Effect of structural modifications on the spectroscopic properties and dynamics of the excited states of peridinin

The spectroscopic properties and dynamics of the lowest excited singlet states of peridinin and two derivatives have been studied by steady-state absorption and fast-transient optical spectroscopic techniques. One derivative denoted PerOlEs, possesses a double bond and a methyl ester group instead of the r-ylidenebutenolide of peridinin. Another derivative denoted PerAcEs, is the biosynthetic precursor of peridinin and possesses a triple bond and a methyl ester group corresponding to the r-ylidenbutenolide function. Ultrafast time-resolved spectroscopic experiments in the visible and near-infrared regions were performed on the molecules and reveal the energies and regarding the structural features and interactions responsible for the unusual solvent-induced changes in the steady-state and transient absorption spectra and dynamics of dynamics of the excited electronic states. The data also provide information peridinin.     

Ultrafast excited state proton transfer dynamics of 1,2-dihydroquinolines in methanol solution.

Femtosecond and picosecond dynamics of 2,2,4,6-tetramethyl-1,2-dihydroquinoline (1) and 1,2,2,4,6-pentamethyl-1,2-dihydroquinoline (2) were studied in MeOH, MeOD, and Pr(i)OH to probe the early events of the photoinduced proton transfer (PT) between 1,2-dihydroquinolines (DHQ) and a solvent. From studies in the two solvents MeOH and Pr(i)OH and by examining the effect of deuterium replacement of proton, it has been established that PT takes 150-200 fs in MeOH, but does not occur in Pr(i)OH. The formation of PT products in the ground state proceeds concurrently to the relaxation of the higher vibrational excited singlet state to the thermally equilibrated state S(1) of DHQ. The absorption spectrum of the S(1) state was registered, and the time constant of its decay in MeOH (ca. 1 ns) agrees well with the lifetime of fluorescence measured recently by single photon counting.     

Chirality of peridinin and dinoxanthin

Details are reported for the configurational assignment of peridinin as 3S, 5R, 6R, 3′S, 5′R, 6′S including ozonolytic degradation of its p-bromobenzoate to derivatives of known chirality obtained from fucoxanthin and violaxanthin. Details regarding derivatization and CD correlations in favour of the same chirality for dinoxanthin = neoxanthin 3-acetate are given.     

Protonation of excited state pyrene-1-carboxylate by phosphate and organic acids in aqueous solution studied by fluorescence spectroscopy

Pyrene-1-carboxylic acid has a pK of 4.0 in the ground state and 8.1 in the singlet electronic excited state. In the pH range of physiological interest (pH approximately 5-8), the ground state compound is largely ionized as pyrene-1-carboxylate, but protonation of the excited state molecule occurs when a proton donor reacts with the carboxylate during the excited state lifetime of the fluorophore. Both forms of the pyrene derivatives are fluorescent, and in this work the protonation reaction was measured by monitoring steady-state and time-resolved fluorescence. The rate of protonation of pyrene-COO(-) by acetic, chloroacetic, lactic, and cacodylic acids is a function of DeltapK, as predicted by Marcus theory. The rate of proton transfer from these acids saturates at high concentration, as expected for the existence of an encounter complex. Trihydrogen-phosphate is a much better proton donor than dihydrogen- and monohydrogen-phosphate, as can be seen by the pH dependence. The proton-donating ability of phosphate does not saturate at high concentrations, but increases with increasing phosphate concentration. We suggest that enhanced rate of proton transfer at high phosphate concentrations may be due to the dual proton donating and accepting nature of phosphate, in analogy to the Grotthuss mechanism for proton transfer in water. It is suggested that in molecular structures containing multiple phosphates, such as membrane surfaces and DNA, proton transfer rates will be enhanced by this mechanism.     

Multidimensional spectroscopy of beta-carotene: vibrational cooling in the excited state

Pump-degenerate four wave mixing (Pump-DFWM) is used for investigating the vibrational dynamics in the excited state of beta-carotene in solution. In this 2D technique, an initial pump pulse promotes the system to the excited state, which is then probed by the succeeding DFWM sequence. We focus particularly on the internal conversion between the S(2) and S(1) state with high temporal and spectral resolution. The frequency shift of the excited state vibrations is measured and is explained as mode-specific vibrational cooling. Our results suggest an internal conversion in a time range between 260 and 500 fs without any intermediate states.     

Convergence to the equilibrium state in the Volterra-Lotka diffusion equations

Summary We introduce a diffusion term in the Volterra-Lotka model for two interacting species. For certain simple boundary conditions there exists a Lyapunov functional which allows to investigate the asymptotic behavior. Either the solution converges to equilibrium or sustained oscillations occur.     

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 alpha- and beta-protons of the peridinin conjugated chain. Assignments of beta-protons belonging to two different methyl groups, with aiso=7.0 MHz and aiso=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 pi-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.     

Migration of the plastid genome to the nucleus in a peridinin dinoflagellate

Dinoflagellate algae are important primary producers and of significant ecological and economic impact because of their ability to form "red tides". They are also models for evolutionary research because of an unparalleled ability to capture photosynthetic organelles (plastids) through endosymbiosis. The nature and extent of the plastid genome in the dominant perdinin-containing dinoflagellates remain, however, two of the most intriguing issues in plastid evolution. The plastid genome in these taxa is reduced to single-gene minicircles encoding an incomplete (until now 15) set of plastid proteins. The location of the remaining photosynthetic genes is unknown. We generated a data set of 6,480 unique expressed sequence tags (ESTs) from the toxic dinoflagellate Alexandrium tamarense (for details, see the Experimental Procedures in the Supplemental Data) to find the missing plastid genes and to understand the impact of endosymbiosis on genome evolution. Here we identify 48 of the non-minicircle-encoded photosynthetic genes in the nuclear genome of A. tamarense, accounting for the majority of the photosystem. Fifteen genes that are always found on the plastid genome of other algae and plants have been transferred to the nucleus in A. tamarense. The plastid-targeted genes have red and green algal origins. These results highlight the unique position of dinoflagellates as the champions of plastid gene transfer to the nucleus among photosynthetic eukaryotes.     

The open/closed conformational equilibrium of aspartate aminotransferase. Studies in the crystalline state and with a fluorescent probe in solution

Aspartate aminotransferase undergoes major shifts in the conformational equilibrium of the protein matrix during transamination. The present study defines the two conformational states of the enzyme by crystallographic analysis, examines the conditions under which the enzyme crystallizes in each of these conformations, and correlates these conditions with the conformational behaviour of the enzyme in solution, as monitored by a fluorescent reporter group. Cocrystallization of chicken mitochondrial aspartate aminotransferase with inhibitors and covalent coenzymesubstrate adducts yields three different crystal forms. Unliganded enzyme forms triclinic crystals of the open conformation, the structure of which has been solved (space group P1) [Ford, G. C., Eichele, G. & Jansonius, J. N. (1980) Proc. Natl Acad. Sci. USA 77, 2559-2563; Kirsch, J. F., Eichele, G., Ford, G. C., Vincent, M. G., Jansonius, J. N., Gehring, H. & Christen, P. (1984) J. Mol. Biol. 174, 487-525]. Complexes of the enzyme with dicarboxylate ligands form monoclinic or orthorhombic crystals of the closed conformation. The results of structure determinations of the latter two crystal forms at 0.44 nm resolution are described here. In the closed conformation, the small domain has undergone a rigid-body rotation of 12-14 which closes the active-site pocket. Shifts in the conformational equilibrium of aspartate aminotransferase in solution, as induced by substrates, substrate analogues and specific dicarboxylic inhibitors, can be monitored by changes in the relative fluoresence yield of the enzyme labelled at Cys166 with monobromotrimethylammoniobimane. The pyridoxal and pyridoxamine forms of the labelled enzyme show the same fluorescence properties, whereas in the apoenzyme the fluorescence intensity is reduced by 30%. All active-site ligands, if added to the labelled pyridoxal enzyme at saturating concentrations, cause a decrease in the fluorescence intensity by 40-70% and a blue shift of maximally 5 nm. Comparison of the fluorescence properties of the enzyme in various functional states with the crystallographic data shows that both techniques probe the same conformational equilibrium. The conformational change that closes the active site seems to be ligand-induced in the reaction of the pyridoxal form of the enzyme and syncatalytic in the reverse reaction with the pyridoxamine enzyme.     

High resolution spectroscopy of the lowest excited state in Re tetra-carbonyl complexes

The luminescence and absorption properties of [Re(bpy)(CO)₄](PF₆) and [Re(phen)(CO)₄](PF₆) are consistent with representation of the lowest excited states as nominally ³LC with an admixture of ¹CT character. Using high resolution spectroscopic techniques at cryogenic temperatures, such as luminescence line narrowing spectroscopy or spectroscopy in single crystals, the vibrational sideband information which is normally lost in the ‘natural’ solution environment can be observed in the luminescence and absorption spectra. Mixing between the ³LC and ¹CT excitation (3%) has previously been reported in [Re(bpy)(CO)₄](PF₆), resulting in metal-ligand sidebands at 184 and 198 cm⁻¹ in the absorption spectrum and a short luminescence lifetime (33.0 μs). In the luminescence spectra (line narrowed) the metal-ligand sidebands are observed at 194 cm⁻¹. Weak mixing ( 1%) of the ¹CT excitation (32 100 cm⁻¹) with the ³LC excitation (22 100 cm⁻¹) in [Re(phen)(CO)₄](PF₆) gives rise to the observation of metal-ligand vibrational sidebands in the luminescence spectrum (204 cm⁻¹) and a luminescence lifetime of τ= 295±5 μs at 20 K. A spin-orbit mixing matrix element of ³LC|H_so|¹CT for [Re(phen)(CO)₄](PF₆) of 65 cm⁻¹ is calculated, compared to 261 cm⁻¹ in [Re(bpy)(CO)₄](PF₆).     

Multidimensional spectroscopy of β-carotene: Vibrational cooling in the excited state

Pump-degenerate four wave mixing (Pump-DFWM) is used for investigating the vibrational dynamics in the excited state of β-carotene in solution. In this 2D technique, an initial pump pulse promotes the system to the excited state, which is then probed by the succeeding DFWM sequence. We focus particularly on the internal conversion between the S₂ and S₁ state with high temporal and spectral resolution. The frequency shift of the excited state vibrations is measured and is explained as mode-specific vibrational cooling. Our results suggest an internal conversion in a time range between 260 and 500 fs without any intermediate states.     

Genome fragmentation is not confined to the peridinin plastid in dinoflagellates

When plastids are transferred between eukaryote lineages through series of endosymbiosis, their environment changes dramatically. Comparison of dinoflagellate plastids that originated from different algal groups has revealed convergent evolution, suggesting that the host environment mainly influences the evolution of the newly acquired organelle. Recently the genome from the anomalously pigmented dinoflagellate Karlodinium veneficum plastid was uncovered as a conventional chromosome. To determine if this haptophyte-derived plastid contains additional chromosomal fragments that resemble the mini-circles of the peridin-containing plastids, we have investigated its genome by in-depth sequencing using 454 pyrosequencing technology, PCR and clone library analysis. Sequence analyses show several genes with significantly higher copy numbers than present in the chromosome. These genes are most likely extrachromosomal fragments, and the ones with highest copy numbers include genes encoding the chaperone DnaK(Hsp70), the rubisco large subunit (rbcL), and two tRNAs (trnE and trnM). In addition, some photosystem genes such as psaB, psaA, psbB and psbD are overrepresented. Most of the dnaK and rbcL sequences are found as shortened or fragmented gene sequences, typically missing the 3'-terminal portion. Both dnaK and rbcL are associated with a common sequence element consisting of about 120 bp of highly conserved AT-rich sequence followed by a trnE gene, possibly serving as a control region. Decatenation assays and Southern blot analysis indicate that the extrachromosomal plastid sequences do not have the same organization or lengths as the minicircles of the peridinin dinoflagellates. The fragmentation of the haptophyte-derived plastid genome K. veneficum suggests that it is likely a sign of a host-driven process shaping the plastid genomes of dinoflagellates.     

Evidence of excited state absorption in PS II membrane fragments

Utilizing a two-beam technique in the frequency domain, the pumped absorption of PS II membrane fragments from spinach and of acetonic chlorophyll-a solutions was measured at room temperature. In a very narrow wavelength region (0.2 nm around the pump pulse wavelength) the relative test beam transmission exhibited either a decrease or an increase, respectively, dependent on the intensity of a strong pump beam. In contrast, the transmission changes of chl-a solutions were not affected by the wavelength mistuning between pump and test beam. The data obtained for PS II membrane fragments were interpreted in terms of excited state absorption of pigment-protein clusters within the light-harvesting complex of PS II. The interpretation of the small absorption band as a homogeneously broadened line led to a transversal relaxation time for chlorophyll in vivo of about 1 ps.Abbreviations PS I photosystem I of green plants - PS II photosystem II of green plants - P700 primary donor of PS I - P680 primary donor of PS II     

Characterization of the indole triplet excited state in proteins utilizing laser flash photolysis

The triplet-triplet absorption spectrum of the sole indole side chain of human serum albumin and its decay kinetics were previously characterized, at room temperature, by using a conventional flash photolysis method [(1978) Proc. Natl. Acad. Sci. USA 75, 1172-1175]. Exploitation of this potentially useful long lived reporter group in protein studies was limited by the excessively large sample size required by that apparatus. The 265 nm laser flash instrument used in the present work avoids this problem at the price of a loss in photo-selectivity. We report that the latter concern can be mitigated. Melittin was studied first because this polypeptide contains a single aromatic residue (W-19), and because its monomeric and tetrameric forms are good models for solvent exposed and buried indole side chains of proteins. For both forms, the indole triplet and neutral radical absorption spectra could be readily time resolved and identified on the basis of shape and differential dioxygen sensitivity. The single tryptophan containing protein human serum albumin was studied next because it contains a large number of other 265 nm absorbing moieties whose transient spectra might complicate the detection of the indole triplet. These transients were shown to not interfere significantly in the wavelength region 450 nm to 600 nm, and, in contrast to the indole triplet, they were relatively dioxygen insensitive. Thus, a facile means is available by which the indole triplet of proteins may be characterized. Subsequently the question of whether this species could be detected in the presence of nuclei acid components was investigated by flashing the phage fd. The putative nucleic acid transients were shown not to interfere and the absorbance of the indole triplet was readily time resolved. The spectral assignment was persuasively confirmed by showing that the indole triplet absorption and phosphorescence emission spectra decay with the same lifetime. The present work thus provides additional evidence for the general applicability of the indole triplet excited state as a long lived intrinsic protein reporter group.     

DT diaphorase exists as a dimer-tetramer equilibrium in solution

The quaternary behaviour of DT diaphorase in solution has been investigated by hydrodynamics under a range of conditions. At neutral pH DT diaphorase is shown to exist as a tightly-associated homodimer in a dimer-tetramer equilibrium. Concentrations of the chaotropic agent potassium thiocyanate (KSCN) of greater than 200 mm result in irreversible loss of the FAD cofactor and denaturation of the homodimer though this agent appears to be ineffective in disrupting intermolecular association. These data conform to a model in which under extreme dissociation conditions, the folded dimer is in equilibrium with the unfolded monomer and are consistent with evidence from the X-ray structure and proposed catalytic mechanism where both monomers are catalytically interdependent. Received: 1 November 1996 / Accepted: 30 December 1996     

Transient state isoelectric focusing. Resolving power and zone resolution

A digital on-line data acquisition system has been used in conjunction with a scanning isoelectric focusing assembly for the direct calculation of the resolving power and zone resolution in transient state isoelectric focusing experiments. The application of the method to the evaluation of these two parameters in relation to (a) the applied electric field strength during focusing, and (b) to the diffusion in the absence of current is presented. A linear relationship between $\text{1}\text{σ}{}^2$ (where σ is the standard deviation of the concentration distribution of a focused zone) and the applied voltage was demonstrated. The resolving power and resolution were generally improved with increased electric field strength.