Molecular Anatomy of Plant Photoprotective Switches: The Sensitivity of PsbS to the Environment, Residue by Residue

Photosynthetic advantages of conifers in the boreal forest

Boreal conifers - the 'Christmas trees' - maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.

Distinct features of PsbS essential for mediating plant photoprotection

For optimum photosynthetic productivity, it is crucial for plants to swiftly transition between light-harvesting and photoprotective states as light conditions change in the field. The PsbS protein plays a pivotal role in this process by switching the light-harvesting antenna, light-harvesting complex II (LHCII), into the photoprotective state, energy-dependent chlorophyll fluorescence quenching (qE), to avoid photoinhibition in high-light environments. However, the molecular mechanism by which PsbS acts upon LHCII has remained unclear. In our study, we identified the specific amino acid domains that are essential for PsbS function. Using amino-acid point mutagenesis of PsbS in vivo, we found that the activation of photoprotection involves dynamic changes in the oligomeric state and conformation of PsbS, with two residues, E67 and E173, playing a key role in this process. Further, the replacement of hydrophobic phenylalanine residues in transmembrane helixes II (F83, F84, F87) and IV (F191, F193, F194) with tyrosine revealed that phenylalanine localized in helix IV can play a significant role in hydrophobic interactions of PsbS with LHCII. Removal of the 310 helix (H3) amino acids I74, Y75, and E76 did not affect the amplitude but strongly delayed the recovery of qE in darkness. Moreover, an AI-assisted protein-folding evolutionary scale model approach (ESMFold) was adopted to intelligently manipulate protein functions in silico and thus streamline and evaluate experimental point mutagenesis strategies. This provides new insights into the molecular architecture of PsbS that are essential for regulating light harvesting in higher plants.

Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis

As a critical step in advancing the simulation of photosynthetic complexes, we present the Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting (LHCII) proteins and the photosystem II (PSII) core complex. Our work focuses on the parametrization of beta-carotene, plastoquinone/quinol, violaxanthin, lutein, neoxanthin, chlorophyll A, chlorophyll B, and heme. We derived the CG parameters to match the all-atom reference simulations, while structural and thermodynamic properties of the cofactors were compared to experimental values when available. To further assess the reliability of the parameterization, we tested the behavior of these cofactors within their physiological environments, specifically in a lipid bilayer and bound to photosynthetic complexes. The results demonstrate that our CG models maintain the essential features required for realistic simulations. This work lays the groundwork for detailed simulations of the PSII-LHCII super-complex, providing a robust parameter set for future studies.

ATP regeneration by ATPases for in vitro biotransformation

Adenosine triphosphate (ATP) regeneration is a significant step in both living cells and in vitro biotransformation (ivBT). Rotary motor ATP synthases (ATPases), which regenerate ATP in living cells, have been widely assembled in biomimetic structures for in vitro ATP synthesis. In this review, we present a comprehensive overview of ATPases, including the working principle, orientation and distribution density properties of ATPases, as well as the assembly strategies and applications of ATPase-based ATP regeneration modules. The original sources of ATPases for in vitro ATP regeneration include chromatophores, chloroplasts, mitochondria, and inverted Escherichia coli (E. coli) vesicles, which are readily accessible but unstable. Although significant advances have been made in the assembly methods for ATPase-artificial membranes in recent decades, it remains challenging to replicate the high density and orientation of ATPases observed in vivo using in vitro assembly methods. The use of bioproton pumps or chemicals for constructing proton motive forces (PMF) enables the versatility and potential of ATPase-based ATP regeneration modules. Additionally, overall robustness can be achieved via membrane component selection, such as polymers offering great mechanical stability, or by constructing a solid supporting matrix through layer-by-layer assembly techniques. Finally, the prospects of ATPase-based ATP regeneration modules can be expected with the technological development of ATPases and artificial membranes.

Structural Diversity in Eukaryotic Photosynthetic Light Harvesting

Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided angstrom-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein-environment interactions will improve our capacity to engineer more productive crops.

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

Designing a structure-function alphabet of helix based on reduced amino acid clusters

Several simple secondary structures could form complex and diverse functional proteins, meaning that secondary structures may contain a lot of hidden information and are arranged according to certain principles, to carry enough information of functional specificity and diversity. However, these inner information and principles have not been understood systematically. In our study, we designed a structure-function alphabet of helix based on reduced amino acid clusters to describe the typical features of helices and delve into the information. Firstly, we selected 480 typical helices from membrane proteins, zymoproteins, transcription factors, and other proteins to define and calculate the interval range, and the helices are classified in terms of hydrophilicity, charge and length: (1) hydrophobic helix (≤43%), amphiphilic helix (43%∼71%), and hydrophilic helix (≥71%). (2) positive helix, negative helix, electrically neutral helix and uncharged helix. (3) short helix (≤8 aa), medium-length helix (9-28 aa), and long helix (≥29 aa). Then, we designed an alphabet containing 36 triplet codes according to the above classification, so that the main features of each helix can be represented by only three letters. This alphabet not only preliminarily defined the helix characteristics, but also greatly reduced the informational dimension of protein structure. Finally, we present an application example to demonstrate the value of the structure-function alphabet in protein functional determination and differentiation.

Photosystem II Subunit S (PsbS): A Nano Regulator of Plant Photosynthesis

Light is required for photosynthesis, but plants are often exposed to excess light, which can lead to photodamage and eventually cell death. To prevent this, they evolved photoprotective feedback mechanisms that regulate photosynthesis and trigger processes that dissipate light energy as heat, called non-photochemical quenching (NPQ). In excess light conditions, the light reaction and activity of Photosystem II (PSII) generates acidification of the thylakoid lumen, which is sensed by special pH-sensitive proteins called Photosystem II Subunit S (PsbS), actuating a photoprotective "switch" in the light-harvesting antenna. Despite its central role in regulating photosynthetic energy conversion, the molecular mechanism of PsbS as well as its interaction with partner proteins are not well understood. This review summarizes the current knowledge on the molecular structure and mechanistic aspects of the light-stress sensor PsbS and addresses open questions and challenges in the field regarding a full understanding of its functional mechanism and role in NPQ.

The Photoprotective Protein PsbS from Green Microalga Lobosphaera incisa: The Amino Acid Sequence, 3D Structure and Probable pH-Sensitive Residues

PsbS is one of the key photoprotective proteins, ensuring the tolerance of the photosynthetic apparatus (PSA) of a plant to abrupt changes in irradiance. Being a component of photosystem II, it provides the formation of quenching centers for excited states of chlorophyll in the photosynthetic antenna with an excess of light energy. The signal for "turning on" the photoprotective function of the protein is an excessive decrease in pH in the thylakoid lumen occurring when all the absorbed light energy (stored in the form of transmembrane proton potential) cannot be used for carbon assimilation. Hence, lumen-exposed protonatable amino acid residues that could serve as pH sensors are the essential components of PsbS-dependent photoprotection, and their pKa values are necessary to describe it. Previously, calculations of the lumen-exposed protonatable residue pKa values in PsbS from spinach were described in the literature. However, it has recently become clear that PsbS, although typical of higher plants and charophytes, can also provide photoprotection in green algae. Namely, the stress-induced expression of PsbS was recently shown for two green microalgae species: Chlamydomonas reinhardtii and Lobosphaera incisa. Therefore, we determined the amino acid sequence and modeled the three-dimensional structure of the PsbS from L. incisa, as well as calculated the pKa values of its lumen-exposed protonatable residues. Despite significant differences in amino acid sequence, proteins from L. incisa and Spinacia oleracea have similar three-dimensional structures. Along with the other differences, one of the two pH-sensing glutamates in PsbS from S. oleracea (namely, Glu-173) has no analogue in L. incisa protein. Moreover, there are only four glutamate residues in the lumenal region of the L. incisa protein, while there are eight glutamates in S. oleracea. However, our calculations show that, despite the relative deficiency in protonatable residues, at least two residues of L. incisa PsbS can be considered probable pH sensors: Glu-87 and Lys-196.

Altered lipid acyl chain length controls energy dissipation in light-harvesting complex II proteoliposomes by hydrophobic mismatch

In plants, the major light-harvesting antenna complex (LHCII) is vital for both light harvesting and photoprotection in photosystem II. Previously, we proposed that the thylakoid membrane itself could switch LHCII into the photoprotective state, qE, via a process known as hydrophobic mismatch. The decrease in the membrane thickness that followed the formation of ΔpH was a key fact that prompted this idea. To test this, we made proteoliposomes from lipids with altered acyl chain length (ACL). Here, we show that ACL regulates the average chlorophyll fluorescence lifetime of LHCII. For liposomes made of lipids with an ACL of 18 carbons, the lifetime was ∼2 ns, like that for the thylakoid membrane. Furthermore, LHCII appears to be quenched in proteoliposomes with an ACL both shorter and longer than 18 carbons. The proteoliposomes made of short ACL lipids display structural heterogeneity revealing two quenched conformations of LHCII, each having characteristic 77 K fluorescence spectra. One conformation spectrally resembles isolated LHCII aggregates, whilst the other resembles LHCII immobilized in polyacrylamide gels. Overall, the decrease in the ACL appears to produce quenched conformations of LHCII, which renders plausible the idea that the trigger of qE is the hydrophobic mismatch.

Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers

Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the Q_B site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to Q_B. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with Q_B^•- are compared with earlier results obtained with Q_B [Wei et. al Photosynthesis Research volume 152, pages153-165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation.

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.

Recent progress in atomistic modeling of light-harvesting complexes: a mini review

In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.

pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer

The photosystem II PsbS protein triggers the photoprotective mechanism of plants by sensing the acidification of the thylakoid lumen. Despite the mechanism of action of PsbS would require a pH-dependent monomerization of the dimeric form, a clear connection between the pH-induced structural changes and the dimer stability is missing. Here, by applying constant pH coarse-grained and all-atom molecular dynamics simulations, we investigate the pH-dependent structural response of the PsbS dimer. We find that the pH variation leads to structural changes in the lumen-exposed helices, located at the dimeric interface, providing an effective switch between PsbS inactive and active form. Moreover, the monomerization free energies reveal that in the neutral pH conformation, where the network of H-bond interactions at the dimeric interface is destroyed, the protein-protein interaction is weaker. Our results show how the pH-dependent conformations of PsbS affect their dimerization propensity, which is at the basis of the photoprotective mechanism.

A kaleidoscope of photosynthetic antenna proteins and their emerging roles

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

Photoprotective energy quenching in the red alga Porphyridium purpureum occurs at the core antenna of the photosystem II but not at its reaction center

Photosynthetic organisms have evolved light-harvesting antennae over time. In cyanobacteria, external phycobilisomes (PBSs) are the dominant antennae, whereas in green algae and higher plants, PBSs have been replaced by proteins of the Lhc family that are integrated in the membrane. Red algae represent an evolutionary intermediate between these two systems, as they employ both PBSs and membrane LHCR proteins as light-harvesting units. Understanding how red algae cope with light is not only interesting for biotechnological applications, but is also of evolutionary interest. For example, energy-dependent quenching (qE) is an essential photoprotective mechanism widely used by species from cyanobacteria to higher plants to avoid light damage; however, the quenching mechanism in red algae remains largely unexplored. Here, we used both pulse amplitude-modulated (PAM) and time-resolved chlorophyll fluorescence to characterize qE kinetics in the red alga Porphyridium purpureum. PAM traces confirmed that qE in P. purpureum is activated by a decrease in the thylakoid lumen pH, whereas time-resolved fluorescence results further revealed the quenching site and ultrafast quenching kinetics. We found that quenching exclusively takes place in the photosystem II (PSII) complexes and preferentially occurs at PSII’s core antenna rather than at its reaction center, with an overall quenching rate of 17.6 ± 3.0 ns⁻¹. In conclusion, we propose that qE in red algae is not a reaction center type of quenching, and that there might be a membrane-bound protein that resembles PsbS of higher plants or LHCSR of green algae that senses low luminal pH and triggers qE in red algae.

Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin

Protein-protein association is often mediated by electrostatic interactions and modulated by pH. However, experimental and computational studies have often overlooked the effect of association on the protonation state of the protein. In this work, we present a methodological approach based on constant-pH molecular dynamics (MD), which aims to provide a detailed description of a pH-dependent protein-protein association, and apply it to the dimerization of β-lactoglobulin (BLG). A selection of analyses is performed using the data generated by constant-pH MD simulations of monomeric and dimeric forms of bovine BLG, in the pH range 3-8. First, we estimate free energies of dimerization using a computationally inexpensive approach based on the Wyman-Tanford linkage theory, calculated in a new way through the use of thermodynamically based splines. The individual free energy contribution of each titratable site is also calculated, allowing for identification of relevant residues. Second, the correlations between the proton occupancies of pairs of sites are calculated (using the Pearson coefficient), and extensive networks of correlated sites are observed at acidic pH values, sometimes involving distant pairs. In general, strongly correlated sites are also slow proton exchangers and contribute significantly to the pH-dependency of the dimerization free energy. Third, we use ionic density as a fingerprint of protein charge distribution and observe electrostatic complementarity between the monomer faces that form the dimer interface, more markedly at the isoionic point (where maximum dimerization occurs) than at other pH values, which might contribute to guide the association. Finally, the pH-dependent dimerization modes are inspected using PCA, among other analyses, and two states are identified: a relaxed state at pH 4-8 (with the typical alignment of the crystallographic structure) and a compact state at pH 3-4 (with a tighter association and rotated alignment). This work shows that an approach based on constant-pH MD simulations can produce rich detailed pictures of pH-dependent protein associations, as illustrated for BLG dimerization.

Dual Singlet Excited-State Quenching Mechanisms in an Artificial Caroteno-Phthalocyanine Light Harvesting Antenna

Under excess illumination, photosystem II of plants dissipates excess energy through the quenching of chlorophyll fluorescence in the light harvesting antenna. Various models involving chlorophyll quenching by carotenoids have been proposed, including (i) direct energy transfer from chlorophyll to the low-lying optically forbidden carotenoid S₁ state, (ii) formation of a collective quenched chlorophyll–carotenoid S₁ excitonic state, (iii) chlorophyll–carotenoid charge separation and recombination, and (iv) chlorophyll–chlorophyll charge separation and recombination. In previous work, the first three processes were mimicked in model systems: in a Zn-phthalocyanine–carotenoid dyad with an amide linker, direct energy transfer was observed by femtosecond transient absorption spectroscopy, whereas in a Zn-phthalocyanine–carotenoid dyad with an amine linker excitonic quenching was demonstrated. Here, we present a transient absorption spectroscopic study on a Zn-phthalocyanine–carotenoid dyad with a phenylene linker. We observe that two quenching phases of the phthalocyanine excited state exist at 77 and 213 ps in addition to an unquenched phase at 2.7 ns. Within our instrument response of ∼100 fs, carotenoid S₁ features rise which point at an excitonic quenching mechanism. Strikingly, we observe an additional rise of carotenoid S₁ features at 3.6 ps, which shows that a direct energy transfer mechanism in an inverted kinetics regime is also in effect. We assign the 77 ps decay component to excitonic quenching and the 3.6 ps/213 ps rise and decay components to direct energy transfer. Our results indicate that dual quenching mechanisms may be active in the same molecular system, in addition to an unquenched fraction. Computational chemistry results indicate the presence of multiple conformers where one of the dihedral angles of the phenylene linker assumes distinct values. We propose that the parallel quenching pathways and the unquenched fraction result from such conformational subpopulations. Our results suggest that it is possible to switch between different regimes of quenching and nonquenching through a conformational change on the same molecule, offering insights into potential mechanisms used in biological photosynthesis to adapt to light intensity changes on fast time scales.

The Mechanism of Non-Photochemical Quenching in Plants: Localization and Driving Forces

Non-photochemical chlorophyll fluorescence quenching (NPQ) remains one of the most studied topics of the 21st century in photosynthesis research. Over the past 30 years, profound knowledge has been obtained on the molecular mechanism of NPQ in higher plants. First, the largely overlooked significance of NPQ in protecting the reaction center of photosystem II (RCII) against damage, and the ways to assess its effectiveness are highlighted. Then, the key in vivo signals that can monitor the life of the major NPQ component, qE, are presented. Finally, recent knowledge on the site of qE and the possible molecular events that transmit ΔpH into the conformational change in the major LHCII [the major trimeric light harvesting complex of photosystem II (PSII)] antenna complex are discussed. Recently, number of reports on Arabidopsis mutants lacking various antenna components of PSII confirmed that the in vivo site of qE rests within the major trimeric LHCII complex. Experiments on biochemistry, spectroscopy, microscopy and molecular modeling suggest an interplay between thylakoid membrane geometry and the dynamics of LHCII, the PsbS (PSII subunit S) protein and thylakoid lipids. The molecular basis for the qE-related conformational change in the thylakoid membrane, including the possible onset of a hydrophobic mismatch between LHCII and lipids, potentiated by PsbS protein, begins to unfold.

Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study

Diatoms generate a large portion of the oxygen produced on earth due to their exceptional light-harvesting properties involving fucoxanthin and chlorophyll-binding proteins (FCP). At the same time, an efficient adaptation of these complexes to fluctuating light conditions is necessary to protect the diatoms against photodamage. So far, structural and dynamic data for the interaction between FCP and the photoprotective LHCX family of proteins in diatoms are lacking. In this computational study, we provide a structural basis for a remarkable pH-dependent adaptation at the molecular level. Upon binding of the LHCX1 protein to the FCP complex together with a change in pH, conformational changes within the FCP protein result in a variation of the electronic coupling in a specific chlorophyll-fucoxanthin pair, leading to a change in the exciton transfer rate by almost an order of magnitude. A common strategy for photoprotection between diatoms and higher plants is identified and discussed.

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.

The molecular pH-response mechanism of the plant light-stress sensor PsbS

Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lumen-faced glutamates. However, how PsbS is activated under low-pH conditions is unknown. To reveal the molecular response of PsbS to low pH, here we perform an NMR, FTIR and 2DIR spectroscopic analysis of Physcomitrella patens PsbS and of the E176Q mutant in which an active glutamate has been replaced. The PsbS response mechanism at low pH involves the concerted action of repositioning of a short amphipathic helix containing E176 facing the lumen and folding of the luminal loop fragment adjacent to E71 to a 310-helix, providing clear evidence of a conformational pH switch. We propose that this concerted mechanism is a shared motif of proteins of the light-harvesting family that may control thylakoid inter-protein interactions driving photoregulatory responses.

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.

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.

Efficient photosynthesis in dynamic light environments: a chloroplast's perspective

In nature, light availability for photosynthesis can undergo massive changes on a very short timescale. Photosynthesis in such dynamic light environments requires that plants can respond swiftly. Expanding our knowledge of the rapid responses that underlie dynamic photosynthesis is an important endeavor: it provides insights into nature's design of a highly dynamic energy conversion system and hereby can open up new strategies for improving photosynthesis in the field. The present review focuses on three processes that have previously been identified as promising engineering targets for enhancing crop yield by accelerating dynamic photosynthesis, all three of them involving or being linked to processes in the chloroplast, i.e. relaxation of non-photochemical quenching, Calvin–Benson–Bassham cycle enzyme activation/deactivation and dynamics of stomatal conductance. We dissect these three processes on the functional and molecular level to reveal gaps in our understanding and critically discuss current strategies to improve photosynthesis in the field.

Rapid regulation of photosynthetic light harvesting in the absence of minor antenna and reaction centre complexes

Plants are subject to dramatic fluctuations in the intensity of sunlight throughout the day. When the photosynthetic machinery is exposed to high light, photons are absorbed in excess, potentially leading to oxidative damage of its delicate membrane components. A photoprotective molecular process called non-photochemical quenching (NPQ) is the fastest response carried out in the thylakoid membranes to harmlessly dissipate excess light energy. Despite having been intensely studied, the site and mechanism of this essential regulatory process are still debated. Here, we show that the main NPQ component called energy-dependent quenching (qE) is present in plants with photosynthetic membranes largely enriched in the major trimeric light-harvesting complex (LHC) II, while being deprived of all minor LHCs and most photosystem core proteins. This fast and reversible quenching depends upon thylakoid lumen acidification (ΔpH). Enhancing ΔpH amplifies the extent of the quenching and restores qE in the membranes lacking PSII subunit S protein (PsbS), whereas the carotenoid zeaxanthin modulates the kinetics and amplitude of the quenching. These findings highlight the self-regulatory properties of the photosynthetic light-harvesting membranes in vivo, where the ability to switch reversibly between the harvesting and dissipative states is an intrinsic property of the major LHCII.

Molecular dynamics simulations in photosynthesis

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.

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.

Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants

Depending on the amount of light, the photosystem II (PSII) antennae or Light Harvesting Complexes (LHCII) switch between two states within the thylakoid membranes of higher plants, i.e., a light-harvesting and a photoprotective mode. This switch is co-regulated by a pH gradient (ΔpH) across the membrane and the interaction with the PSII subunit S (PsbS) that is proposed to induce LHCII aggregation. Herein we employ all-atom and coarse-grained molecular simulations of the major LHCII trimer at low and excess ΔpH, as well as in complexation with PsbS within a native thylakoid membrane model. Our results demonstrate the aggregation potential of LHCII and, consistent with the experimental literature, reveal the role of PsbS at atomic resolution. PsbS alters the LHCII-thylakoid lipid interactions and restores the LHCII mobility that is lost in the transition to photoprotective conditions (low lumenal pH). In agreement with this finding, diffusion of the integral membrane protein LHCII is dependent on both, electrostatic interactions and hydrophobic mismatch, while it does not obey the Saffman-Delbrück diffusion model.

A New Light on Photosystem II Maintenance in Oxygenic Photosynthesis

Life on earth is sustained by oxygenic photosynthesis, a process that converts solar energy, carbon dioxide, and water into chemical energy and biomass. Sunlight is essential for growth and productivity of photosynthetic organisms. However, exposure to an excessive amount of light adversely affects fitness due to photooxidative damage to the photosynthetic machinery, primarily to the reaction center of the oxygen-evolving photosystem II (PSII). Photosynthetic organisms have evolved diverse photoprotective and adaptive strategies to avoid, alleviate, and repair PSII damage caused by high-irradiance or fluctuating light. Rapid and harmless dissipation of excess absorbed light within antenna as heat, which is measured by chlorophyll fluorescence as non-photochemical quenching (NPQ), constitutes one of the most efficient protective strategies. In parallel, an elaborate repair system represents another efficient strategy to maintain PSII reaction centers in active states. This article reviews both the reaction center-based strategy for robust repair of photodamaged PSII and the antenna-based strategy for swift control of PSII light-harvesting (NPQ). We discuss evolutionarily and mechanistically diverse strategies used by photosynthetic organisms to maintain PSII function for growth and productivity under static high-irradiance light or fluctuating light environments. Knowledge of mechanisms underlying PSII maintenance would facilitate bioengineering photosynthesis to enhance agricultural productivity and sustainability to feed a growing world population amidst climate change.