Peridinin Molecules Research Articles

Classical Force Fields Tailored for QM Applications: Is It Really a Feasible Strategy?

Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the molecular systems are seldom parametrized to reproduce electronic processes, such as electronic excitations, which are instead very sensitive to the underlining description of the molecular structure. Here, we analyze the challenging case of the peridinin molecule, a natural apocarotenoid responsible for the light-harvesting process in the PCP antenna protein of dinoflagellates. Ground-state structural and vibrational properties, as well as electronic transitions of the pigment are studied by means of quantum-mechanical static and dynamic calculations. Thereafter, classical molecular dynamics simulations are performed with a number of different force-fields, ranging from a popular, general purpose one to refined potentials of increasing level of complexity. From the comparison of classical results with their quantum mechanical counterparts, it appears that, while very poor results are obtained from standard transferrable force-fields, specifically tuned potentials are able to correctly characterize most of the structural and vibrational features of the pigment. Nonetheless, only an advanced parametrization technique is able to give a semiquantitative description of the coupling between vibrations and electronic excitations, thus suggesting that the use of classical MD in combination of QM calculations for the study of photoinduced processes, albeit possible, should be considered with care.

Distance measurements in peridinin-chlorophyll a-protein by light-induced PELDOR spectroscopy. Analysis of triplet state localization

Triplet-triplet energy transfer from chlorophylls to carotenoids is the mechanism underlying the photoprotective role played by carotenoids in many light harvesting complexes, during photosynthesis. The peridinin–chlorophyll-a protein (PCP) is a water-soluble light harvesting protein of the dinoflagellate Amphidinium carterae, employing peridinin as the main carotenoid to fulfil this function.The dipolar coupling of the triplet state of peridinin, populated under light excitation in isolated PCP, to the MTSSL nitroxide, introduced in the protein by site-directed mutagenesis followed by spin labeling, has been measured by Pulse ELectron-electron DOuble Resonance (PELDOR) spectroscopy. The triplet-nitroxide distance derived by this kind of experiments, performed for the first time in a protein system, allowed the assignment of the triplet state to a specific peridinin molecule belonging to the pigment cluster. The analysis strongly suggests that this peridinin is the one in close contact with the water ligand to the chlorophyll a, thus supporting previous evidences based on ENDOR and time resolved-EPR.

Excitation Energy Transfer in the Peridinin-Chlorophyll a-Protein Complex Modeled Using Configuration Interaction

We modeled excitation energy transfer (EET) in the peridinin-chlorophyll a-protein (PCP) complex of dinoflagellate Amphidinium carterae to determine which pathways contribute dominantly to the high efficiency of this process. We used complete active space configuration interaction (CAS-CI) to calculate electronic structure properties of the peridinin (PID) and chlorophyll a (CLA) pigments in PCP and the transition density cube (TDC) method to calculate Coulombic couplings between energy transfer donors and acceptors. Our calculations show that the S1 → Qy EET pathway from peridinin to chlorophyll a is the dominant energy transfer pathway in PCP, with two sets of interactions-between PID612 and CLA601 and between PID622 and CLA602-contributing most strongly. EET lifetimes for these two interactions were calculated to be 2.66 and 2.90, with quantum efficiencies of 85.75 and 84.65%, respectively. The calculated Coulombic couplings for EET between two peridinin molecules in the strongly allowed S2 excited states are extremely large and suggest excitonic coupling between pairs of peridinin S2 states. This methodology is also broadly applicable to the study of EET in other photosynthetic complexes and/or organic photovoltaics, where both single and double excitations are present and donor and acceptor molecules are tightly packed.

The electronic structure of the lutein triplet state in plant light-harvesting complex II

Carotenoid molecules are essential for the life of photosynthetic organisms in that they protect the cell from the photo-oxidative damage induced by light-stress conditions. One of the photo-protective mechanisms involves triplet-triplet energy transfer from the chlorophyll molecules to the carotenoids: a process that is strongly dependent on the electronic properties of the triplet states involved. Here, we obtain a clear description of the triplet state of lutein in LHCII from higher plants for the first time by density functional theory (DFT) calculations. DFT predictions have been validated by comparison with hyperfine couplings obtained with pulsed-ENDOR spectroscopy. Knowledge of the spin density distribution, the frontier orbitals and orbital excitations forms a basis for discussing the requirements for an efficient triplet-triplet energy transfer. The results obtained for the lutein in LHCII are compared with those of the highly-substituted carotenoid peridinin in PCP from Amphidinium carterae [Di Valentin et al., Biochim. Biophys. Acta, 2008, 1777, 295-307]. The presence of substituents in the peridinin molecule does not alter significantly the triplet state electronic structure compared to lutein. Despite the unusual spectroscopic behaviour of the peridinin excited singlet state, lutein and peridinin have similar triplet state properties. In both molecules the unpaired spins are delocalized uniformly over the whole π-conjugated system in an alternating even-odd pattern.

Identification of a single peridinin sensing Chl- a excitation in reconstituted PCP by crystallography and spectroscopy

The peridinin-chlorophyll a-protein (PCP) of dinoflagellates is unique among the large variety of natural photosynthetic light-harvesting systems. In contrast to other chlorophyll protein complexes, the soluble PCP is located in the thylakoid lumen, and the carotenoid pigments outnumber the chlorophylls. The structure of the PCP complex consists of two symmetric domains, each with a central chlorophyll a (Chl-a) surrounded by four peridinin molecules. The protein provides distinctive surroundings for the pigment molecules, and in PCP, the specific environment around each peridinin results in overlapping spectral line shapes, suggestive of different functions within the protein. One particular Per, Per-614, is hypothesized to show the strongest electronic interaction with the central Chl-a. We have performed an in vitro reconstitution of pigments into recombinant PCP apo-protein (RFPCP) and into a mutated protein with an altered environment near Per-614. Steady-state and transient optical spectroscopic experiments comparing the RFPCP complex with the reconstituted mutant protein identify specific amino acid-induced spectral shifts. The spectroscopic assignments are reinforced by a determination of the structures of both RFPCP and the mutant by x-ray crystallography to a resolution better than 1.5 A. RFPCP and mutated RFPCP are unique in representing crystal structures of in vitro reconstituted light-harvesting pigment-protein complexes.

Inter-pigment interactions in the peridinin chlorophyll protein studied by global and target analysis of time resolved absorption spectra

Inter-pigment interactions define the functioning of light-harvesting protein complexes. To describe the particularly complex molecular dynamics and interactions of peridinin and chlorophyll in the peridinin chlorophyll protein of Amphidinium carterae, we applied global and target analysis to a series of ultrafast transient absorption experiments. We have created and validated a model that consistently describes and characterizes the interactions and evolution of excited and ground-state populations after excitation in all different experiments. The series of energy transfer steps that follow excitation are described by our model of cascading populations and numerous rate constants that correspond to intra-molecular thermal relaxation, fast and slow peridinin-to-chlorophyll energy transfer steps, and chlorophyll excited-state annihilation. By analyzing the spectral response of ground-state peridinins to excited chlorophylls we have identified which specific peridinin molecule is most closely coupled to the chlorophylls. No evidence was found that the intra-molecular charge transfer (ICT) state of peridinin, identified in studies of peridinin in solution, is a separate entity in the protein. The peridinin that exhibited slow peridinin-to-chlorophyll energy transfer was characterized by a difference spectrum free from ICT features, consistent with the importance of coupled ICT and S 1 states for energy transfer.

Spectroscopic properties of the peridinins involved in chlorophyll triplet quenching in high-salt peridinin–chlorophyll a-protein from Amphidinium carterae as revealed by optically detected magnetic resonance, pulse EPR and pulse ENDOR spectroscopies

The photoexcited triplet state of the carotenoid peridinin in the high-salt peridinin–chlorophyll a-protein (HSPCP) of the dinoflagellate Amphidinium carterae was investigated by ODMR (optically detected magnetic resonance), pulse EPR and pulse ENDOR spectroscopies. The properties of peridinins associated to the triplet state formation in HSPCP were compared to those of peridinins involved in triplet state population in the main-form peridinin–chlorophyll protein (MFPCP), previously reported. In HSPCP no signals due to the presence of chlorophyll triplet state have been detected, during either steady-state illumination or laser-pulse excitation, meaning that peridinins play the photo-protective role with 100% efficiency as in MFPCP. The general spectroscopic features of the peridinin triplet state are very similar in the two complexes and allow drawing the conclusion that the triplet formation pathway and the triplet localization in one specific peridinin in each subcluster are the same in HSPCP and MFPCP. However some significant differences also emerged from the analysis of the spectra. Zero field splitting parameters of the peridinin triplet states are slightly smaller in HSPCP and small changes are also observed for the hyperfine splittings measured by pulse ENDOR and assigned to the β-protons belonging to one of the two methyl groups present in the conjugated chain, (aiso=10.3 MHz in HSPCP vs aiso=10.6 MHz in MFPCP). The differences are explained in terms of local distortion of the tails of the conjugated chains of the peridinin molecules, in agreement with the conformational data resulting from the X-ray structures of the two complexes.

Pulse ENDOR and density functional theory on the peridinin triplet state involved in the photo-protective mechanism in the peridinin–chlorophyll a–protein from Amphidinium carterae

The photoexcited triplet state of the carotenoid peridinin in the Peridinin–chlorophyll a–protein of the dinoflagellate Amphidinium carterae has been investigated by pulse EPR and pulse ENDOR spectroscopies at variable temperatures. This is the first time that the ENDOR spectra of a carotenoid triplet in a naturally occurring light-harvesting complex, populated by energy transfer from the chlorophyll a triplet state, have been reported. From the electron spin echo experiments we have obtained the information on the electron spin polarization dynamics and from Mims ENDOR experiments we have derived the triplet state hyperfine couplings of the α- and β-protons of the peridinin conjugated chain. Assignments of β-protons belonging to two different methyl groups, with a iso = 7.0 MHz and a iso = 10.6 MHz respectively, have been made by comparison with the values predicted from density functional theory. Calculations provide a complete picture of the triplet spin density on the peridinin molecule, showing that the triplet spins are delocalized over the whole π-conjugated system with an alternate pattern, which is lost in the central region of the polyene chain. The ENDOR investigation strongly supports the hypothesis of localization of the triplet state on one peridinin in each subcluster of the PCP complex, as proposed in [Di Valentin et al. Biochim. Biophys. Acta 1777 (2008) 186–195]. High spin density has been found specifically at the carbon atom at position 12 (see Fig. 1B), which for the peridinin involved in the photo-protective mechanism is in close contact with the water ligand to the chlorophyll a pigment. We suggest that this ligated water molecule, placed at the interface between the chlorophyll–peridinin pair, is functioning as a bridge in the triplet–triplet energy transfer between the two pigments.

Transient Absorption Study of Peridinin and Peridinin−Chlorophyll a−Protein after Two-Photon Excitation

Two-photon excited pump−probe spectroscopy was carried out on the peridinin−chlorophyll a−protein complex (PCP) and on the peridinin molecule in methanol solution. Our data are consistent with earlier two-photon fluorescence excitation spectra1,2 and lead to the conclusion that, for peridinin in methanol solution, a separate two-photon-allowed transition exists just to the red of the strongly allowed S0 − S2(Bu+) band. In the PCP complex, two-photon excitation at 1150 nm can also be interpreted as preparing a new state. In both cases, the new state is most likely the S1(Ag-) state. It is not yet possible to conclude experimentally whether peridinin possesses a single low lying state with solvent dependent properties or two distinct states, the Ag- and the charge transfer states.

Model for Triplet−Triplet Energy Transfer in Natural Clusters of Peridinin Molecules Contained in Dinoflagellate's Outer Antenna Proteins

Triplet−triplet energy transfer among peridinin molecules in peridinin−chlorophyll−protein (PCP) complexes from two different dinoflagellate species is quantitatively evaluated by the use of the optically detected magnetic resonance technique supplemented by triplet-state decay rate measurements. The two complexes are related by a dimer−monomer relationship in the sense that the four peridinins−one chlorophyll cluster of the Heterocapsa pygmeae PCP (H−PCP) is a copy of the two clusters contained in the larger protein Amphidinium carterae PCP (A−PCP), which are related by a local 2-fold symmetry axis. The system is conveniently discussed as a multistate Frenkel exciton system performing stochastic jumps from one exciton state to another. The rate of triplet−triplet energy exchange among peridinin molecules is obtained through the simulation of the spectral line shapes of optically detected magnetic resonance in zero field. Measurements were collected in a range of temperatures between 2 and 40 K and supplemented by the determination of the decay rate of the triplet to ground state in the same temperature range. The latter is of the order of 0.005 MHz and is relevant in determining the line shapes, especially at the lowest temperatures where the exchange rates are low. Exchange rates within the four-member peridinin cluster of H−PCP exactly match those within each of the two clusters of A−PCP and span a range from 0 to 20 MHz for the uphill rate and from 10 to 300 MHz for the downhill rate, corresponding to an energy difference of 41 cm-1. The intercluster exchange rate in A−PCP goes from 0 to 12 MHz uphill and from 0.05 to 30 MHz downhill, with an energy difference of only 12.5 cm-1. The kinetics conform to phonon-stimulated radiationless transition theory, and coupling parameters and reorganization energies are evaluated and discussed.

Circular dichroism (CD) study of peridinin[ndash ]chlorophyll a protein (PCP) complexes from marine dinoflagellate algae The tetramer approach

The absorption and circular dichroism spectra of PCP (peridinin–chlorophyll a protein) light-harvesting complexes from Glenodiniumsp. and Gonyaulaxpolyedra are studied in terms of vibronic coupling theory. Analysis based on a tetramer model allows the determination of the relative positions of peridinin molecules in the PCP complexes studied. The tetrameric arrangementof four peridinins around the chlorophyll a is suggested to favour the efficient transfer of energy from the peridinin to thechlorophyll. The simple arguments presented suggest that the energy transfer from peridin to chlorophyll might occur from theΨ1± states of the peridinin tetramer to the Bx, and By states of the chlorophyll a.

Carotenoid interactions in peridinin chlorophyll a proteins from dinoflagellates. Evidence for optical excitions and triplet migration

Optical and magnetic resonance spectroscopy has been used to investigate two peridinin–chlorophyll a–protein (PCP) complexes constituting the peripheral antenna of the photosystem of two dinoflagellate species. One protein contains a cluster of four peridinins and one chlorophyll molecule, the other contains two such clusters in a ‘quasi’ dimer of the former. Evidence of intra-cluster excitonic interactions between peridinins is provided by low-temperature absorption and circular dichroism spectra. Peridinin triplets are detected in zero-field magnetic resonance spectroscopy by both optical emission and absorption. Interaction among peridinin molecules causes a fast intra-cluster and a slow inter-cluster triplet migration. The origin of the interactions is discussed by correlating optical and magnetic spectroscopic data.

A novel peridinin—chlorophyll a protein (PCP) from the marine dinoflagellate Alexandrium cohorticula: A high pigment content and plural spectral forms of peridinin and chlorophyll a

A new type of peridinin—chlorophyll a protein (PCP) was isolated from the marine dinoflagellate Alexandrium cohorticula. Unlike previous studies, PCP was obtained as a single component in the presence of a protease inhibitor. The monomer had a molecular mass of 37 kDa with 12 peridinin molecules associated with 2 chl a molecules. This pigment content was much higher than that reported previously. We observed a partial amino acid sequence of the N-terminus that is novel among photosynthetic pigment—protein complexes. Magnetic circular dichroism clearly indicated that chl a in PCP had monomeric features. Multiple spectral components were suggested for both chl a and peridinin. Based on the high pigment content, the optical properties were compared with those for a reported PCP containing 4 chl a and 1 peridinin.

PROTECTION OF CHLOROPHYLL a BY CAROTENOID FROM PHOTODYNAMIC DECOMPOSITION

Abstract— The order of inhibition of the photooxidation of chlorophyll a in ethanol and ethanol‐benzene is as follows: β‐carotene, α‐tocopherol, benzoquinone, DABCO, menadione, cholesterol and KI. The quenching of singlet oxygen by β‐carotene occurs by a collisional quenching mechanism with a diffusion‐controlled rate of 1.7 × 1010M‐1 s‐1. Photodecomposition of Chi a is faster in ethanol‐D2O than in ethanol‐H2O. Photoirradiation (660 nm) of the peridinin‐Chl a‐protein complex, a photosynthetic light‐harvesting pigment isolated from marine dinoflagellates, did not show any photo‐decomposition of its Chi a in H2O or D2O, even after an extended period (12 h) of irradiation. However, the carotenoid, peridinin, in the photosynthetic antenna pigment was photobleached (ca. 10%) during the irradiation. We conclude that the singlet oxygen formed as a result of the Chi photosensitization is immediately quenched by the low‐lying triplet state of four peridinin molecules (per Chl a) bound within the same protein crevice. The carotenoid thus effectively protects Chl a from photodynamic damage, providing a direct proof for the protective role of carotenoids in the photosynthetic pigment complex.

Molecular topology of the photosynthetic light-harvesting pigment complex, peridinin-chlorophyll a-protein, from marine dinoflagellates.

The photosynthetic light-harvesting complex, peridinin-chlorophyll a-protein, was isolated from several marine dinoflagellates including Glenodinium sp. by Sephadex and ion-exchange chromatography. The carotenoid (peridinin)-chlorophyll a ratio in the complex is estimated to be 4:1. The fluorescence excitation spectrum of the complex indicates that energy absorbed by the carotenoid is transferred to the chlorophyll a molecule with 100% efficiency. Fluorescence lifetime measurements indicate that the energy transfer is much faster than fluorescence emission from chlorophyll a. The four peridinin molecules within the complex appear to form two allowed exciton bands which split the main absorption band of the carotenoid into two circular dichronic bands (with negative ellipticity band at 538 nm and positive band at 463 nm in the case of peridinin-chlorophyl a-protein complex from Glenodinium sp.). The fluorescence polarization of chlorophyll a in the complex at 200 K is about 0.1 in both circular dichroic excitation bands of the carotenoid chromophore. From these circular dichroic and fluorescence polarization data, a possible molecular arrangement of the four peridinin and chlorophyll molecules has been deduced for the complex. The structure of the complex deduced is also consistent with the magnitude of the exciton spliting (ca. greater than 3000 cm-1) at the intermolecular distance in the dimer pair of peridinin (ca. 12 A). This structural feature accounts for the efficient light-harvesting process of dinoflagellates as the exciton interaction lengthens the lifetime of peridinin (radiative) and the complex topology increases the energy transfer probability. The complex is, therefore, a useful molecular model for elucidating the mechanism and efficiency of solar energy conversion in vivo as well as in vitro.