On the influence of pigment-protein interactions on the energy transfer processes in photosynthetic membrane structures. 2. LH2 complex of Rhodobacter sphaeroides

Low-temperature heterogeneous absorption and circular dichroism spectra of the Rb. sphaeroides LH2 complexes are calculated within the framework of the mini-exciton theory and diagonal static random disorder for the pure electronic transitions of the monomeric Bchl molecules. The coupling of Bchl molecules with the surrounding amino acid residues has been shown to change both the exciton distribution between the pigment molecules in each of the exciton states. The value of the delocalization index depends on the excitation wavelength and varies between 2-6 Bchl molecules. The optical transitions occurring at 780-790 and 820 nm have been found to be strongly mixed so that all Bchl molecules of the LH2 complex predetermine absorption in these spectral regions. On the other hand, absorption at 800 and 850 nm is mainly determined by the cycles of 9 and 18 Bchl molecules, respectively. Thus, the light energy absorbed by the B800 molecules at 800 nm is transferred to the B850 molecules by the interlevel exciton relaxation processes due to the population of the heavily mixed 820-nm exciton levels. The width of the heterogeneous absorption band for the cyclic monomeric aggregate has been shown to decrease as compared with the monomeric absorption band by square root(Ndel) time, where Ndel is the mean number of pigments over which the exciton is delocalized within the excited absorption band.     

On the influence of pigment-protein interactions on the energy transfer processes in photosynthetic membrane structures

Low-temperature heterogeneous absorption and circular dichroism spectra of the Prosthecochloris aestuarii FMO complex were calculated within the framework of the mini-exciton theory including both the inhomogeneous distribution of exciton line frequencies and static random disorder of the pure electronic transitions of Bchl molecules. The frequencies of the Qy pure electronic transitions of Bchl molecules immobilized by the FMO complex polypeptides were found by minimization of a functional which links the parameters of the theoretical and experimental optical spectra. The interactions of Bchl molecules with surrounding amino acid residues was shown to change both the exciton delocalization index and exciton distribution between the pigment molecules in each exciton energetic state. As a consequence, the interlevel exciton relaxation processes, being accompanied by essential changes in the exciton distribution between pigment molecules, lead to the energy transfer within the FMO complex. The model spectra calculations within the framework of the static random disorder approach were shown to give unacceptable results.     

Red Chlorophylls in the Exciton Model of Photosystem I

Structural arrangement of pigment molecules of Photosystem I of photosynthetic cyanobacterium Synechococcus elongatus is used for theoretical modeling of the excitation energy spectrum. It is demonstrated that a straightforward application of the exciton theory with the assumption of the same molecular transition energy does not describe the red side of the absorption spectrum. Since the inhomogeneity in the molecular transition energies caused by a dispersive interaction with the molecular surrounding cannot be identified directly from the structural model, the evolutionary search procedure is used for fitting the low temperature absorption and circular dichroism spectra. As a result, one dimer, three trimers and one tetramer of chlorophyll molecules responsible for the red side of the absorption spectrum with their assignment to the spectroscopically established three bands at 708, 714 and 719 nm are determined. All of them are found to be situated not in the very close vicinity of the reaction center but are encircling it almost at the same distance. In order to explain the unusual broadening on the red side of the spectrum the exciton state mixing with the charge transfer (CT) states is considered. It is shown that two effects can be distinguished as caused by mixing of those states: (i) the oscillator strength borrowing by the CT state from the exciton transition and (ii) the borrowing of the high density of the CT state by the exciton state. The intermolecular vibrations between two counter-charged molecules determine the high density in the CT state. From the broad red absorption wing it is concluded that the CT state should be the lowest state in the complexes under consideration. Such mixing effect enables resolving the diversity in the molecular transition energies as determined by different theoretical approaches.     

Exciton dynamics in circular aggregates: application to antenna of photosynthetic purple bacteria.

A theoretical model of exciton dynamics in circular molecular aggregates of light-harvesting bacteriochlorophyll of photosynthetic bacteria is proposed. The spectra and anisotropy of photoinduced absorption changes in the femto- and picosecond time domain are under its scope. The excited state of aggregate was treated due to the standard exciton theory, taking into account a pigment inhomogeneity. Dephasing processes via the exciton-phonon interactions were described by means of the Haken-Strobl equation. It was shown that only two exciton levels are dipole-allowed in the case of homogeneous circular aggregate. The pigment inhomogeneity results in the appearance of several weak transitions to higher exciton levels. It was proposed that the minor band (B896) in an absorption spectrum of the B875 complex as well as the similar minor band in spectra of B800-850 complex correspond to electron transition from the ground to the lowest exciton level, whereas the major band corresponds to transition to the higher exciton level. The proposed model shows the subpicosecond decay of anisotropy at the short-wavelength side of absorption band and a high degree of anisotropy at the long-wavelength side, even at high temperatures.     

Molecular evolution of color vision of zebra finch

We have isolated and sequenced the RH1(Tg), RH2(Tg), SWS2(Tg), and LWS(Tg) opsin cDNAs from zebra finch retinas. Upon binding to 11-cis-retinal, these opsins regenerate the corresponding photosensitive molecules, visual pigments. The absorption spectra of visual pigments have a broad bell shape, with the peak being called lambda(max). Previously, SWS1(Tg) opsin cDNA was isolated from zebra finch retinal RNA, expressed in cultured COS1 cells, reconstituted with 11-cis-retinal, and the lambda(max) of the resulting visual pigment was shown to be 359nm. Here, the lambda(max) values of the RH1(Tg), RH2(Tg), SWS2(Tg), and LWS(Tg) pigments are determined to be 501, 505, 440, and 560nm, respectively. Molecular evolutionary analyses suggest that specific amino acid replacements in the SWS1 and SWS2 pigments, resulting from accelerated evolution, must have been responsible for their functional divergences among the avian pigments.     

Exciton delocalization in the B808-866 antenna of the green bacterium Chloroflexus aurantiacus as revealed by ultrafast pump-probe spectroscopy.

A model of pigment organization in the B808-866 bacteriochlorophyll a antenna of the green photosynthetic bacterium Chloroflexus aurantiacus based on femtosecond pump-probe studies is proposed. The building block of the antenna was assumed to be structurally similar to that of the B800-850 light-harvesting 2 (LH2) antenna of purple bacteria and to have the form of two concentric rings of N strongly coupled BChl866 pigments and of N/2 weakly coupled BChl808 monomers, where N = 24 or 32. We have shown that the Qy transition dipoles of BChl808 and BChl866 molecules form the angles 43 degrees +/- 3 degrees and 8 degrees +/- 4 degrees, respectively, with the plane of the corresponding rings. Using the exciton model, we have obtained a quantitative fit of the pump-probe spectra of the B866 and B808 bands. The anomalously high bleaching value of the B866 band with respect to the B808 monomeric band provided the direct evidence for a high degree of exciton delocalization in the BChl866 ring antenna. The coherence length of the steady-state exciton wave packet corresponds to five or six BChl866 molecules at room temperature.     

Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekko

We have isolated a full-length cDNA encoding a putative ultraviolet (UV)-sensitive visual pigment of the Tokay gecko (Gekko gekko). This clone has 57 and 59% sequence similarities to the gecko RH2 and MWS pigment genes, respectively, but it shows 87% similarity to the UV pigment gene of the American chameleon (Anolis carolinensis). The evolutionary rates of amino acid replacement are significantly higher in the three gecko pigments than in the corresponding chameleon pigments. The accelerated evolutionary rates reflect not only the transition from cones to rods in the retina but also the blue-shift in the absorption spectra of the gecko pigments.     

Phosphorylation of iodopsin, chicken red-sensitive cone visual pigment

The amino acid sequence has been determined for the carboxyl-terminal 41 amino acids of chicken red-sensitive cone pigment, iodopsin. This sequence is distinct from but structurally homologous to that of other visual pigments. It contains a region rich in the hydroxy amino acids serine and threonine. In the related rod cell visual pigment, rhodopsin, such serines and threonines have previously been identified as sites for phosphorylation by rhodopsin kinase. Phosphorylation of photolyzed rhodopsin serves to terminate its ability to function in visual transduction as an activator of G-protein. We have purified and reconstituted both chicken rhodopsin and chicken iodopsin and shown them to be phosphorylated by bovine rhodopsin kinase. Chicken iodopsin has a Km and Vmax similar to but distinguishably different from that for bovine rhodopsin. These results, in conjunction with other data, suggest that visual pigments in cone cells, upon absorption of light, undergo functional processes similar to those of the visual pigments in rod cells.     

Analysis by exciton theory of the optical properties of the Chloroflexus aurantiacus reaction center

The optical properties of the reaction center of the filamentous green bacterium Chloroflexus aurantiacus, that contains three bacteriochlorophyll (BChl) a and three bacteriopheophytin (BPh) a molecules, were analyzed in the near-infrared region with the aid of exciton theory. The coordinates obtained from the X-ray analysis of the reaction center of Rhodopseudomonas viridis (Deisenhofer, J., Epp, O., Miki, K., Huber, R. and Michel, H. (1984) J. Mol. Biol. 180, 385–398) were used for the geometry of the reaction center of C. aurantiacus, with the replacement of one of the ‘accessory’ BChl molecules by BPh. The results were found to be in good agreement with experimental low-temperature absorption spectra, linear and circular dichroism and fluorescence polarization spectra and lead to the following conclusions. The allowed, low-energy exciton transition of the primary electron donor (P-865) is located at 887 nm and carries the dipole strength of approx. two BChl a monomers; the high-energy exciton transition, around 790 nm, is mixed with wave functions of other pigments, which explains its relatively small angle with respect to the 887 nm transition. The optical transition of the accessory BChl a molecule near 812 nm has some contribution of the BChls that constitute P-865. This can account for the experimentally observed reorientation and shift of this transition upon oxidation of P-865. Two of the BPh molecules are located on the same (probably the M) polypeptide subunit and show a clear splitting of absorption bands (11 nm) due to exciton coupling; the single BPh on the opposite branch shows hardly any exciton shift. Similar calculations for reaction centers of purple bacteria that contain four BChl a and two BPh a molecules resulted in a very low dipole strength for the high-energy transition of the primary donor due to antisymmetric mixing with both accessory BChl a wave functions and gave very little splitting of the absorption bands of BPh a. Our results indicate that the arrangement of the chromophores in reaction centers of C. aurantiacus is very similar to that in purple bacteria. The functional L-chains of the reaction centers of purple and filamentous green bacteria consist of pigments of the same type in a probably very similar arrangement.     

Introduction of hydroxyl-bearing amino acids causes bathochromic spectral shifts in rhodopsin. Amino acid substitutions responsible for red-green color pigment spectral tuning.

Comparisons of the deduced amino acid sequences of eight primate photopigment genes led to the proposal that three amino acid substitutions produce the approximately 1,000 cm-1 difference in the absorption maxima of human red and green pigments (Neitz, M., Neitz, J., and Jacobs, G.H. (1991) Science 252, 971-974). We tested this proposal by mutating these three residues in rhodopsin and evaluating the effects on spectral properties. Nonpolar residues normally present in rhodopsin and in the green pigment were substituted by hydroxyl-bearing residues normally present in the red pigment. Two of these substitutions (Phe-261 to Tyr or Ala-269 to Thr) caused significant red shifts in the absorption maxima of the resulting mutant pigments. A third substitution (Ala-164 to Ser) caused only a slight effect. Combinations of substitutions caused additive shifts in absorption maxima. A double mutant (Phe-261 to Tyr/Ala-269 to Thr) displayed an absorption maximum that was red-shifted by 775 cm-1. Wavelength modulation in the visual pigments responsible for red-green color vision is likely to be governed by retinal-protein interactions involving primarily these two amino acid residues. Furthermore, interactions of hydroxyl-bearing amino acids with the chromophore may be a general mechanism of the opsin shift in visual pigments.     

Characterization of a Drosophila melanogaster orthologue of muskelin

Visual systems of vertebrates exhibit a striking level of diversity, reflecting their adaptive responses to various color environments. The photosensitive molecules, visual pigments, can be synthesized in vitro and their absorption spectra can be determined. Comparing the amino acid sequences and absorption spectra of various visual pigments, we can identify amino acid changes that have modified the absorption spectra of visual pigments. These hypotheses can then be tested using the in vitro assay. This approach has been a powerful tool in elucidating not only the molecular bases of color vision, but the processes of adaptive evolution at the molecular level.     

Dichroism and polarized fluorescence of chlorophyll a, chlorophyll c and bacteriochlorophyll a dissolved in liquid crystals

Three photosynthetic pigments were studied: chlorophyll a, chlorophyll c and bacteriochlorcphyll a in nematic liquid crystal matrixes. The polarized absorption and fluorescence spectra as a function of the electric field have been measured. From the polarized components of the absorption A( parallel) and A( perpendicular) of the pigments in liquid crystals two reduced components A(x) and A(y) are calculated (x and y are the direction of the axis which is going through the second, fourth pyrrol rings, and the first, third rings, respectively). From these results the orientation of chlorophylls in liquid crystals and the configuration of the transition moments in the skeleton of the pigment molecules were determined.     

Genetic basis of spectral tuning in the violet-sensitive visual pigment of African clawed frog, Xenopus laevis

Ultraviolet (UV) and violet vision in vertebrates is mediated by UV and violet visual pigments that absorb light maximally (lambdamax) at approximately 360 and 390-440 nm, respectively. So far, a total of 11 amino acid sites only in transmembrane (TM) helices I-III are known to be involved in the functional differentiation of these short wavelength-sensitive type 1 (SWS1) pigments. Here, we have constructed chimeric pigments between the violet pigment of African clawed frog (Xenopus laevis) and its ancestral UV pigment. The results show that not only are the absorption spectra of these pigments modulated strongly by amino acids in TM I-VII, but also, for unknown reasons, the overall effect of amino acid changes in TM IV-VII on the lambdamax-shift is abolished. The spectral tuning of the contemporary frog pigment is explained by amino acid replacements F86M, V91I, T93P, V109A, E113D, L116V, and S118T, in which V91I and V109A are previously unknown, increasing the total number of critical amino acid sites that are involved in the spectral tuning of SWS1 pigments in vertebrates to 13.     

Interactions between purine derivatives: Electronic spectral studies. I. Electronic transitions in caffeine monomer and exciton coupling in caffeine dimer

The concentration dependence of the ultraviolet absorption spectrum of aqueous solutions of caffeine has been studied. Individual species spectra have been derived for the monomer, dimer, and tetramer of caffeine. The emission spectrum of caffeine in aqueous solution and the dichroic spectra in oriented poly(vinyl alcohol) and polyethylene films have been measured. The long-wavelength tail of the absorption spectrum of caffeine in non-polar environment has been found to incorporate at least one carbonyl(π*, n) transition. Dichroic spectral data and molecular orbital calculations have been used to assign transition moment directions to the (π*,π) transitions. The lowest energy (π*,π) transition, responsible for the near-ultraviolet absorption peak in aqueous solution of caffeine, has been used for the study of degenerate exciton interactions in the dimeric species of caffeine. Assuming that the caffeine molecules in the dimer are stacked in parallel planes, theoretical calculations of the ground-state interactions and of the degenerate exciton interactions have been combined with experimental data and a unique model for the dimer of caffeine has been derived. The transfer rate of energy between the molecules in the dimer is of the order of 10¹³_S^?1.     

Near edge X-ray absorption fine structure spectroscopy (NEXAFS) of pigment–protein complexes: Peridinin–chlorophyll a protein (PCP) of Amphidinium carterae

Peridinin–chlorophyll a protein (PCP) is a unique water soluble antenna complex that employs the carotenoid peridinin as the main light-harvesting pigment. In the present study the near edge X-ray absorption fine structure (NEXAFS) spectrum of PCP was recorded at the carbon K-edge. Additionally, the NEXAFS spectra of the constituent pigments, chlorophyll a and peridinin, were measured. The energies of the lowest unoccupied molecular levels of these pigments appearing in the carbon NEXAFS spectrum were resolved. Individual contributions of the pigments and the protein to the measured NEXAFS spectrum of PCP were determined using a “building block” approach combining NEXAFS spectra of the pigments and the amino acids constituting the PCP apoprotein. The results suggest that absorption changes of the pigments in the carbon near K-edge region can be resolved following excitation using a suitable visible pump laser pulse. Consequently, it may be possible to study excitation energy transfer processes involving “optically dark” states of carotenoids in pigment–protein complexes by soft X-ray probe optical pump double resonance spectroscopy (XODR).     

Circular dichroism and magnetic circular dichroism spectra of chlorophylls in nematic liquid crystals. I. Electric and weak magnetic field effects on the dichroism spectra

Dichroism spectra of chlorophyll a, chlorophyll b and bacteriochlorophyll a in various nematic liquid crystals are reported. The initial orientation of chlorophylls in such a sample is determined by the interaction of the aggregate formed from the pigment and the liquid crystal molecules with the electrode surface on the cell windows. Reorientation is carried out by either an electric or magnetic field. The analysis of the circular dichroism spectra obtained from these samples on the basis of the Mueller matrix shows that the intensity is predominantly related to the texture of the sample. Chlorophyll molecules can be aggregated with liquid crystals in two ways: (1) through the chlorin magnesium atom, which results in the liquid crystal chain being almost perpendicular to the porphyrin ring, or (2) attached parallel to the line connecting the first and third pyrrole rings of the chlorin, the chlorin now lying in the plane of the liquid crystal chains. By comparing the dichroism spectra of various chlorophylls in the same liquid crystal we can draw conclusions concerning the preferred type of aggregation, not only with liquid crystals, but also with biological molecules. These liquid crystal systems are models of the orientation effects found for chlorophyll in lamellae. The model studied in this work is much simpler than the lamellar system but it does exhibit several common properties with the latter. Both systems are anisotropic and show much more intense dichroism signals, often of opposite sign, compared with those observed for photosynthetic pigments in isotropic solutions. Dichroism signals of organism fragments are much more complex than those of our model, which can either be related to the occurrence in the organism of several types of pigments or, for a given type of pigment, could be the result of exciton splitting. On the basis of our model it is shown that small changes in the anisotropy of the pigment in the surroundings have a strong influence on the sign and amplitude of the observed circular dichroism signal. Such effects may be responsible for the structure of the dichroism spectra observed for biological samples. Such structures can be partially related to the superposition of the dichroism signal from various ‘domains’ of chromophore which are different in both pigment arrangement and in the anisotropy of the surroundings of the pigment molecules themselves.     

Excitation energy transfer in the LHC-II trimer: a model based on the new 2.72 Å structure

Energy transfer of the light harvesting complex LHC-II trimer, extracted from spinach, was studied in the Q(y) region at room temperature by femtosecond transient absorption spectroscopy. Configuration interaction exciton method [Linnanto et al. (1999) J Phys Chem B 103: 8739-8750] and 2.72 A structural information reported by Liu et al. was used to calculate spectroscopic properties and excitation energy transfer rates of the complex. Site energies of the pigments and coupling constants of pigment pairs in close contact were calculated by using a quantum chemical configuration interaction method. Gaussian random variation of the diagonal and off-diagonal exciton matrix elements was used to account for inhomogeneous broadening. Rate calculations included only the excitonic states initially excited and probed in the experiments. A kinetic model was used to simulate time and wavelength dependent absorption changes after excitation on the blue side of the Q(y) transition and compared to experimentally recorded rates. Analysis of excitonic wavefunctions allowed identification of pigments initially excited and probed into later. It was shown that excitation of the blue side of the Q(y) band of a single LHC-II complex results in energy transfer from chlorophyll b's of the lumenal side to chlorophyll a's located primarly on one of the monomers of the stromal side.     

Spectral properties of a mixture of fluorescent pigments produced by Pseudomonas aeruginosa

The major chromophore of a mixture of fluorescent pigments produced by Pseudomonas aeruginosa ATCC 9027 had pH-dependent absorption, excitation, and emission spectra, such that two ionic forms existed in the ground state and three in the excited states. The pigments could complex with several metal ions to change fluorescence and absorption spectra. Although the pigments were separable into several components, spectra indicated that the same fluorescent chromophore was present in each component. Hydrolysis of the mixture of pigments gave amino acids which did not include alanine or lysine. These pigments must therefore differ from those described by other workers, even though similarities of the chromophores were evident from comparisons with data in the literature, and from comparisons of a hydrolytic product of the mixture of pigments, termed compound F, with the chromophore of the fluorescent pigment of Azotobacter vinelandii. Drastic hydrolysis of the latter chromophore also yielded compound F.     

Solvation effect of bacteriochlorophyll excitons in light-harvesting complex LH2

We have characterized the influence of the protein environment on the spectral properties of the bacteriochlorophyll (Bchl) molecules of the peripheral light-harvesting (or LH2) complex from Rhodobacter sphaeroides. The spectral density functions of the pigments responsible for the 800 and 850 nm electronic transitions were determined from the temperature dependence of the Bchl absorption spectra in different environments (detergent micelles and native membranes). The spectral density function is virtually independent of the hydrophobic support that the protein experiences. The reorganization energy for the B850 Bchls is 220 cm(-1), which is almost twice that of the B800 Bchls, and its Huang-Rhys factor reaches 8.4. Around the transition point temperature, and at higher temperatures, both the static spectral inhomogeneity and the resonance interactions become temperature-dependent. The inhomogeneous distribution function of the transitions exhibits less temperature dependence when LH2 is embedded in membranes, suggesting that the lipid phase protects the protein. However, the temperature dependence of the fluorescence spectra of LH2 cannot be fitted using the same parameters determined from the analysis of the absorption spectra. Correct fitting requires the lowest exciton states to be additionally shifted to the red, suggesting the reorganization of the exciton spectrum.     

A comparative study of the infrared difference spectra for octopus and bovine rhodopsins and their bathorhodopsin photointermediates

Fourier-transform infrared difference spectroscopy has been used to detect the vibrational modes in the chromophore and protein that change in position and intensity between octopus rhodopsin and its photoproducts formed at low temperature (85 K), bathorhodopsin and isorhodopsin. The infrared difference spectra between octopus rhodopsin and octopus bathorhodopsin, octopus bathorhodopsin and octopus isorhodopsin, and octopus isorhodopsin and octopus rhodopsin are compared to analogous difference spectra for the well-studied bovine pigments, in order to understand the similarities in pigment structure and photochemical processes between the vertebrate and invertebrate systems. The structure-sensitive fingerprint region of the infrared spectra for octopus bathorhodopsin shows strong similarities to spectra of both all-trans-retinal and bovine bathorhodopsin, thus confirming chemical extraction data that suggest that octopus bathorhodopsin contains an all-trans-retinal chromophore. In contrast, we find dramatic differences in the hydrogen out-of-plane modes of the two bathorhodopsins, and in the fingerprint lines of the rhodopsins and isorhodopsins for the two pigments. These observations suggest that while the primary effect of light in the octopus rhodopsin system, as in the bovine rhodopsin system, is 11-cis/11-trans isomerization, the protein-chromophore interactions for the two systems are quite different. Finally, striking similarities and differences in infrared lines attributable to changes in amino acid residues in the opsin are found between the two pigment systems. They suggest that no carboxylic acid or tyrosine residues are affected in the initial changes of light-energy transduction in octopus rhodopsin. Comparing the amino acid sequences for octopus and bovine pigments also allows us to suggest that the carboxylic acid residues altered in the bovine transitions are Glu-122 and/or Glu-134.