Dynamical and allosteric regulation of photoprotection in light harvesting complex II

Hydrophobic Mismatch in the Thylakoid Membrane Regulates Photosynthetic Light Harvesting

The ability to harvest light effectively in a changing environment is necessary to ensure efficient photosynthesis and crop growth. One mechanism, known as qE, protects photosystem II (PSII) and regulates electron transfer through the harmless dissipation of excess absorbed photons as heat. This process involves reversible clustering of the major light-harvesting complexes of PSII (LHCII) in the thylakoid membrane and relies upon the ΔpH gradient and the allosteric modulator protein PsbS. To date, the exact role of PsbS in the qE mechanism has remained elusive. Here, we show that PsbS induces hydrophobic mismatch in the thylakoid membrane through dynamic rearrangement of lipids around LHCII leading to observed membrane thinning. We found that upon illumination, the thylakoid membrane reversibly shrinks from around 4.3 to 3.2 nm, without PsbS, this response is eliminated. Furthermore, we show that the lipid digalactosyldiacylglycerol (DGDG) is repelled from the LHCII-PsbS complex due to an increase in both the pKa of lumenal residues and in the dipole moment of LHCII, which allows for further conformational change and clustering in the membrane. Our results suggest a mechanistic role for PsbS as a facilitator of a hydrophobic mismatch-mediated phase transition between LHCII-PsbS and its environment. This could act as the driving force to sort LHCII into photoprotective nanodomains in the thylakoid membrane. This work shows an example of the key role of the hydrophobic mismatch process in regulating membrane protein function in plants.

Unraveling the excited-state vibrational cooling dynamics of chlorophyll-a using femtosecond broadband fluorescence spectroscopy

Understanding the dynamics of excited-state vibrational energy relaxation in photosynthetic pigments is crucial for elucidating the mechanisms underlying energy transfer processes in light-harvesting complexes. Utilizing advanced femtosecond broadband transient fluorescence (TF) spectroscopy, we explored the excited-state vibrational dynamics of Chlorophyll-a (Chl-a) both in solution and within the light-harvesting complex II (LHCII). We discovered a vibrational cooling (VC) process occurring over ∼6 ps in Chl-a in ethanol solution following Soret band excitation, marked by a notable ultrafast TF blueshift and spectral narrowing. This VC process, crucial for regulating the vibronic lifetimes, was further elucidated through the direct observation of the population dynamics of higher vibrational states within the Qy electronic state. Notably, Chl-a within LHCII demonstrated significantly faster VC dynamics, unfolding within a few hundred femtoseconds and aligning with the ultrafast energy transfer processes observed within the complex. Our findings shed light on the complex interaction between electronic and vibrational states in photosynthetic pigments, underscoring the pivotal role of vibrational dynamics in enabling efficient energy transfer within light-harvesting complexes.

Energy transfer from two luteins to chlorophylls in light-harvesting complex II study by using exciton models with phase correction

In light-harvesting complex II of plants, the two lutein pigments (LUT1 and LUT2) are always paired and an energy transfer pathway between them is believed to exist. However, it remains unclear whether this pathway is essential for the energy transfer between carotenoids and chlorophylls. In this work, we performed hybrid quantum mechanics/molecular mechanics simulations with Frenkel exciton models to investigate this energy transfer. The results show that the energy transfer pathways between the S2 state of LUT1 and CLAs are not affected by LUT2 S2. The energy transfer between LUT and chlorophyll-a (CLA) also follows a resonance mechanism. The two LUTs have different energy transfer pathways according to their energy gaps and coupling strengths with each CLA. The present work sheds light on the energy transfer pathways involved in the two LUTs.

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.

Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation

The major light-harvesting complex of photosystem II (LHCII) has a dual regulatory function in a process called non-photochemical quenching to avoid the formation of reactive oxygen. LHCII undergoes reversible conformation transitions to switch between a light-harvesting state for excited-state energy transfer and an energy-quenching state for dissipating excess energy under full sunshine. Here we report cryo-electron microscopy structures of LHCII in membrane nanodiscs, which mimic in vivo LHCII, and in detergent solution at pH 7.8 and 5.4, respectively. We found that, under low pH conditions, the salt bridges at the lumenal side of LHCII are broken, accompanied by the formation of two local α-helices on the lumen side. The formation of α-helices in turn triggers allosterically global protein conformational change, resulting in a smaller crossing angle between transmembrane helices. The fluorescence decay rates corresponding to different conformational states follow the Dexter energy transfer mechanism with a characteristic transition distance of 5.6 Å between Lut1 and Chl612. The experimental observations are consistent with the computed electronic coupling strengths using multistate density function theory.

Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations

The contradictory behaviors in light harvesting and non-photochemical quenching make xanthophyll lutein the most attractive functional molecule in photosynthesis. Despite several theoretical simulations on the spectral properties and excited-state dynamics, the atomic-level photophysical mechanisms need to be further studied and established, especially for an accurate description of geometric and electronic structures of conical intersections for the lowest several electronic states of lutein. In the present work, semiempirical OM2/MRCI and multi-configurational restricted active space self-consistent field methods were performed to optimize the minima and conical intersections in and between the 1Ag-, 2Ag-, 1Bu+, and 1Bu- states. Meanwhile, the relative energies were refined by MS-CASPT2(10,8)/6-31G*, which can reproduce correct electronic state properties as those in the spectroscopic experiments. Based on the above calculation results, we proposed a possible excited-state relaxation mechanism for lutein from its initially populated 1Bu+ state. Once excited to the optically bright 1Bu+ state, the system will propagate along the key reaction coordinate, i.e., the stretching vibration of the conjugated carbon chain. During this period of time, the 1Bu- state will participate in and forms a resonance state between the 1Bu- and 1Bu+ states. Later, the system will rapidly hop to the 2Ag- state via the 1Bu+/2Ag- conical intersection. Finally, the lutein molecule will survive in the 2Ag- state for a relatively long time before it internally converts to the ground state directly or via a twisted S1/S0 conical intersection. Notably, though the photophysical picture may be very different in solvents and proteins, the current theoretical study proposed a promising calculation protocol and also provided many valuable mechanistic insights for lutein and similar carotenoids.

Multistate Energy Decomposition Analysis of Molecular Excited States

A multistate energy decomposition analysis (MS-EDA) method is described to dissect the energy components in molecular complexes in excited states. In MS-EDA, the total binding energy of an excimer or an exciplex is partitioned into a ground-state term, called local interaction energy, and excited-state contributions that include exciton excitation energy, superexchange stabilization, and orbital and configuration-state delocalization. An important feature of MS-EDA is that key intermediate states associated with different energy terms can be variationally optimized, providing quantitative insights into widely used physical concepts such as exciton delocalization and superexchange charge-transfer effects in excited states. By introducing structure-weighted adiabatic excitation energy as the minimum photoexcitation energy needed to produce an excited-state complex, the binding energy of an exciplex and excimer can be defined. On the basis of the nature of intermolecular forces through MS-EDA analysis, it was found that molecular complexes in the excited states can be classified into three main categories, including (1) encounter excited-state complex, (2) charge-transfer exciplex, and (3) intimate excimer or exciplex. The illustrative examples in this Perspective highlight the interplay of local excitation polarization, exciton resonance, and superexchange effects in molecular excited states. It is hoped that MS-EDA can be a useful tool for understanding photochemical and photobiological processes.

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.

Excimer Energies

A multistate energy decomposition analysis (MS-EDA) method is introduced for excimers using density functional theory. Although EDA has been widely applied to intermolecular interactions in the ground state, few methods are currently available for excited-state complexes. Here, the total energy of an excimer state is separated into exciton excitation energy ΔE_Ex(|Ψ_X·Ψ_Y⟩*), resulting from the state interaction between locally excited monomer states |Ψ_X^*·Ψ_Y⟩ and |Ψ_X·Ψ_Y^*⟩ , a superexchange stabilization energy ΔE_SE, originating from the mutual charge transfer between two monomers |Ψ_X⁺·Ψ_Y⟩ and |Ψ_X^-·Ψ_Y⁺⟩ , and an orbital-and-configuration delocalization term ΔE_OCD due to the expansion of configuration space and block-localized orbitals to the fully delocalized dimer system. Although there is no net charge transfer in symmetric excimer cases, the resonance of charge-transfer states is critical to stabilizing the excimer. The monomer localized excited and charge-transfer states are variationally optimized, forming a minimal active space for nonorthogonal state interaction (NOSI) calculations in multistate density functional theory to yield the intermediate states for energy analysis. The present MS-EDA method focuses on properties unique to excited states, providing insights into exciton coupling, superexchange and delocalization energies. MS-EDA is illustrated on the acetone and pentacene excimer systems; three configurations of the latter case are examined, including the optimized excimer, a stacked configuration of two pentacene molecules and the fishbone orientation. It is found that excited-state energy splitting is strongly dependent on the relative energies of the monomer excited states and the phase-matching of the monomer wave functions.

Target State Optimized Density Functional Theory for Electronic Excited and Diabatic States

A flexible self-consistent field method, called target state optimization (TSO), is presented for exploring electronic excited configurations and localized diabatic states. The key idea is to partition molecular orbitals into different subspaces according to the excitation or localization pattern for a target state. Because of the orbital-subspace constraint, orbitals belonging to different subspaces do not mix. Furthermore, the determinant wave function for such excited or diabatic configurations can be variationally optimized as a ground state procedure, unlike conventional ΔSCF methods, without the possibility of collapsing back to the ground state or other lower-energy configurations. The TSO method can be applied both in Hartree-Fock theory and in Kohn-Sham density functional theory (DFT). The density projection procedure and the working equations for implementing the TSO method are described along with several illustrative applications. For valence excited states of organic compounds, it was found that the computed excitation energies from TSO-DFT and time-dependent density functional theory (TD-DFT) are of similar quality with average errors of 0.5 and 0.4 eV, respectively. For core excitation, doubly excited states and charge-transfer states, the performance of TSO-DFT is clearly superior to that from conventional TD-DFT calculations. It is shown that variationally optimized charge-localized diabatic states can be defined using TSO-DFT in energy decomposition analysis to gain both qualitative and quantitative insights on intermolecular interactions. Alternatively, the variational diabatic states may be used in molecular dynamics simulation of charge transfer processes. The TSO method can also be used to define basis states in multistate density functional theory for excited states through nonorthogonal state interaction calculations. The software implementing TSO-DFT can be accessed from the authors.

Cold-induced calreticulin OsCRT3 conformational changes promote OsCIPK7 binding and temperature sensing in rice

Unusually low temperatures caused by global climate change adversely affect rice production. Sensing cold to trigger signal network is a key base for improvement of chilling tolerance trait.  Here, we report that Oryza sativa Calreticulin 3 (OsCRT3) localized at the endoplasmic reticulum (ER) exhibits conformational changes under cold stress, thereby enhancing its interaction with CBL-interacting protein kinase 7 (OsCIPK7) to sense cold. Phenotypic analyses of OsCRT3 knock-out mutants and transgenic overexpression lines demonstrate that OsCRT3 is a positive regulator in chilling tolerance. OsCRT3 localizes at the ER and mediates increases in cytosolic calcium levels under cold stress. Notably, cold stress triggers secondary structural changes of OsCRT3 and enhances its binding affinity with OsCIPK7, which finally boosts its kinase activity. Moreover, Calcineurin B-like protein 7 (OsCBL7) and OsCBL8 interact with OsCIPK7 specifically on the plasma membrane. Taken together, our results thus identify a cold-sensing mechanism that simultaneously conveys cold-induced protein conformational change, enhances kinase activity, and Ca²⁺ signal generation to facilitate chilling tolerance in rice.

The mechanism for thermal-enhanced chaperone-like activity of α-crystallin against UV irradiation-induced aggregation of γD-crystallin

Exposure to solar UV irradiation damages γ-crystallin, leading to cataract formation via aggregation. α-Crystallin, as a small heat-shock protein (sHsps), efficiently suppresses this irreversible aggregation by selectively binding the denatured γ-crystallin monomer. In this study, liquid chromatography tandem mass spectrometry (LC-MS) was used to evaluate UV-325 nm irradiation-induced photodamage of human γD-crystallin in the presence of bovine α-crystallin, atomic force microscope (AFM) and dynamic light scattering (DLS) techniques were used to detect the quaternary structure changes of α-crystallin oligomer, and Fourier transform infrared (FTIR) spectroscopy and temperature-jump (T-jump) nanosecond time-resolved IR absorbance difference spectroscopy were used to probe the secondary structure changes of bovine α-crystallin. We find that the thermal-induced subunit dissociation of α-crystallin oligomer involves the breaking of hydrogen bonds at the dimeric interface, leading to three different spectral components at varied temperature regions as resolved from temperature-dependent IR spectra. Under UV-325 nm irradiation, unfolded γD-crystallin binds to the dissociated α-crystallin subunit to form αγ-complex, then follows the reassociation of αγ-complex to the partially dissociated α-crystallin oligomer. This prevents the aggregation of denatured γD-crystallin. The formation of the γD-bound α-crystallin oligomer is further confirmed by AFM and DLS analysis, which reveals an obvious size expansion in the reassociated αγ-oligomers. In addition, UV-325 nm irradiation causes a peptide bond cleavage of γD-crystallin at Ala158 in presence of α-crystallin. Our results suggest a very effective protection mechanism for subunits dissociated from α-crystallin oligomers against UV irradiation-induced aggregation of γD-crystallin, at an expense of a loss of a short C-terminal peptide in γD-crystallin.

Lipid-Enhanced Photoprotection of LHCII in Membrane Nanodisc by Reducing Chlorophyll Triplet Production

Carotenoid (Car) quenching chlorophyll triplet state (³Chl a*), an unwanted photosensitizer yielding harmful reactive oxygen species, is crucial for the survival of oxygenic photosynthetic organisms. For the major light-harvesting complex of photosystem II (LHCII) in isolated form, ³Chl a* is deactivated via sub-nanosecond Chl-to-Car triplet excitation energy transfer by lutein in the central domain of LHCII; however, the mechanistic difference from LHCII in vivo remains to be explored. To investigate the intrinsic Car-photoprotection properties of LHCII in a bio-mimicking circumstance, we reconstituted trimeric spinach LHCII into the discoidal membrane of nanosize made from l-α-phosphatidylcholine and examined the triplet excited dynamics. Time-resolved optical absorption combined with circular dichroism spectroscopies revealed that, with reference to LHCII in buffer, LHCII in the membrane nanodisc shows appreciable conformational variation in the neoxanthin and the Lut621 domains and in the Chl a-terminal cluster owing to the lipid-protein interactions, which, in turn, alters the triplet population of Lut620 and Lut621 and their partition. Importantly, the unquenched ³Chl a* population in the complex was reduced by 60%, indicating that LHCII in the membrane adopts a conformation that is optimized for the alleviation of photoinhibition.

Vibrational and vibronic coherences in the energy transfer process of light-harvesting complex II revealed by two-dimensional electronic spectroscopy

The presence of quantum coherence in light-harvesting complex II (LHCII) as a mechanism to understand the efficiency of the light-harvesting function in natural photosynthetic systems is still debated due to its structural complexity and weak-amplitude coherent oscillations. Here, we revisit the coherent dynamics and clarify different types of coherences in the energy transfer processes of LHCII using a joint method of the high-S/N transient grating and two-dimensional electronic spectroscopy. We find that the electronic coherence decays completely within 50 fs at room temperature. The vibrational coherences of chlorophyll a dominate over oscillations within 1 ps, whereas a low-frequency mode of 340 cm−1 with a vibronic mixing character may participate in vibrationally assisted energy transfer between chlorophylls a. Our results may suggest that vibronic mixing is relevant for rapid energy transfer processes among chlorophylls in LHCII.

A different perspective for nonphotochemical quenching in plant antenna complexes

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

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.

Bridging Carotenoid-to-Bacteriochlorophyll Energy Transfer of Purple Bacteria LH2 With Temperature Variations: Insights From Conformational Changes

Photosynthesis is a key process for converting light energy into chemical energy and providing food for lives on Earth. Understanding the mechanism for the energy transfers could provide insights into regulating energy transfers in photosynthesis and designing artificial photosynthesis systems. Many efforts have been devoted to exploring the mechanism of temperature variations affecting the excitonic properties of LH2. In this study, we performed all-atom molecular dynamics (MD) simulations and quantum mechanics calculations for LH2 complex from purple bacteria along with its membrane environment under three typical temperatures: 270, 300, and 330 K. The structural analysis from validated MD simulations showed that the higher temperature impaired interactions at N-terminus of both α and β polypeptide helices and led to the dissociation of this hetero polypeptide dimer. Rhodopin-β-D-glucosides (RG1) moved centripetally with α polypeptide helices when temperature increased and enlarged their distances with bacteriochlorophylls molecules that have the absorption peak at 850 nm (B850), which resulted in reducing the coupling strengths between RG1 and B850 molecules. The present study reported a cascading mechanism for temperature regulating the energy transfers in LH2 of purple bacteria.

Exact-two-component block-localized wave function: A simple scheme for the automatic computation of relativistic ΔSCF

Block-localized wave function is a useful method for optimizing constrained determinants. In this article, we extend the generalized block-localized wave function technique to a relativistic two-component framework. Optimization of excited state determinants for two-component wave functions presents a unique challenge because the excited state manifold is often quite dense with degenerate states. Furthermore, we test the degree to which certain symmetries result naturally from the ΔSCF optimization such as time-reversal symmetry and symmetry with respect to the total angular momentum operator on a series of atomic systems. Variational optimizations may often break the symmetry in order to lower the overall energy, just as unrestricted Hartree-Fock breaks spin symmetry. Overall, we demonstrate that time-reversal symmetry is roughly maintained when using Hartree-Fock, but less so when using Kohn-Sham density functional theory. Additionally, maintaining total angular momentum symmetry appears to be system dependent and not guaranteed. Finally, we were able to trace the breaking of total angular momentum symmetry to the relaxation of core electrons.

Block-Localized Excitation for Excimer Complex and Diabatic Coupling

We describe a block-localized excitation (BLE) method to carry out constrained optimization of block-localized orbitals for constructing valence bond-like, diabatic excited configurations using multistate density functional theory (MSDFT). The method is an extension of the previous block-localized wave function method through a fragment-based ΔSCF approach to optimize excited determinants within a molecular complex. In BLE, both the number of electrons and the electronic spin of different fragments in a whole system can be constrained, whereas electrostatic, exchange, and polarization interactions among different blocks can be fully taken into account of. To avoid optimization collapse to unwanted states, a ΔSCF projection scheme and a maximum overlap of wave function approach have been presented. The method is illustrated by the excimer complex of two naphthalene molecules. With a minimum of eight spin-adapted configurational state functions, it was found that the inversion of L_a^- and L_b^- states near the optimal structure of the excimer complex is correctly produced, which is in quantitative agreement with DMRG-CASPT2 calculations and experiments. Trends in the computed transfer integrals associated with excited-state energy transfer both in the singlet and triplet states are discussed. The results suggest that MSDFT may be used as an efficient approach to treat intermolecular interactions in excited states with a minimal active space (MAS) for interpretation of the results and for dynamic simulations, although the selection of a small active space is often system dependent.

The robustness of the terminal emitter site in major LHCII complexes controls xanthophyll function during photoprotection

Xanthophylls in light harvesting complexes perform a number of functions ranging from structural support to light-harvesting and photoprotection. In the major light harvesting complex of photosystem II in plants (LHCII), the innermost xanthophyll binding pockets are occupied by lutein molecules. The conservation of these sites within the LHC protein family suggests their importance in LHCII functionality. In the present work, we induced the photoprotective switch in LHCII isolated from the Arabidopsis mutant npq1lut2, where the lutein molecules are exchanged with violaxanthin. Despite the differences in the energetics of the pigments and the impairment of chlorophyll fluorescence quenching in vivo, we show that isolated complexes containing violaxanthin are still able to induce the quenching switch to a similar extent to wild type LHCII monomers. Moreover, the same spectroscopic changes take place, which suggest the involvement of the terminal emitter site (L1) in energy dissipation in both complexes. These results indicate the robust nature of the L1 xanthophyll binding domain in LHCII, where protein structural cues are the major determinant of the function of the bound carotenoid.

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.