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

Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning

Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes more complicated not only because of structural effects induced by the protein pocket but also because the protein environment is highly anisotropic. This is particularly evident for highly conjugated and flexible molecules such as carotenoids, whose excitation energy is strongly dependent on both the geometry and the electrostatics of the environment. Here, we introduce a machine learning (ML) strategy trained on quantum mechanics/molecular mechanics calculations of geometrical and electrochromic contributions to carotenoids' excitation energies. We employ this strategy to compare solvatochromism in protein and solvent environments. Despite the important specifities of the protein, ML models trained on solvents can faithfully predict excitation energies in the protein environment, demonstrating the robustness of the chosen descriptors.

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes

Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.

Relaxation dynamics of high-energy excited states of carotenoids studied by UV excitation and pump-repump-probe transient absorption spectroscopy

The excited states of carotenoids have been a subject of numerous studies. While a majority of these reports target the excited state dynamics initiated by the excitation of the S2 state, the upper excited state(s) absorbing in the UV spectral region (denoted as SUV) has been only scarcely studied. Moreover, the relation between the SUV and Sn, the final state of the well-known S1-Sn transition of carotenoids, remains unknown. To address this yet-unresolved issue, we compared the excited state dynamics of two carotenoids, namely, β-carotene and astaxanthin, after excitation of either the SUV or Sn state. The SUV state was excited directly by UV light, and the excitation of the Sn state was achieved via re-pumping the S1-Sn transition. The results indicated that direct SUV excitation produces an S1-Sn band that is significantly broader than that obtained after S2 excitation, most probably due to the generation of multiple S1 conformations produced by excess energy. No such broadening is observed if the Sn state is excited by the re-pump pulse. This shows that the Sn and SUV states are different, each initializing a specific relaxation pathway. We propose that the Sn state retains the coupled triplet pair character of the S1 state, while the SUV state is the higher state of Bu+ symmetry accessible by one-photon transition.

The role of the local environment on the structural heterogeneity of carotenoid β-ionone rings

Our analysis of the X-ray crystal structure of canthaxanthin (CAN) showed that its ketolated β-ionone rings can adopt two energetically equal, but structurally distinct puckers. Quantum chemistry calculations revealed that the potential energy surface of the β-ionone ring rotation over the plane of the conjugated π-system in carotenoids depends on the pucker state of the β-ring. Considering different pucker states and β-ionone ring rotation, we found six separate local minima on the potential energy surface defining the geometry of the keto-β-ionone ring-two cis and one trans orientation for each of two pucker states. We observed a small difference in energy and no difference in relative orientation for the cis-minima, but a pronounced difference for the position of trans-minimum in alternative pucker configurations. An energetic advantage of β-ionone ring rotation from a specific pucker type can reach up to 8 kJ/mol ([Formula: see text]). In addition, we performed the simulation of linear absorption of CAN in hexane and in a unit cell of the CAN crystal. The electronic energies of [Formula: see text] transition were estimated both for the CAN monomer and in the CAN crystal. The difference between them reached [Formula: see text], which roughly corresponds to the energy gap between A and B pucker states predicted by theoretical estimations. Finally, we have discussed the importance of such effects for biological systems whose local environment determines conformational mobility, and optical/functional characteristics of carotenoid.

Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization

Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows concerted isomerization of C9'-C8' and C7'-C6' single bonds in the bicycle-pedal (s-BP) manner and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven recovery of the s-BP isomer to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. Solution FTIR and UV/Vis spectroscopy support the single bond isomerization of the carotenoid in the s-BP manner and subsequent thermal structural reactions as the basis of OCP photoreception.

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae^1,2. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching^3-6. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties⁷, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

Simulation of Ab Initio Optical Absorption Spectrum of β-Carotene with Fully Resolved S0 and S2 Vibrational Normal Modes

The electronic absorption spectrum of β-carotene (β-Car) is studied using quantum chemistry and quantum dynamics simulations. Vibrational normal modes were computed in optimized geometries of the electronic ground state S₀ and the optically bright excited S₂ state using the time-dependent density functional theory. By expressing the S₂-state normal modes in terms of the ground-state modes, we find that no one-to-one correspondence between the ground- and excited-state vibrational modes exists. Using the ab initio results, we simulated the β-Car absorption spectrum with all 282 vibrational modes in a model solvent at 300 K using the time-dependent Dirac-Frenkel variational principle and are able to qualitatively reproduce the full absorption line shape. By comparing the 282-mode model with the prominent 2-mode model, widely used to interpret carotenoid experiments, we find that the full 282-mode model better describes the high-frequency progression of carotenoid absorption spectra; hence, vibrational modes become highly mixed during the S₀ → S₂ optical excitation. The obtained results suggest that electronic energy dissipation is mediated by numerous vibrational modes.

Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein

Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion.

Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion.

Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach

The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid-protein interactions.

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.

Spectral Signatures of Canthaxanthin Translocation in the Orange Carotenoid Protein

The orange carotenoid protein (OCP) is involved in the photoprotective processes in cyanobacteria via nonphotochemical quenching. Triggered by blue-green light absorption, the carotenoid chromophore undergoes translocation, displacing around 12 Å from the C-terminal domain (CTD) to the N-terminal domain (NTD). The detailed molecular rearrangements that occur within the carotenoid and the protein during this process remain largely elusive. By using a combination of molecular dynamics, well-tempered metadynamics, and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations, we were able to mimic the translocation of the carotenoid from the inactive OCP^O and obtain metastable red-shifted states in the photoactivation mechanism, replicating the λ_max values of reference experimental spectra. In addition, our simulations give insight into the structure of the red-shifted form of the inactive state of OCP.

Excited state geometry of β-carotene influenced by environments: the nature and decisive role of solvent revealing by two-dimensional resonance Raman correlation spectroscopy

Resonance Raman scattering can be used to investigate the ground and excited state information of carotenoid. It is known that the Dushinsky rotation can significantly influence the resonant Raman intensity of β-carotene (β-car). The excited state geometry revealed by the double components feature of the C = C stretching vibrational modes and the environmental dependence of the Raman intensity for each component remain unknown. We explore the influence of environmental factors on the relative intensity of these two C = C stretching vibration modes and perform two-dimensional resonance Raman correlation analysis to reveal the changes on β-car excited state geometry. The results show that the relative wavelength difference between the 0-0 absorption and the excitation is the key factor that decides the intensity ratio of the two components and that the intensity of each mode is modulated by environmental factors. This modulation is closely related to the excited state geometry and dynamics, effective conjugation length, and electron-phonon coupling constant. It also shows that the asynchronous cross-peaks in the two-dimensional resonance Raman correlation spectrum (2DRRCOS) can effectively characterize the degree of the varied electron-phonon coupling with the changing conditions. These results are not only complementary to the research on the excited states of carotenoids but also applicable to investigate the environmental dependence of Raman intensity for a lot of π-conjugated molecules.

Fluorescence Anisotropy Detection of Barrier Crossing and Ultrafast Conformational Dynamics in the S2 State of β-Carotene

Carotenoids are usually only weakly fluorescent despite being very strong absorbers in the mid-visible region because their first two excited singlet states, S₁ and S₂, have very short lifetimes. To probe the structural mechanisms that promote the nonradiative decay of the S₂ state to the S₁ state, we have carried out a series of fluorescence lineshape and anisotropy measurements with a prototype carotenoid, β-carotene, in four aprotic solvents. The anisotropy values observed in the fluorescence emission bands originating from the S₂ and S₁ states reveal that the large internal rotations of the emission transition dipole moment, as much as 50° relative to that of the absorption transition dipole moment, are initiated during ultrafast evolution on the S₂ state potential energy surface and persist upon nonradiative decay to the S₁ state. Electronic structure calculations of the orientation of the transition dipole moment account for the anisotropy results in terms of torsional and pyramidal distortions near the center of the isoprenoid backbone. The excitation wavelength dependence of the fluorescence anisotropy indicates that these out-of-plane conformational motions are initiated by passage over a low-activation energy barrier from the Franck-Condon S₂ structure. This conclusion is consistent with detection over the 80-200 K range of a broad, red-shifted fluorescence band from a dynamic intermediate evolving on a steep gradient of the S₂ state potential energy surface after crossing the activation barrier. The temperature dependence of the oscillator strength and anisotropy indicate that nonadiabatic passage from S₂ through a conical intersection seam to S₁ is promoted by the out-of-plane motions of the isoprenoid backbone with strong hindrance by solvent friction.

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

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

Spectroscopy and excited state dynamics of nearly infinite polyenes

Steady-state and transient absorption spectra with <50 fs time resolution were obtained for two conjugated polymers, both with ≈200 conjugated double bonds (N), constrained in planar, stable, polyene frameworks. Solutions of the polymers exhibit the same S2 → S1 → S* → S0 decay pathway observed for the N = 11-19 polyene oligomers and for zeaxanthin homologues with N = 11-23. Comparisons with the excited state dynamics of polydiactylene and a much longer, more disordered polyene polymer (poly(DEDPM)) show that the S2, S1, and S* lifetimes of the four polymers are almost identical. The S* signals in the polymers are assigned to absorption from vibrationally excited ground states. In spite of significant heterogeneities and variations in conjugation lengths in these long polyenes, their S0 → S2 absorptions are vibronically-resolved in room temperature solutions with electronic origins at ≈600 nm. The limiting wavelength for the S0 → S2 transitions is consistent with the persistence of bond length alternation in the electronic ground states and a HOMO-LUMO band gap in polyenes with N ≈ 200. The coincidence of the well-resolved S0 → S2 electronic origins and the convergence of the excited state lifetimes in the four polymers point to a common, "nearly infinite" polyene limit.

Structural peculiarities of keto-carotenoids in water-soluble proteins revealed by simulation of linear absorption

To prevent irreversible damage caused by an excess of incident light, the photosynthetic machinery of many cyanobacteria uniquely utilizes the water-soluble orange carotenoid protein (OCP) containing a single keto-carotenoid molecule. This molecule is non-covalently embedded into the two OCP domains which are interconnected by a flexible linker. The phenomenon of OCP photoactivation, causing significant changes in carotenoid absorption in the orange and red form of OCP, is currently being thoroughly studied. Numerous additional spectral forms of natural and synthetic OCP-like proteins have been unearthed. The optical properties of carotenoids are strongly determined by the interaction of their electronic states with vibrational modes, the surrounding protein matrix, and the solvent. In this work, the effects of the pigment-protein interaction and vibrational relaxation in OCP were studied by computational simulation of linear absorption. Taking into account Raman spectroscopy data and applying the multimode Brownian oscillator model as well as the cumulant expansion technique, we have calculated a set of characteristic microparameters sufficient to demarcate different carotenoid states in OCP forms, using the model carotenoids spheroidene and spheroidenone in methanol/acetone solution as benchmarks. The most crucial microparameters, which determine the effect of solvent and protein environment, are the Huang-Rhys factors and the frequencies of C[double bond, length as m-dash]C and C-C stretching modes, the low-frequency mode and the FWHM due to inhomogeneous line broadening. Considering the difference of linear absorption between spheroidene and spheroidenone, which remarkably resembles the photoinduced changes of OCP absorption, and applying quantum chemical calculations, we discuss structural and functional determinants of carotenoid binding proteins.