Protein Regulation of Carotenoid Binding

Photoactivation and conformational gating for manganese binding and oxidation in bacterial reaction centers

The influence of illumination history of native bacterial reaction centers (BRCs) on the ability of binding and photo-induced oxidation of manganous ions was investigated in the pH range between 8.0 and 9.4. Binding of manganous ions to a buried site required 6 to 11-fold longer incubation periods, depending on the pH, in dark-adapted BRCs than in BRCs that were previously illuminated prior to manganese binding. The intrinsic electron transfer from the bound manganese ion to the photo-oxidized primary electron donor was found to be limited by a 2 to 5-fold slower precursor conformational step in the dark-adapted samples for the same pH range. The conformational gating could be eliminated by photoactivation, namely if the BRCs were illuminated prior to binding. Unlike in Photosystem II, photoactivation in BRCs did not involve cluster assembly. Photoactivation with manganese already bound was only possible at elevated detergent concentration. In addition, also exclusively in dark-adapted BRCs, a marked breaking point in the Arrhenius-plot was discovered around 15 °C at pH 9.4 indicating a change in the reaction mechanism, most likely caused by the change of orientation of the 2-acetyl group of the inactive bacteriochlorophyll monomer located near the manganese binding site.

Pigment-modified reaction centers of Chloroflexus aurantiacus: chemical exchange of bacteriopheophytins with plant-type pheophytins

The pigment composition of isolated reaction centers (RCs) of the green filamentous bacterium Chloroflexus (Cfl.) aurantiacus was changed by chemical exchange of native bacteriopheophytin a (BPheo) molecules with externally added pheophytin a (Pheo) or [3-acetyl]-Pheo upon incubation of RC/pheophytin mixtures at room temperature and 45 °C. The modified RCs were characterized by Vis/NIR absorption spectroscopy, and the effect of pigment exchange on RC photochemical activity was assessed by measuring the photoaccumulation of the reduced pigment at the binding site H_A. It is shown that both pheophytins can be exchanged into the H_A site instead of BPheo by incubation at room temperature. While the newly introduced Pheo molecule is not active in electron transfer, the [3-acetyl]-Pheo molecule is able to replace functionally the photoreducible H_A BPheo molecule with the formation of the [3-acetyl]-Pheo^- radical anion instead of the BPheo^-. After incubation at 45 °C, the majority (~ 90%) of H_A BPheo molecules is replaced by both Pheo and [3-acetyl]-Pheo. Only a partial replacement of inactive BPheo molecules with pheophytins is observed even when the incubation temperature is raised to 50 °C. The results are discussed in terms of (i) differences in the accessibility of BPheo binding sites for extraneous pigments depending on structural constraints and incubation temperature and (ii) the effect of the reduction potential of pigments introduced into the H_A site on the energetics of the charge separation process. The possible implication of Pheo-exchanged preparations for studying early electron-transfer events in Cfl. aurantiacus RCs is considered.

Uncovering the interactions driving carotenoid binding in light-harvesting complexes

Carotenoids are essential constituents of plant light-harvesting complexes (LHCs), being involved in protein stability, light harvesting, and photoprotection. Unlike chlorophylls, whose binding to LHCs is known to require coordination of the central magnesium, carotenoid binding relies on weaker intermolecular interactions (such as hydrogen bonds and van der Waals forces), whose character is far more elusive. Here we addressed the key interactions responsible for carotenoid binding to LHCs by combining molecular dynamics simulations and polarizable quantum mechanics/molecular mechanics calculations on the major LHC, LHCII. We found that carotenoid binding is mainly stabilized by van der Waals interactions with the surrounding chlorophyll macrocycles rather than by hydrogen bonds to the protein, the latter being more labile than predicted from structural data. Furthermore, the interaction network in the binding pockets is relatively insensitive to the chemical structure of the embedded carotenoid. Our results are consistent with a number of experimental data and challenge the role played by specific interactions in the assembly of pigment-protein complexes.

Bound detergent molecules in bacterial reaction centers facilitate detection of tetryl explosive

Bacterial reaction centers (BRC) from Rhodobacter sphaeroides were found to accelerate, about 100-fold, the reaction between tetryl (2,4,6-trinitrophenylmethylnitramine) explosive and n-lauryl-N-N-dimethylamine-N-oxide (LDAO) that results in the formation of picric acid-like product with characteristic UV-VIS absorption spectrum with peaks at 345 and 415 nm. Moreover, this product also affects the spectra of BRC cofactors in the NIR spectral region and stabilizes the conformational changes associated with slow charge recombination. The evolution of the NIR absorption changes correlated with the kinetics of the product formation. Comparison between the wild-type and the R26 carotenoid-less strain indicates that tetryl-LDAO reaction is roughly five times faster for R26, which allows for identifying the carotenoid binding site as the optimal reaction site. Another, less-defined reaction site is located in the BRC's hydrophobic cavity. These effects are highly selective for tetryl and not observed for several other widespread nitric explosives; slowed-down charge recombination allows for distinguishing between tetryl and Q_B-site herbicides. The current limit of detection is in the ppb range or ~ 100 nM. Details of the molecular mechanisms of the reactions and perspectives of using these effects in bioassays or biosensors for explosives detection are also discussed.

Energetic insights into two electron transfer pathways in light-driven energy-converting enzymes

We report E_m values of (bacterio-)chlorophylls for one-electron reduction in both electron-transfer branches of PbRC, PSI, and PSII.

We report redox potentials (E_m) for one-electron reduction for all chlorophylls in the two electron-transfer branches of water-oxidizing enzyme photosystem II (PSII), photosystem I (PSI), and purple bacterial photosynthetic reaction centers (PbRC). In PSI, E_m values for the accessory chlorophylls were similar in both electron-transfer branches. In PbRC, the corresponding E_m value was 170 mV less negative in the active L-branch (B_L) than in the inactive M-branch (B_M), favoring B_L˙^– formation. This contrasted with the corresponding chlorophylls, Chl_D1 and Chl_D2, in PSII, where E_m(Chl_D1) was 120 mV more negative than E_m(Chl_D2), implying that to rationalize electron transfer in the D1-branch, Chl_D1 would need to serve as the primary electron donor. Residues that contributed to E_m(Chl_D1) < E_m(Chl_D2) simultaneously played a key role in (i) releasing protons from the substrate water molecules and (ii) contributing to the larger cationic population on the chlorophyll closest to the Mn₄CaO₅ cluster (P_D1), favoring electron transfer from water molecules. These features seem to be the nature of PSII, which needs to possess the proton-exit pathway to use a protonated electron source—water molecules.

Protein Vibration Effects on Primary Electron Transfer Dynamics in Rhodobacter sphaeroides Photosynthetic Reaction Center

Primary electron transfer (ET) in the chromophore subsystem in a bacterial reaction center (RC) is a unique process, and is coupled with the protein motion, which, like the ET, is caused by photoexcitation of these chromophores. ET is also coupled with dissipative processes, which are caused by interaction between chromophores and vibrations of its surrounding protein. We propose a new dynamics calculation method that accounts for both these effects of protein vibrations. Within this method, the photoinduced protein motion causes an addition of coherent component to the ET rate. We performed dynamics calculation using this method and parameters, which were determined from the ab initio wave functions of the chromophore subsystem and protein normal vibrational modes. We showed that it is this protein motion that causes oscillations in the time-dependencies of stimulated emission intensities and of absorption at 1020 nm. Moreover, the latter oscillations are related to the coherent component of the ET rate.

Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs

Contents 937 I. 937 II. 938 III. 939 IV. 943 V. 947 VI. 948 948 References 949 SUMMARY: The orange carotenoid protein (OCP) is a water-soluble, photoactive protein involved in thermal dissipation of excess energy absorbed by the light-harvesting phycobilisomes (PBS) in cyanobacteria. The OCP is structurally and functionally modular, consisting of a sensor domain, an effector domain and a keto-carotenoid. On photoactivation, the OCP converts from a stable orange form, OCP^O , to a red form, OCP^R . Activation is accompanied by a translocation of the carotenoid deeper into the effector domain. The increasing availability of cyanobacterial genomes has enabled the identification of new OCP families (OCP1, OCP2, OCPX). The fluorescence recovery protein (FRP) detaches OCP1 from the PBS core, accelerating its back-conversion to OCP^O ; by contrast, other OCP families are not regulated by FRP. N-terminal domain homologs, the helical carotenoid proteins (HCPs), have been found among diverse cyanobacteria, occurring as multiple paralogous groups, with two representatives exhibiting strong singlet oxygen (¹ O₂ ) quenching (HCP2, HCP3) and another capable of dissipating PBS excitation (HCP4). Crystal structures are presently available for OCP1 and HCP1, and models of other HCP subtypes can be readily produced as a result of strong sequence conservation, providing new insights into the determinants of carotenoid binding and ¹ O₂ quenching.

Carotenoids and Photosynthesis

Carotenoids are ubiquitous and essential pigments in photosynthesis. They absorb in the blue-green region of the solar spectrum and transfer the absorbed energy to (bacterio-)chlorophylls, and so expand the wavelength range of light that is able to drive photosynthesis. This is an example of singlet-singlet energy transfer, and so carotenoids serve to enhance the overall efficiency of photosynthetic light reactions. Carotenoids also act to protect photosynthetic organisms from the harmful effects of excess exposure to light. Triplet-triplet energy transfer from chlorophylls to carotenoids plays a key role in this photoprotective reaction. In the light-harvesting pigment-protein complexes from purple photosynthetic bacteria and chlorophytes, carotenoids have an additional role of structural stabilization of those complexes. In this article we review what is currently known about how carotenoids discharge these functions. The molecular architecture of photosynthetic systems will be outlined first to provide a basis from which to describe carotenoid photochemistry, which underlies most of their important functions in photosynthesis.

Energy dissipative photoprotective mechanism of carotenoid spheroidene from the photoreaction center of purple bacteria Rhodobacter sphaeroides

Carotenoid spheroidene (SPO) functions for photoprotection in the photosynthetic reaction centers (RCs) and effectively dissipates its triplet excitation energy. Sensitized cis-to-trans isomerization was proposed as a possible mechanism for a singlet-triplet energy crossing for the 15,15'-cis-SPO; however, it has been questioned recently. To understand the dissipative photoprotective mechanism of this important SPO and to overcome the existing controversies on this issue, we carried out a theoretical investigation using density functional theory on the possible triplet energy relaxation mechanism through the cis-to-trans isomerization. Together with the earlier experimental observations, the possible mechanism was discussed for the triplet energy relaxation of the 15,15'-cis-SPO. The result shows that complete cis-to-trans isomerization is not necessary. Twisting the C15-C15' bond leads to singlet-triplet energy crossing at ϕ(14,15,15',14') = 77° with an energy 32.5 kJ mol(-1) (7.7 kcal mol(-1)) higher than that of the T1 15,15'-cis minimum. Further exploration of the minimum-energy intersystem crossing (MEISC) point shows that triplet relaxation could occur at a less distorted structure (ϕ = 58.4°) with the energy height of 26.5 KJ mol(-1) (6.3 kcal mol(-1)). Another important reaction coordinate to reach the MEISC point is the bond-length alternation. The model truncation effect, solvent effect, and spin-orbit coupling were also investigated. The singlet-triplet crossing was also investigated for the 13,14-cis stereoisomer and locked-13,14-cis-SPO. We also discussed the origin of the natural selection of the cis over trans isomer in the RC.

Comparative ENDOR study at 34 GHz of the triplet state of the primary donor in bacterial reaction centers of Rb. sphaeroides and Bl. viridis

The primary electron donor (P) in the photosynthetic bacterial reaction center of Rhodobacter sphaeroides and Blastochloris viridis consists of a dimer of bacteriochlorophyll a and b cofactors, respectively. Its photoexcited triplet state in frozen solution has been investigated by time resolved ENDOR spectroscopy at 34 GHz. The observed ENDOR spectra for (3)P865 and (3)P960 are essentially the same, indicating very similar spin density distributions. Exceptions are the ethylidene groups unique to the bacteriochlorophyll b dimer in (3)P960. Strikingly, the observed hyperfine coupling constants of the ethylidene groups are larger than in the monomer, which speaks for an asymmetrically delocalized wave function over both monomer halves in the dimer. The latter observation corroborates previous findings of the spin density in the radical cation states P 865 (•+) (Lendzian et al. in Biochim Biophys Acta 1183:139-160, 1993) and P 960 (•+) (Lendzian et al. in Chem Phys Lett 148:377-385, 1988). As compared to the bacteriochlorophyll monomer, the hyperfine coupling constants of the methyl groups 2(1) and 12(1) are reduced by at least a factor of two, and quantitative analysis of these couplings gives rise to a ratio of approximately 3:1 for the spin density on the halves PL:PM. Our findings are discussed in light of the large difference in photosynthetic activity of the two branches of cofactors present in the bacterial reaction center proteins.

Determination of Excited-State Energies and Dynamics in the B Band of the Bacterial Reaction Center with 2D Electronic Spectroscopy

Photosynthetic organisms convert photoenergy to chemical energy with near-unity quantum efficiency. This occurs through charge transfer in the reaction center, which consists of two branches of pigments. In bacteria, both branches are energy-transfer pathways, but only one is also an electron transfer pathway. One barrier to a full understanding of the asymmetry is that the two branches contain excited states close in energy that produce overlapping spectroscopic peaks. We apply polarization-dependent, 2D electronic spectroscopy to the B band of the oxidized bacterial reaction center. The spectra reveal two previously unresolved peaks, corresponding to excited states localized on each of the two branches. Furthermore, a previously unknown interaction between these two states is observed on a time scale of ∼100 fs. This may indicate an alternative pathway to electron transfer for the oxidized reaction center and thus may be a mechanism to prevent energy from becoming trapped in local minima.

New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory

Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.

Neutron and light scattering studies of light-harvesting photosynthetic antenna complexes

Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been employed in studying the structural information of various biological systems, particularly in systems without high-resolution structural information available. In this report, we briefly present some principles and biological applications of neutron scattering and DLS, compare the differences in information that can be obtained with small-angle X-ray scattering (SAXS), and then report recent studies of SANS and DLS, together with other biophysical approaches, for light-harvesting antenna complexes and reaction centers of purple and green phototrophic bacteria.

Lipid binding to the carotenoid binding site in photosynthetic reaction centers

Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S.; Williams, J. C.; Allen, J. P.; Kalman, L. Biochemistry 2011, 50, 340). Here in the R-26 reaction centers, the combination of light-induced structural changes and lipid binding resulted in a 5 orders of magnitude increase in the lifetime of the charge-separated state involving the oxidized dimer and the reduced primary quinone in proteoliposomes. Only saturated phospholipids with fatty acid chains of 12 and 14 carbon atoms long were bound successfully at 8 °C by cooling the reaction center protein slowly from room temperature. In addition to reporting a dramatic increase of the lifetime of the charge-separated state at physiologically relevant temperatures, this study reveals a novel lipid binding site in photosynthetic reaction center. These results shed light on a new potential application of the reaction center in energy storage as a light-driven biocapacitor since the charges separated by ∼30 Å in a low-dielectric medium can be prevented from recombination for hours.

Removal and reconstitution of the carotenoid antenna of xanthorhodopsin

Salinixanthin, a C₄₀-carotenoid acyl glycoside, serves as a light-harvesting antenna in the retinal-based proton pump xanthorhodopsin of Salinibacter ruber. In the crystallographic structure of this protein, the conjugated chain of salinixanthin is located at the protein–lipid boundary and interacts with residues of helices E and F. Its ring, with a 4-keto group, is rotated relative to the plane of the π-system of the carotenoid polyene chain and immobilized in a binding site near the β-ionone retinal ring. We show here that the carotenoid can be removed by oxidation with ammonium persulfate, with little effect on the other chromophore, retinal. The characteristic CD bands attributed to bound salinixanthin are now absent. The kinetics of the photocycle is only slightly perturbed, showing a 1.5-fold decrease in the overall turnover rate. The carotenoid-free protein can be reconstituted with salinixanthin extracted from the cell membrane of S. ruber. Reconstitution is accompanied by restoration of the characteristic vibronic structure of the absorption spectrum of the antenna carotenoid, its chirality, and the excited-state energy transfer to the retinal. Minor modification of salinixanthin, by reducing the carbonyl C=O double bond in the ring to a C-OH, suppresses its binding to the protein and eliminates the antenna function. This indicates that the presence of the 4-keto group is critical for carotenoid binding and efficient energy transfer.

Reconstitution of gloeobacter rhodopsin with echinenone: role of the 4-keto group

In previous work, we reconstituted salinixanthin, the C(40)-carotenoid acyl glycoside that serves as a light-harvesting antenna to the light-driven proton pump xanthorhodopsin, into a different protein, gloeobacter rhodopsin expressed in Escherichia coli, and demonstrated that it transfers energy to the retinal chromophore [Imasheva, E. S., et al. (2009) Biochemistry 48, 10948]. The key to binding of salinixanthin was the accommodation of its ring near the retinal β-ionone ring. Here we examine two questions. Do any of the native Gloeobacter carotenoids bind to gloeobacter rhodopsin, and does the 4-keto group of the ring play a role in binding? There is no salinixanthin in Gloeobacter violaceous, but a simpler carotenoid, echinenone, also with a 4-keto group but lacking the acyl glycoside, is present in addition to β-carotene and oscillol. We show that β-carotene does not bind to gloeobacter rhodopsin, but its 4-keto derivative, echinenone, does and functions as a light-harvesting antenna. This indicates that the 4-keto group is critical for carotenoid binding. Further evidence of this is the fact that salinixanthol, an analogue of salinixanthin in which the 4-keto group is reduced to hydroxyl, does not bind and is not engaged in energy transfer. According to the crystal structure of xanthorhodopsin, the ring of salinixanthin in the binding site is turned out of the plane of the polyene conjugated chain. A similar conformation is expected for echinenone in the gloeobacter rhodopsin. We suggest that the 4-keto group in salinixanthin and echinenone allows for the twisted conformation of the ring around the C6-C7 bond and probably is engaged in an interaction that locks the carotenoid in the binding site.

Percentile-based spread: a more accurate way to compare crystallographic models

The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.

Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria

The photoprotective processes of photosynthetic organisms involve the dissipation of excess absorbed light energy as heat. Photoprotection in cyanobacteria is mechanistically distinct from that in plants; it involves the orange carotenoid protein (OCP), a water-soluble protein containing a single carotenoid. The OCP is a new member of the family of blue light-photoactive proteins; blue-green light triggers the OCP-mediated photoprotective response. Here we report structural and functional characterization of the wild type and two mutant forms of the OCP, from the model organism Synechocystis PCC6803. The structural analysis provides high resolution detail of the carotenoid-protein interactions that underlie the optical properties of the OCP, unique among carotenoid-proteins in binding a single pigment per polypeptide chain. Collectively, these data implicate several key amino acids in the function of the OCP and reveal that the photoconversion and photoprotective responses of the OCP to blue-green light can be decoupled.

The conformation of end-groups is one determinant of carotenoid topology suitable for high fidelity molecular recognition: a study of beta- and epsilon-end-groups

Conformation affects a carotenoid's ability to bind selectively to proteins. We calculated adiabatic energy profiles for rotating the ring end-groups around the C6C7 bond and for flexing of the ring with respect to the polyene chain. The choice of computational methods is important. A low, 4.2 kcal/mol barrier to rotation exists for a beta-ring. An 8.3 kcal/mol barrier exists for rotation of an epsilon-ring. Rotation of the epsilon-ring is sensitive to substitution at C3. In the absence of external forces neither beta- nor epsilon-rings are rotationally constrained. The nearly parallel alignment of the beta-ring to the C6C7 bond axis contrasts to the more perpendicular orientation of the epsilon-ring. Flexion of a beta-ring to the minimized epsilon-ring conformation requires approximately 23 kcal/mol; extension of the epsilon-ring to the minimized beta-ring conformation requires approximately 8 kcal/mol. Selectivity associated with beta- versus epsilon-rings is dominated by the inability of the beta-ring to flex to minimize protein/ring steric interactions and maximize van der Waal's attractions with the binding site.

Probing the effect of the binding site on the electrostatic behavior of a series of carotenoids reconstituted into the light-harvesting 1 complex from purple photosynthetic bacterium Rhodospirillum rubrum detected by stark spectroscopy

Reconstitutions of the LH1 complexes from the purple photosynthetic bacterium Rhodospirillum rubrum S1 were performed with a range of carotenoid molecules having different numbers of C=C conjugated double bonds. Since, as we showed previously, some of the added carotenoids tended to aggregate and then to remain with the reconstituted LH1 complexes (Nakagawa, K.; Suzuki, S.; Fujii, R.; Gardiner, A.T.; Cogdell, R.J.; Nango, M.; Hashimoto, H. Photosynth. Res. 2008, 95, 339-344), a further purification step using a sucrose density gradient centrifugation was introduced to improve purity of the final reconstituted sample. The measured absorption, fluorescence-excitation, and Stark spectra of the LH1 complex reconstituted with spirilloxanthin were identical with those obtained with the native, spirilloxanthin-containing, LH1 complex of Rs. rubrum S1. This shows that the electrostatic environments surrounding the carotenoid and bacteriochlorophyll a (BChl a) molecules in both of these LH1 complexes were essentially the same. In the LH1 complexes reconstituted with either rhodopin or spheroidene, however, the wavelength maximum at the BChl a Qy absorption band was slightly different to that of the native LH1 complexes. These differences in the transition energy of the BChl a Qy absorption band can be explained using the values of the nonlinear optical parameters of this absorption band, i.e., the polarizability change Tr(Deltaalpha) and the static dipole-moment change |Deltamu| upon photoexcitation, as determined using Stark spectroscopy. The local electric field around the BChl a in the native LH1 complex (ES) was determined to be approximately 3.0x10(6) V/cm. Furthermore, on the basis of the values of the nonlinear optical parameters of the carotenoids in the reconstituted LH1 complexes, it is possible to suggest that the conformations of carotenoids, anhydrorhodovibrin and spheroidene, in the LH1 complex were similar to that of rhodopin glucoside in crystal structure of the LH2 complex from Rhodopseudomonas acidophila 10050.

Chromophore interaction in xanthorhodopsin--retinal dependence of salinixanthin binding

Xanthorhodopsin is a light-driven proton pump in the extremely halophilic bacterium Salinibacter ruber. Its unique feature is that besides retinal it has a carotenoid, salinixanthin, with a light harvesting function. Tight and specific binding of the carotenoid antenna is controlled by binding of the retinal. Addition of all-trans retinal to xanthorhodopsin bleached with hydroxylamine restores not only the retinal chromophore absorption band, but causes sharpening of the salinixanthin bands reflecting its rigid binding by the protein. In this report we examine the correlation of the changes in the two chromophores during bleaching and reconstitution with native all-trans retinal, artificial retinal analogs and retinol. Bleaching and reconstitution both appear to be multistage processes. The carotenoid absorption changes during bleaching occurred not only upon hydrolysis of the Schiff base but continued while the retinal was leaving its binding site. In the case of reconstitution, the 13-desmethyl analog formed the protonated Schiff base slower than retinal, and provided the opportunity to observe changes in carotenoid binding at various stages. The characteristic sharpening of the carotenoid bands, indicative of its reduced conformational heterogeneity in the binding site, occurs when the retinal occupies the binding site but the covalent bond to Lys-240 via a Schiff base is not yet formed. This is confirmed by the results for retinol reconstitution, where the Schiff base does not form but the carotenoid exhibits its characteristic spectral change from the binding.

Probing binding site of bacteriochlorophyll a and carotenoid in the reconstituted LH1 complex from Rhodospirillum rubrum S1 by Stark spectroscopy

Stark spectroscopy is a powerful technique to investigate the electrostatic interactions between pigments as well as between the pigments and the proteins in photosynthetic pigment-protein complexes. In this study, Stark spectroscopy has been used to determine two nonlinear optical parameters (polarizability change Tr(Deltaalpha) and static dipole-moment change |Deltamu| upon photoexcitation) of isolated and of reconstituted LH1 complexes from the purple photosynthetic bacterium, Rhodospirillum (Rs.) rubrum. The integral LH1 complex was prepared from Rs. rubrum S1, while the reconstituted complex was assembled by addition of purified carotenoid (all-trans-spirilloxanthin) to the monomeric subunit of LH1 from Rs. rubrum S1. The reconstituted LH1 complex has its Q(y) absorption maximum at 878 nm. This is shifted to the blue by 3 nm in comparison to the isolated LH1 complex. The energy transfer efficiency from carotenoid to bacteriochlorophyll a (BChl a), which was determined by fluorescence excitation spectroscopy of the reconstituted LH1 complex, is increased to 40%, while the efficiency in the isolated LH1 complex is only 28%. Based on the differences in the values of Tr(Deltaalpha) and |Deltamu|, between these two preparations, we can calculate the change in the electric field around the BChl a molecules in the two situations to be E (Delta) approximately 3.4 x 10(5) [V/cm]. This change can explain the 3 nm wavelength shift of the Q(y) absorption band in the reconstituted LH1 complex.

Two stereoisomers of spheroidene in the Rhodobacter sphaeroides R26 reaction center: a DFT analysis of resonance Raman spectra

From a theoretical analysis of the resonance Raman spectra of 19 isotopomers of spheroidene reconstituted into the reaction center (RC) of Rhodobacter sphaeroides R26, we conclude that the carotenoid in the RC occurs in two configurations. The normal mode underlying the resonance Raman transition at 1239 cm(-1), characteristic for spheroidene in the RC, has been identified and found to uniquely refer to the cis nature of the 15,15' carbon-carbon double bond. Detailed analysis of the isotope-induced shifts of transitions in the 1500-1550 cm(-1) region proves that, besides the 15,15'-cis configuration, spheroidene in the RC adopts another cis-configuration, most likely the 13,14-cis configuration.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

Lipidic Sponge Phase Crystallization of Membrane Proteins

Bicontinuous lipidic cubic phases can be used as a host for growing crystals of membrane proteins. Since the cubic phase is stiff, handling is difficult and time-consuming. Moreover, the conventional cubic phase may interfere with the hydrophilic domains of membrane proteins due to the limited size of the aqueous pores. Here, we introduce a new crystallization method that makes use of a liquid analogue of the cubic phase, the sponge phase. This phase facilitates a considerable increase in the allowed size of aqueous domains of membrane proteins, and is easily generalised to a conventional vapour diffusion crystallisation experiment, including the use of nanoliter drop crystallization robots. The appearance of the sponge phase was confirmed by visual inspection, small-angle X-ray scattering and NMR spectroscopy. Crystals of the reaction centre from Rhodobacter sphaeroides were obtained by a conventional hanging-drop experiment, were harvested directly without the addition of lipase or cryoprotectant, and the structure was refined to 2.2 Angstroms resolution. In contrast to our earlier lipidic cubic phase reaction centre structure, the mobile ubiquinone could be built and refined. The practical advantages of the sponge phase make it a potent tool for crystallization of membrane proteins.

Triplet state spectra and dynamics of geometric isomers of carotenoids

The observation of preferential binding of cis-carotenoids in purple bacterial photosynthetic reaction centers versus trans-isomers in antenna pigment protein complexes has led to the hypothesis that the natural selection of stereoisomers has physiological significance. In order to test this hypothesis, we have undertaken a systematic series of investigations comparing the optical spectroscopic properties and excited state dynamics of cis and trans isomers of carotenoids. The present work compares the triplet state spectra, lifetimes, and energy transfer rates of all-trans-spheroidene and 13,14-locked-cis-spheroidene, the latter of which is incapable of isomerizing to the all-trans configuration, and therefore provides a unique opportunity to examine the triplet state properties of a structurally stable cis molecule. The data reveal only small differences in spectra, decay dynamics, and transfer times and suggest there is little intrinsic advantage in either triplet energy transfer or triplet state decay arising from the inherently different isomeric forms of cis compared to trans carotenoids.

Biogenesis, molecular regulation and function of plant isoprenoids

Isoprenoids represent the oldest class of known low molecular-mass natural products synthesized by plants. Their biogenesis in plastids, mitochondria and the endoplasmic reticulum-cytosol proceed invariably from the C5 building blocks, isopentenyl diphosphate and/or dimethylallyl diphosphate according to complex and reiterated mechanisms. Compounds derived from the pathway exhibit a diverse spectrum of biological functions. This review centers on advances obtained in the field based on combined use of biochemical, molecular biology and genetic approaches. The function and evolutionary implications of this metabolism are discussed in relation with seminal informations gathered from distantly but related organisms.

Strong Effects of an Individual Water Molecule on the Rate of Light-driven Charge Separation in the Rhodobacter sphaeroides Reaction Center

The role of a water molecule (water A) located between the primary electron donor (P) and first electron acceptor bacteriochlorophyll (B(A)) in the purple bacterial reaction center was investigated by mutation of glycine M203 to leucine (GM203L). The x-ray crystal structure of the GM203L reaction center shows that the new leucine residue packs in such a way that water A is sterically excluded from the complex, but the structure of the protein-cofactor system around the mutation site is largely undisturbed. The results of absorbance and resonance Raman spectroscopy were consistent with either the removal of a hydrogen bond interaction between water A and the keto carbonyl group of B(A) or a change in the local electrostatic environment of this carbonyl group. Similarities in the spectroscopic properties and x-ray crystal structures of reaction centers with leucine and aspartic acid mutations at the M203 position suggested that the effects of a glycine to aspartic acid substitution at the M203 position can also be explained by steric exclusion of water A. In the GM203L mutant, loss of water A was accompanied by an approximately 8-fold slowing of the rate of decay of the primary donor excited state, indicating that the presence of water A is important for optimization of the rate of primary electron transfer. Possible functions of this water molecule are discussed, including a switching role in which the redox potential of the B(A) acceptor is rapidly modulated in response to oxidation of the primary electron donor.

Local Electrostatic Field Induced by the Carotenoid Bound to the Reaction Center of the Purple Photosynthetic Bacterium Rhodobacter Sphaeroides

Electroabsorption (EA) spectra were recorded in the region of the reaction center (RC) Qy absorption bands of bacteriochlorophyll (Bchl) and bacteriopheophytin, to investigate the effect of carotenoid (Car) on the electrostatic environment of the RCs of the purple bacterium Rhodobacter (Rb.) sphaeroides. Two different RCs were prepared from Rb. sphaeroides strain R26.1 (R26.1-RC); R26.1 RC lacking Car and a reconstituted RC (R26.1-RC+ Car) prepared by incorporating a synthetic Car (3,4-dihydrospheroidene). Although there were no detectable differences between these two RCs in their near infrared (NIR) absorption spectra at 79 and 293 K, or in their EA spectra at 79 K, significant differences were detected in their EA spectra at 293 K. Three nonlinear optical parameters of each RC were determined in order to evaluate quantitatively these differences; transition dipole-moment polarizability and hyperpolarizability (D factor), the change in polarizability upon photoexcitation (Deltaalpha), and the change in dipole-moment upon photoexcitation (Deltamu). The value of D or Deltaalpha determined for each absorption band of the two RC samples showed similar values at 77 or 293 K. However, the Deltamu values of the special pair Bchls (P) and the monomer Bchls absorption bands showed significant differences between the two RCs at 293 K. X-ray crystallography of the two RCs has revealed that a single molecule of the solubilizing detergent LDAO occupies part of the carotenoid binding site in the absence of a carotenoid. The difference in the value of Deltamu therefore represents the differential effect of the detergent LDAO and the carotenoid on P. The change of electrostatic field around P induced by the presence of Car was determined to be 1.7 x 10(5) [V/cm], corresponding to a approximately 10% change in the electrostatic field around P.