2D Spectroscopy Study of Water-Soluble Chlorophyll-Binding Protein from Lepidium virginicum

Exciton interactions of chlorophyll tetramer in water-soluble chlorophyll-binding protein BoWSCP

The exciton interaction of four chlorophyll a (Chl a) molecules in a symmetrical tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP was analyzed in the pH range of 3-11. Exciton splitting ΔE = 232 ± 2 cm-1 of the Qy band of Chl a into two subcomponents with relative intensities of 78.1 ± 0.7 % and 21.9 ± 0.7 % was determined by a joint decomposition of the absorption and circular dichroism spectra into Gaussian functions. The exciton coupling parameters were calculated based on the BoWSCP atomic structure in three approximations: the point dipole model, the distributed atomic monopoles, and direct ab initio calculations in the TDDFT/PCM approximation. The Coulomb interactions of monomers were calculated within the continuum model using three values of optical permittivity. The models based on the properties of free Chl a in solution suffer from significant errors both in estimating the absolute value of the exciton interaction and in the relative intensity of exciton transitions. Calculations within the TDDFT/PCM approximation reproduce the experimentally determined parameters of the exciton splitting and the relative intensities of the exciton bands. The following factors of pigment-protein and pigment-pigment interactions were examined: deviation of the macrocycle geometry from the planar conformation of free Chl; the formation of hydrogen bonds between the macrocycle and water molecules; the overlap of wave functions of monomers at close distances. The most significant factor is the geometrical deformation of the porphyrin macrocycle, which leads to an increase in the dipole moment of Chl monomer from 5.5 to 6.9 D and to a rotation of the dipole moment by 15° towards the cyclopentane ring. The contributions of resonant charge-transfer states to the wave functions of the Chl dimer were determined and the transition dipole moments of the symmetric and antisymmetric charge-transfer states were estimated.

Femtosecond Dynamics of Excited States of Chlorophyll Tetramer in Water-Soluble Chlorophyll-Binding Protein BoWSCP

The paper reports on the absorption dynamics of chlorophyll a in a symmetric tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP. It was measured by a broadband femtosecond laser pump-probe spectroscopy within the range from 400 to 750 nm and with a time resolution of 20 fs-200 ps. When BoWSCP was excited in the region of the Soret band at a wavelength of 430 nm, nonradiative intramolecular conversion S3→S1 was observed with a characteristic time of 83 ± 9 fs. When the complex was excited in the region of the Qy band at 670 nm, relaxation transition between two excitonic states of the chlorophyll dimer was observed in the range of 105 ± 10 fs. Absorption spectra of the excited singlet states S1 and S3 of chlorophyll a were obtained. The delocalization of the excited state between exciton-coupled Chl molecules in BoWSCP tetramer changed in time and depended on the excitation energy. When BoWSCP is excited in the Soret band region, an ultrafast photochemical reaction is observed. This could result from the reduction of tryptophan in the vicinity of chlorophyll.

Measuring the Ultrafast Correlation Dynamics of a Multilevel System Using the Center Line Slope Analysis in Two-Dimensional Electronic Spectroscopy

In a two-dimensional (2D) optical spectrum of a multilevel system, there are diagonal peaks and off-diagonal cross-peaks that correlate the different levels. The time-dependent properties of these diagonal peaks and cross-peaks contain much information about the dynamics of the multilevel system. The time-dependent diagonal peakshape that depends on the spectral diffusion dynamics of the associated transition and characterized by the frequency-fluctuation correlation function (FFCF) is well studied. However, the time-dependent peakshape of a cross-peak that provides the correlation dynamics between different transitions is much less studied or understood. We derived the third-order nonlinear response functions that describe the cross-peaks in a 2D electronic spectrum of a multilevel system that arise from processes sharing a common ground state and/or from internal conversion and population transfer. We can use the center line slope (CLS) analysis to characterize the cross-peaks in conjunction with the diagonal peaks. This allows us to recover the frequency-fluctuation cross-correlation functions (FXCFs) between two transitions. The FXCF and its subsidiary quantities such as the initial correlation and the initial covariance between different transitions are important for studying the correlation effects between states in complex systems, such as energy-transfer processes. Furthermore, knowledge of how various molecular processes over different timescales affect simultaneously different transitions can also be obtained from the measured FXCF. We validated and tested our derived equations and analysis process by studying, as an example, the 2D electronic spectra of metal-free phthalocyanine in solution. We measured and analyzed the diagonal peaks of the Qx and Qy transitions and the cross-peaks between these two transitions of this multilevel electronic system and obtained the associated FFCFs and FXCFs. In this model system, we measured negative components of FXCF over the tens of picosecond timescale. This suggests that in phthalocyanine, the Qx and Qy transitions coupling with the solvent molecule motion are anticorrelated to each other.

Signatures of intramolecular vibrational and vibronic Q[Formula: see text]-Q[Formula: see text] coupling effects in absorption and CD spectra of chlorophyll dimers

An electron-vibrational coupling model that includes the vibronic (non-adiabatic) coupling between the Q[Formula: see text] and Q[Formula: see text] transitions of chlorophyll (Chl), created by Reimers and coworkers (Scientific Rep. 3, 2761, 2013) is extended here to chlorophyll dimers with interchlorophyll excitonic coupling. The model is applied to a Chl a dimer of the water-soluble chlorophyll binding protein (WSCP). As for isolated chlorophyll, the vibronic coupling is found to have a strong influence on the high-frequency vibrational sideband in the absorption spectrum, giving rise to a band splitting. In contrast, in the CD spectrum the interplay of vibronic coupling and static disorder leads to a strong suppression of the vibrational sideband in excellent agreement with the experimental data. The conservative nature of the CD spectrum in the low-energy region is found to be caused by a delicate balance of the intermonomer excitonic coupling between the purely electronic Q[Formula: see text] transition and the Q[Formula: see text] transition involving intramolecular vibrational excitations on one hand and the coupling to higher-energy electronic transitions on the other hand.

Magnetophotoselection in the Investigation of Excitonically Coupled Chromophores: The Case of the Water-Soluble Chlorophyll Protein

A magnetophotoselection (MPS) investigation of the photoexcited triplet state of chlorophyll a both in a frozen organic solvent and in a protein environment, provided by the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum, is reported. The MPS experiment combines the photoselection achieved by exciting with linearly polarized light with the magnetic selection of electron paramagnetic resonance (EPR) spectroscopy, allowing the determination of the relative orientation of the optical transition dipole moment and the zero-field splitting tensor axes in both environments. We demonstrate the robustness of the proposed methodology for a quantitative description of the excitonic interactions among pigments. The orientation of the optical transition dipole moments determined by the EPR analysis in WSCP, identified as an appropriate model system, are in excellent agreement with those calculated in the point-dipole approximation. In addition, MPS provides information on the electronic properties of the triplet state, localized on a single chlorophyll a pigment of the protein cluster, in terms of orientation of the zero-field splitting tensor axes in the molecular frame.

Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches

A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening effects. Here, this challenging problem is approached by combining the fragment molecular orbital (FMO) method with the polarizable continuum model (PCM). The method is applied to compute excitonic couplings between chlorophyll a (Chl a) pigments of the water-soluble chlorophyll-binding protein (WSCP). By calibrating the vacuum dipole strength of the 0–0 transition of the Chl a chromophores according to experimental data, an excellent agreement between calculated and experimental linear absorption and circular dichroism spectra of WSCP is obtained. The effect of the mutual polarization of the pigment ground states is calculated to be very small. The simple Poisson-Transition-charge-from-Electrostatic-potential (Poisson-TrEsp) method is found to accurately describe the screening part of the excitonic coupling, obtained with FMO/PCM. Taking into account that the reaction field effects of the latter method can be described by a scalar constant leads to an improvement of Poisson-TrEsp that is expected to provide the basis for simple and realistic calculations of optical spectra and energy transfer in photosynthetic light-harvesting complexes. In addition, we present an expression for the estimation of Huang–Rhys factors of high-frequency pigment vibrations from experimental fluorescence line-narrowing spectra that takes into account the redistribution of oscillator strength by the interpigment excitonic coupling. Application to WSCP results in corrected Huang–Rhys factors that are less than one third of the original values obtained by the standard electronic two-state analysis that neglects the above redistribution. These factors are important for the estimation of the dipole strength of the 0–0 transition of the chromophores and for the development of calculation schemes for the spectral density of the exciton-vibrational coupling.

The importance of reaction field and screening effects on the excitonic couplings is demonstrated, and from quantum-chemical calculations a single scaling factor is derived that can be used to improve simple models based on the Poisson equation.

Spectral tuning of chlorophylls in proteins - electrostatics vs. ring deformation

In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Recombinant type II water soluble chlorophyll-binding proteins from Brassicaceae (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, and the ability to rigorously modify the chlorophyll's protein surroundings. Our previous comparison of the crystal structures of two WSCP homologues suggested that protein-induced chlorophyll ring deformation is the predominant spectral tuning mechanism. Here, we implement a more rigorous analysis based on hybrid quantum mechanics and molecular mechanics calculations to quantify the relative contributions of geometrical and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, geometry distortions such as chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas the direct polarization of the electron density accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes.

The fate of chlorophyll in phytophagous insects goes beyond nutrition

Chlorophyll (Chl) is a natural compound that is found in all autotrophic plants. Since phytophagous insects ingest the photosynthetically active material with the plant leaves, the question arises if and how herbivores deal with Chl and its degradation products. Here we review findings on Chl degradation in phytophagous insects and highlight the role of these ubiquitous plant metabolites for plant-feeding insects. Due to the anaerobic gut of many insects, the degradation is limited to the removal of the peripheral substituents, while the tetrapyrrole core remains intact. Proteins, such as red fluorescent protein, P252 (a novel 252-kDa protein), and chlorophyllide binding protein have been reported to occur in the insect gut and might be indirectly connected to Chl degradation. Besides of an nutritional value, e.g., by taking up Mg²⁺ ions or by sequestration of carbon from the phytol side chain, the Chl degradation products may serve the insect, after binding to certain proteins, as antimicrobial, antifungal, and antiviral factors. The protein complexes may also confer protection against reactive oxygen species. The antibiotic potential of proteins and degradation products does not only benefit phytophagous insects but also human being in medical application of cancer treatment for instance. This review highlights these aspects from a molecular, biochemical, and ecological point of view.

Confronting FCP structure with ultrafast spectroscopy data: evidence for structural variations

Diatoms are a major group of algae, responsible for a quarter of the global primary production on our planet. Their adaptation to marine environments is ensured by their light-harvesting antenna - the fucoxanthin-chlorophyll protein (FCP) complex, which absorbs strongly in the blue-green spectral region. Although these essential proteins have been the subject of many studies, for a long time their comprehensive description was not possible in the absence of structural data. Last year, the 3D structures of several FCP complexes were revealed. The structure of an FCP dimer was resolved by crystallography for the pennate diatom Phaeodactylum tricornutum [W. Wang et al., Science, 2019, 363, 6427] and the structure of the PSII supercomplex from the centric diatom Chaetoceros gracilis, containing several FCPs, was obtained by electron microscopy [X. Pi et al., Science, 2019, 365, 6452; R. Nagao et al., Nat. Plants, 2019, 5, 890]. In this Perspective article, we evaluate how precisely these structures may account for previously published ultrafast spectroscopy results, describing the excitation energy transfer in the FCP from another centric diatom Cyclotella meneghiniana. Surprisingly, we find that the published FCP structures cannot explain several observations obtained from ultrafast spectroscopy. Using the available structures, and results from electron microscopy, we construct a trimer-based FCP model for Cyclotella meneghiniana, consistent with ultrafast experimental data. As a whole, our observations suggest that the structures from the proteins belonging to the FCP family display larger variations than the equivalent LHC proteins in plants, which may reflect species-specific adaptations or original strategies for adapting to rapidly changing marine environments.

How water-soluble chlorophyll protein extracts chlorophyll from membranes

Water-soluble chlorophyll proteins (WSCPs) found in Brassicaceae are non-photosynthetic proteins that bind only a small number of chlorophylls. Their biological function remains unclear, but recent data indicate that WSCPs are involved in stress response and pathogen defense as producers of reactive oxygen species and/or Chl-regulated protease inhibitors. For those functions, WSCP apoprotein supposedly binds Chl to become physiologically active or inactive, respectively. Thus, Chl-binding seems to be a pivotal step for the biological function of WSCP. WSCP can extract Chl from the thylakoid membrane but little is known about the mechanism of how Chl is sequestered from the membrane into the binding sites. Here, we investigate the interaction of WSCP with the thylakoid membrane in detail. The extraction of Chl from the thylakoid by WSCP apoprotein is a slow and inefficient reaction, because WSCP presumably does not directly extract Chl from other Chl-binding proteins embedded in the membrane. WSCP apoprotein interacts with model membranes that contain the thylakoid lipids MGDG, DGDG or PG, and can extract Chl from those. Furthermore, the WSCP-Chl complex, once formed, no longer interacts with membranes. We concluded that the surroundings of the WSCP pigment-binding site are involved in the WSCP-membrane interaction and identified a ring of hydrophobic amino acids with two conserved Trp residues around the Chl-binding site. Indeed, WSCP variants, in which one of the Trp residues was exchanged for Phe, still interact with the membrane but are no longer able to extract Chl.

How the Protein Environment Can Tune the Energy, the Coupling, and the Ultrafast Dynamics of Interacting Chlorophylls: The Example of the Water-Soluble Chlorophyll Protein

The interplay between active molecules and the protein environment in light-harvesting complexes tunes the photophysics and the dynamical properties of pigment-protein complexes in a subtle way, which is not fully understood. Here we characterized the photophysics and the ultrafast dynamics of four variants of the water-soluble chlorophyll protein (WSCP) as an ideal model system to study the behavior of strongly interacting chlorophylls. We found that when coordinated by the WSCP protein, the presence of the formyl group in chlorophyll b replacing the methyl group in chlorophyll a strongly affects the exciton energy and the dynamics of the system, opening up the possibility of tuning the photophysics and the transport properties of multichromophores by engineering specific interactions with the surroundings.

New homologues of Brassicaceae water-soluble chlorophyll proteins shed light on chlorophyll binding, spectral tuning, and molecular evolution

Type-II water-soluble chlorophyll (Chl) proteins (WSCPs) of Brassicaceae are promising models for understanding how protein sequence and structure affect Chl binding and spectral tuning in photosynthetic Chl-protein complexes. However, to date, their use has been limited by the small number of known WSCPs, which also limited understanding their physiological roles. To overcome these limitations, we performed a phylogenetic analysis to compile a more comprehensive and complete set of natural type-II WSCP homologues. The identified homologues were heterologously expressed in Escherichia coli, purified, tested for assembly with chlorophylls, and spectroscopically characterized. The analyses led to the discovery of previously unrecognized type-IIa and IIb subclass WSCPs, as well as of a new subclass that did not bind chlorophylls. Further analysis by ancestral sequence reconstruction yielded sequences of putative ancestors of the three subclasses, which were subsequently recombinantly expressed in E. coli, purified and characterized. Combining the phylogenetic and spectroscopic data with molecular structural information revealed distinct Chl-binding motifs, and identified residues critically impacting spectral tuning. The distinct Chl-binding properties of the WSCP archetypes suggest that the non-Chl-binding subclass evolved from a Chl-binding ancestor that most likely lost its Chl-binding capacity upon localization in the plant tissues with low Chl content. This dual evolutionary trajectory is consistent with WSCPs association with the Kunitz-type protease inhibitors superfamily, and indications of their inhibitory activity in response to various forms of stress in plants. These findings suggest new directions for exploring the physiological roles of WSCPs and the correlation, if any, between Chl-binding and protease inhibition functionality.

Efficient Simulation of Finite-Temperature Open Quantum Systems

Chain-mapping techniques in combination with the time-dependent density matrix renormalization group are a powerful tool for the simulation of open-system quantum dynamics. For finite-temperature environments, however, this approach suffers from an unfavorable algorithmic scaling with increasing temperature. We prove that the system dynamics under thermal environments can be nonperturbatively described by temperature-dependent system-environmental couplings with the initial environment state being in its pure vacuum state, instead of a mixed thermal state. As a consequence, as long as the initial system state is pure, the global system-environment state remains pure at all times. The resulting speed-up and relaxed memory requirements of this approach enable the efficient simulation of open quantum systems interacting with highly structured environments in any temperature range, with applications extending from quantum thermodynamics to quantum effects in mesoscopic systems.

How Well Does the Hole-Burning Action Spectrum Represent the Site-Distribution Function of the Lowest-Energy State in Photosynthetic Pigment-Protein Complexes?

For the first time, we combined Monte Carlo and nonphotochemical hole burning (NPHB) master equation approaches to allow for ultrahigh-resolution (<0.005 cm^-1, smaller than the typical homogeneous line widths at 5 K) simulations of the NPHB spectra of dimers and trimers of interacting pigments. These simulations reveal significant differences between the zero-phonon hole (ZPH) action spectrum and the site-distribution function (SDF) of the lowest-energy state. The NPHB of the lowest-energy pigment, following the excitation energy transfer (EET) from the higher-energy pigments which are excited directly, results in the shifts of all excited states. These shifts affect the ZPH action spectra and EET times derived from the widths of the spectral holes burned in the donor-dominated regions. The effect is present for a broad variety of realistic antihole functions, and it is maximal at relatively low values of interpigment coupling (V ≤ 5 cm^-1) where the use of the Förster approximation is justified. These findings need to be considered in interpreting various optical spectra of photosynthetic pigment-protein complexes for which SDFs (describing the inhomogeneous broadening) are often obtained directly from the ZPH action spectra. Water-soluble chlorophyll-binding protein (WSCP) was considered as an example.

Hole-Burning Spectroscopy on Excitonically Coupled Pigments in Proteins: Theory Meets Experiment

A theory for the calculation of resonant and nonresonant hole-burning (HB) spectra of pigment–protein complexes is presented and applied to the water-soluble chlorophyll-binding protein (WSCP) from cauliflower. The theory is based on a non-Markovian line shape theory (Renger and MarcusJ. Chem. Phys.2002, 116, 9997) and includes exciton delocalization, vibrational sidebands, and lifetime broadening. An earlier approach by Reppert (J. Phys. Chem. Lett.2011, 2, 2716) is found to describe nonresonant HB spectra only. Here we present a theory that can be used for a quantitative description of HB data for both nonresonant and resonant burning conditions. We find that it is important to take into account the excess energy of the excitation in the HB process. Whereas excitation of the zero-phonon transition of the lowest exciton state, that is, resonant burning allows the protein to access only its conformational substates in the neighborhood of the preburn state, any higher excitation gives the protein full access to all conformations present in the original inhomogeneous ensemble. Application of the theory to recombinant WSCP from cauliflower, reconstituted with chlorophyll a or chlorophyll b, gives excellent agreement with experimental data by Pieper et al. (J. Phys. Chem. B2011, 115, 405321417356) and allows us to obtain an upper bound of the lifetime of the upper exciton state directly from the HB experiments in agreement with lifetimes measured recently in time domain 2D experiments by Alster et al. (J. Phys. Chem. B2014, 118, 352424627983).

Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules

Quantum superposition of molecular electronic states is very fragile because of thermal energy fluctuations and the static conformational disorder induced by the intimate surrounding of constituent molecules of the system. However, the nature of the long-lived quantum beats, observed in time-resolved spectra of molecular aggregates at physiological conditions, is still being debated. We present our study of the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer. We show that depending on the amount of inhomogeneous broadening, the excitonically coupled molecular system can establish long-lived electronic coherences, caused by a disordered subensemble, for which the dephasing due to static energy disorder becomes significantly reduced. On the basis of these considerations, we present explanations for why the electronic or vibrational coherences were or were not observed in a range of recent experiments.

Water-soluble chlorophyll-binding proteins from Arabidopsis thaliana and Raphanus sativus target the endoplasmic reticulum body

Background

Non-photosynthetic chlorophyll (Chl) proteins called water-soluble Chl-binding proteins are distributed in Brassicaceae plants. Brassica oleracea WSCP (BoWSCP) and Lepidium virginicum WSCP (LvWSCP) are highly expressed in leaves and stems, while Arabidopsis thaliana WSCP (AtWSCP) and Raphanus sativus WSCP (RshWSCP) are highly transcribed in floral organs. BoWSCP and LvWSCP exist in the endoplasmic reticulum (ER) body. However, the subcellular localization of AtWSCP and RshWSCP is still unclear. To determine the subcellular localization of these WSCPs, we constructed transgenic plants expressing Venus-fused AtWSCP or RshWSCP.

Results

Open reading frames corresponding to full-length AtWSCP and RshWSCP were cloned and ligated between the cauliflower mosaic virus 35S promoter and Venus, a gene encoding a yellow fluorescent protein. We introduced the constructs into A. thaliana by the floral dip method. We succeeded in constructing a number of transformants expressing Venus-fused chimeric AtWSCP (AtWSCP::Venus) or RshWSCP (RshWSCP::Venus). We detected fluorescence derived from the chimeric proteins using a fluorescence microscope system. In cotyledons, fluorescence derived from AtWSCP::Venus and RshWSCP::Venus was detected in spindle structures. The spindle structures altered their shape to a globular form under blue light excitation. In true leaves, the number of spindle structures was drastically reduced. These observations indicate that the spindle structure was the ER body.

Conclusions

AtWSCP and RshWSCP have the potential for ER body targeting like BoWSCP and LvWSCP.