +DCMU leaves n q was <1 per PSII, suggesting pre-reduction of Q A during the dark pre-exposure. A strongly sigmoidal FI curve was constructed by complementing (shifting) the recorded FI curves to n q = 1 excitation per PSII. The full FI curve in +DCMU leaves was well fitted by a model assuming PSII antennae are excitonically connected in domains of four PSII. This result, obtained by gradually reducing Q A in PSII with pre-blocked Q B (by DCMU or PQH2), differs from that obtained by gradually blocking the Q B site (by increasing DCMU or PQH2 level) in leaves during (quasi)steady-state e(-) transport (Oja and Laisk, Photosynth Res 114, 15-28, 2012). Explanations are discussed. Donor side quenching was characterized by comparison of the total n q in one and the same dark-adapted leaf, which apparently increased with increasing PFD during FI. An explanation for the donor side quenching is proposed, based on electron transfer from excited P680* to oxidized tyrosine Z (TyrZ(ox)). At high PFDs the donor side quenching at the J inflection of FI is due mainly to photochemical quenching by TyrZ(ox). This quenching remains active for subsequent photons while TyrZ remains oxidized, following charge transfer to Q A. During further induction this quenching disappears as soon as PQ and Q A become reduced, charge separation becomes impossible and TyrZ is reduced by the water oxidizing complex.

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.

Excitonic connectivity between photosystem II units: what is it, and how to measure it?

In photosynthetic organisms, light energy is absorbed by a complex network of chromophores embedded in light-harvesting antenna complexes. In photosystem II (PSII), the excitation energy from the antenna is transferred very efficiently to an active reaction center (RC) (i.e., with oxidized primary quinone acceptor Q(A)), where the photochemistry begins, leading to O2 evolution, and reduction of plastoquinones. A very small part of the excitation energy is dissipated as fluorescence and heat. Measurements on chlorophyll (Chl) fluorescence and oxygen have shown that a nonlinear (hyperbolic) relationship exists between the fluorescence yield (Φ(F)) (or the oxygen emission yield, (Φ(O2)) and the fraction of closed PSII RCs (i.e., with reduced Q(A)). This nonlinearity is assumed to be related to the transfer of the excitation energy from a closed PSII RC to an open (active) PSII RC, a process called PSII excitonic connectivity by Joliot and Joliot (CR Acad Sci Paris 258: 4622-4625, 1964). Different theoretical approaches of the PSII excitonic connectivity, and experimental methods used to measure it, are discussed in this review. In addition, we present alternative explanations of the observed sigmoidicity of the fluorescence induction and oxygen evolution curves.

Excitonic connectivity between photosystem II units: what is it, and how to measure it?

In photosynthetic organisms, light energy is absorbed by a complex network of chromophores embedded in light-harvesting antenna complexes. In photosystem II (PSII), the excitation energy from the antenna is transferred very efficiently to an active reaction center (RC) (i.e., with oxidized primary quinone acceptor Q(A)), where the photochemistry begins, leading to O2 evolution, and reduction of plastoquinones. A very small part of the excitation energy is dissipated as fluorescence and heat. Measurements on chlorophyll (Chl) fluorescence and oxygen have shown that a nonlinear (hyperbolic) relationship exists between the fluorescence yield (Φ(F)) (or the oxygen emission yield, (Φ(O2)) and the fraction of closed PSII RCs (i.e., with reduced Q(A)). This nonlinearity is assumed to be related to the transfer of the excitation energy from a closed PSII RC to an open (active) PSII RC, a process called PSII excitonic connectivity by Joliot and Joliot (CR Acad Sci Paris 258: 4622-4625, 1964). Different theoretical approaches of the PSII excitonic connectivity, and experimental methods used to measure it, are discussed in this review. In addition, we present alternative explanations of the observed sigmoidicity of the fluorescence induction and oxygen evolution curves.

Functional compartmental modeling of the photosystems in the thylakoid membrane at 77 K

Time-resolved fluorescence spectroscopy measurements at 77 K on thylakoid membrane preparations and isolated photosynthetic complexes thereof were investigated using target analysis with the aim of building functional compartmental models for the photosystems in the thylakoid membrane. Combining kinetic schemes with different spectral constraints enabled us to resolve the energy transfer pathways and decay characteristics of the different emissive species. We determined the spectral and energetic properties of the red Chl pools in both photosystems and quantified the formation of LHCII-LHCI-PSI supercomplexes in the transition from native to unstacked thylakoid membranes.

A structure-based model of energy transfer reveals the principles of light harvesting in photosystem II supercomplexes

Photosystem II (PSII) initiates photosynthesis in plants through the absorption of light and subsequent conversion of excitation energy to chemical energy via charge separation. The pigment binding proteins associated with PSII assemble in the grana membrane into PSII supercomplexes and surrounding light harvesting complex II trimers. To understand the high efficiency of light harvesting in PSII requires quantitative insight into energy transfer and charge separation in PSII supercomplexes. We have constructed the first structure-based model of energy transfer in PSII supercomplexes. This model shows that the kinetics of light harvesting cannot be simplified to a single rate limiting step. Instead, substantial contributions arise from both excitation diffusion through the antenna pigments and transfer from the antenna to the reaction center (RC), where charge separation occurs. Because of the lack of a rate-limiting step, fitting kinetic models to fluorescence lifetime data cannot be used to derive mechanistic insight on light harvesting in PSII. This model will clarify the interpretation of chlorophyll fluorescence data from PSII supercomplexes, grana membranes, and leaves.

Quantum yield of charge separation in photosystem II: functional effect of changes in the antenna size upon light acclimation

We have studied thylakoid membranes of Arabidopsis thaliana acclimated to different light conditions and have related protein composition to excitation energy transfer and trapping kinetics in Photosystem II (PSII). In high light: the plants have reduced amounts of the antenna complexes LHCII and CP24, the overall trapping time of PSII is only ∼180 ps, and the quantum efficiency reaches a value of 91%. In low light: LHCII is upregulated, the PSII lifetime becomes ∼310 ps, and the efficiency decreases to 84%. This difference is largely caused by slower excitation energy migration to the reaction centers in low-light plants due to the LHCII trimers that are not part of the C2S2M2 supercomplex. This pool of "extra" LHCII normally transfers energy to both photosystems, whereas it transfers only to PSII upon far-red light treatment (state 1). It is shown that in high light the reduction of LHCII mainly concerns the LHCII-M trimers, while the pool of "extra" LHCII remains intact and state transitions continue to occur. The obtained values for the efficiency of PSII are compared with the values of Fv/Fm, a parameter that is widely used to indicate the PSII quantum efficiency, and the observed differences are discussed.

On the analysis of non-photochemical chlorophyll fluorescence quenching curves: I. Theoretical considerations

Non-photochemical quenching (NPQ) protects photosynthetic organisms against photodamage by high light. One of the key measuring parameters for characterizing NPQ is the high-light induced decrease in chlorophyll fluorescence. The originally measured data are maximal fluorescence (Fm') signals as a function of actinic illumination time (Fm'(t)). Usually these original data are converted into the so-called Stern-Volmer quenching function, NPQSV(t), which is then analyzed and interpreted in terms of various NPQ mechanisms and kinetics. However, the interpretation of this analysis essentially depends on the assumption that NPQ follows indeed a Stern-Volmer relationship. Here, we question this commonly assumed relationship, which surprisingly has never been proven. We demonstrate by simulation of quenching data that particularly the conversion of time-dependent quenching curves like Fm'(t) into NPQSV(t) is (mathematically) not "innocent" in terms of its effects. It distorts the kinetic quenching information contained in the originally measured function Fm'(t), leading to a severe (often sigmoidal) distortion of the time-dependence of quenching and has negative impact on the ability to uncover the underlying quenching mechanisms and their contribution to the quenching kinetics. We conclude that the commonly applied analysis of time-dependent NPQ in NPQSV(t) space should be reconsidered. First, there exists no sound theoretical basis for this common practice. Second, there occurs no loss of information whatsoever when analyzing and interpreting the originally measured Fm'(t) data directly. Consequently, the analysis of Fm'(t) data has a much higher potential to provide correct mechanistic answers when trying to correlate quenching data with other biochemical information related to quenching.