Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors

Supramolecular arrangement of Rhodospirillum rubrum B880 holochrome as studied by radiation inactivation and electron paramagnetic resonance

Oxidation of the B880 antenna holochrome gives rise to a 3.8-G linewidth electron paramagnetic resonance (EPR) signal that is considerably narrower than the 13-G signal of monomeric bacteriochlorophyll (Bchl) cation. Radiation inactivation was used to verify a model according to which this linewidth narrowing is due to delocalization over several Bchl molecules. Chromatophores of the photoreaction centerless mutant F24 of Rhodospirillum rubrum were subjected to different doses of gamma-radiation. This induced not only a decay of the EPR signal amplitude but also its linewidth broadening. According to target theory, the induced amplitude decay of the EPR signal had a target size of 10.5 kDa. This is attributed to an elementary structure (alpha1beta1Bchl2), whose number in the membrane would limit the rate of encounter with ferricyanide and thus the formation of unpaired spins. We applied Bernoulli statistics to predict, for a given survival probability of the signal, the number of surviving elementary structures in aggregates of (alpha1beta1Bchl2)n where n was varied from 4 to 7. Using an equation that predicted the Bchl special pair in the photo-reaction center, we were able to simulate the observed relationship between the EPR linewidth and the dose of radiation. The best fit was obtained with a hexameric structure alpha1beta1Bchl2)6.

Fourier transform infrared difference spectroscopy shows no evidence for an enolization of chlorophyll a upon cation formation either in vitro or during P700 photooxidation

Molecular changes associated with the photooxidation of the primary electron donor P700 in photosystem I from cyanobacteria have been investigated with Fourier transform infrared (FTIR) difference spectroscopy. Highly resolved signals are observed in the carbonyl stretching frequency region of the light-induced FTIR spectra. In order to assign and to interpret these signals, the FTIR spectra of isolated chlorophyll a and pyrochlorophyll a (lacking the 10a-ester carbonyl) in both their neutral and cation states were investigated. Comparison of the redox-induced FTIR difference spectra of these two model compounds demonstrates that upon chlorophyll a cation formation in tetrahydrofuran the 7c-ester carbonyl is essentially unperturbed while the 10a-ester carbonyl is upshifted from 1738 to 1751 cm-1. For the 9-keto group, the shift is from 1693 to 1718 cm-1 in chlorophyll a and from 1686 to 1712 cm-1 in pyrochlorophyll a. The 1718-cm-1 band in the difference spectrum of chlorophyll a is thus unambiguously assigned to the 9-keto carbonyl of the cation. Comparison of the light-induced FTIR difference spectrum associated with the photooxidation of P700 in vivo with the difference FTIR spectrum of chlorophyll a cation formation leads to the assignment of the frequencies of the 9-keto carbonyl group(s) at 1700 cm-1 in P700 and at 1717 cm-1 in P700+.(ABSTRACT TRUNCATED AT 250 WORDS)

Stark effect in wild-type and heterodimer-containing reaction centers from Rhodobacter capsulatus

The effect of an external electric field on the optical absorption spectra of wild-type Rhodobacter capsulatus and two Rb. capsulatus reaction centers that have been genetically modified through site-directed mutagenesis (HisM200----LeuM200 and HisM200----PheM200) was measured at 77 K. The two genetically modified reaction centers replace histidine M200, the axial ligand to the M-side bacteriochlorophyll of the special pair, with either leucine or phenylalanine. These substitutions result in the replacement of the M-side bacteriochlorophyll with bacteriopheophytin, forming a bacteriochlorophyll-bacteriopheophytin heterodimer. The magnitude of the change in dipole moment from the ground to excited state (delta mu app) and the angle delta between the Qy transition moment and the direction of delta mu app were measured for the special pair absorption band for all three reaction centers. The values for delta mu app and delta obtained for wild-type Rb. capsulatus (delta mu app = 6.7 +/- 1.0 D, delta = 38 +/- 3 degrees) were the same within experimental error as those of Rhodobacter sphaeroides and Rhodopseudomonas viridis. The values for delta mu app and delta obtained for the red-most Stark band of both heterodimers were the same, but delta mu was substantially different from that of wild-type reaction centers (HisM200----LeuM200, delta mu app greater than or equal to 14.1 D and delta = 33 +/- 3 degrees; HisM200----PheM200, delta mu app greater than or equal to 15.7 D and delta = 31 +/- 4 degrees).(ABSTRACT TRUNCATED AT 250 WORDS)

A similar structure of the herbicide binding site in photosystem II of plants and cyanobacteria is demonstrated by site specific mutagenesis of the psbA gene

Many herbicides inhibit the photosynthetic electron transfer in photosystem II by binding to the polypeptide D1. A point mutation in the chloroplast gene psbA, which leads to a change of the amino acid residue 264 of D1 from serine to glycine, is responsible for atrazine resistance in higher plants. We have changed serine 264 to glycine in Synechococcus PCC7942 and compared its phenotype to a mutant with a serine to alanine shift in the same position. The results show that glycine at position 264 in D1 gives rise to a similar phenotype in cyanobacteria and in higher plants, indicating a similar structure of the binding site for herbicides and for the quinone QB in the two systems. A possible mode of binding of phenyl-urea herbicides to D1 is predicted from the difference in herbicidal cross-resistance between glycine and alanine substitutions of serine 264.

Spectral hole burning of the primary electron donor state of Photosystem I

Persistent photochemical hole burned profiles are reported for the primary electron donor state P700 of the reaction center of PS I. The hole profiles at 1.6 K for a wide range of burn wavelengths (λB) are broad (FWHM∼310 cm(-1)) and for the 45:1 enriched particles studied exhibit no sharp zero-phonon hole feature coincident with λB. The λB hole profiles are analyzed using the theory of Hayes et al. [J Phys Chem 1986, 90: 4928] for hole burning in the presence of arbitrarily strong linear electron-phonon coupling. A Huang-Rhys factor S in the range 4-6 and a corresponding mean phonon frequency in the range 35-50 cm(-1) together with an inhomogeneous line broadening of∼100 cm(-1) are found to provide good agreement with experiment. The zero-point level of P700(*) is predicted to lie at∼710 nm at 1.6K with an absorption maximum at∼702 nm. The hole spectra are discussed in the context of the hole spectra for the primary electron donor states of PS II and purple bacteria.

Exciton interactions in synthetic porphyrin dimers

The Soret absorption spectra of six synthetic rigid porphyrin dimers whose crystal structures have been determined are simulated using simple exciton theory. The objective is to test the validity of the point dipole and associated approximations; the electronic interaction parameters are thus calculated using data obtained from the monomer spectra, with no adjustable parameters. Satisfactory agreement between theory and experiment is obtained for one class of dimers but not for a second. This poses a challenge for semiempirical electronic structure methods as to whether improvements over the point dipole calculations can be obtained.

Photoelectric study on the kinetics of trapping and charge stabilization in oriented PS II membranes

Excitation energy trapping and charge separation in Photosystem II were studied by kinetic analysis of the fast photovoltage detected in membrane fragments from peas with picosecond excitation. With the primary quinone acceptor oxidized the photovoltage displayed a biphasic rise with apparent time constants of 100-300 ps and 550±50 ps. The first phase was dependent on the excitation energy whereas the second phase was not. We attribute these two phases to trapping (formation of P-680(+) Phe(-)) and charge stabilization (formation of P-680(+) QA (-)), respectively. A reversibility of the trapping process was demonstrated by the effect of the fluorescence quencher DNB and of artificial quinone acceptors on the apparent rate constants and amplitudes. With the primary quinone acceptor reduced a transient photoelectric signal was observed and attributed to the formation and decay of the primary radical pair. The maximum concentration of the radical pair formed with reduced QA was about 30% of that measured with oxidized QA. The recombination time was 0.8-1.2 ns.The competition between trapping and annihilation was estimated by comparison of the photovoltage induced by short (30 ps) and long (12 ns) flashes. These data and the energy dependence of the kinetics were analyzed by a reversible reaction scheme which takes into account singlet-singlet annihilation and progressive closure of reaction centers by bimolecular interaction between excitons and the trap. To put on firmer grounds the evaluation of the molecular rate constants and the relative electrogenicity of the primary reactions in PS II, fluorescence decay data of our preparation were also included in the analysis. Evidence is given that the rates of radical pair formation and charge stabilization are influenced by the membrane potential. The implications of the results for the quantum yield are discussed.

Dispersed polaron simulations of electron transfer in photosynthetic reaction centers

A microscopic method for simulating quantum mechanical, nuclear tunneling effects in biological electron transfer reactions is presented and applied to several electron transfer steps in photosynthetic bacterial reaction centers. In this "dispersed polaron" method the fluctuations of the protein and the electron carriers are projected as effective normal modes onto an appropriate reaction coordinate and used to evaluate the quantum mechanical rate constant. The simulations, based on the crystallographic structure of the reaction center from Rhodopseudomonas viridis, focus on electron transfer from a bacteriopheophytin to a quinone and the subsequent back-reaction. The rates of both of these reactions are almost independent of temperature or even increase with decreasing temperature. The simulations reproduce this unusual temperature dependence in a qualitative way, without the use of adjustable parameters for the protein's Franck-Condon factors. The observed dependence of the back-reaction on the free energy of the reaction also is reproduced, including the special behavior in the "inverted region."

Role of specific lysine residues in binding cytochrome c2 to the Rhodobacter sphaeroides reaction center in optimal orientation for rapid electron transfer

The role of specific lysine residues in facilitating electron transfer from Rhodobacter sphaeroides cytochrome c2 to the Rb. sphaeroides reaction center was studied by using six cytochrome c2 derivatives each labeled at a single lysine residue with a carboxydinitrophenyl group. The reaction of native cytochrome c2 at low ionic strength has a fast phase with a half-time of 0.6 microseconds that has been assigned to the reaction of bound cytochrome c2 [Overfield, R.E., Wraight, C.A., & DeVault, D. (1979) FEBS Lett. 105, 137]. Modification of lysine-55 did not affect the half-time of this phase but decreased the apparent binding constant by a factor of 2. The derivatives modified at lysines-10, -88, -95, -97, -99, -105, and -106 surrounding the heme crevice did not show any detectable fast phase but only slow second-order phases due to the reaction of solution cytochrome c2. These lysines thus appear to be involved in binding cytochrome c2 to the reaction center in an optimal orientation for electron transfer. The involvement of lysines-95 and -97 is especially significant, since they are located in an extra loop comprising residues 89-98 that is not present in eukaryotic cytochrome c. The reactions of horse cytochrome c derivatives modified at single lysine amino groups with trifluoroacetyl or [(trifluoromethyl)phenyl]carbamoyl were also studied. The derivatives modified at lysines-22, -55, -88, and -99 far removed from the heme crevice had nearly the same half-times for the fast phase as native cytochrome c, 6 microseconds.(ABSTRACT TRUNCATED AT 250 WORDS)

Hydrophobic organization of membrane proteins

Membrane-exposed residues are more hydrophobic than buried interior residues in the transmembrane regions of the photosynthetic reaction center from Rhodobacter sphaeroides. This hydrophobic organization is opposite to that of water-soluble proteins. The relative polarities of interior and surface residues of membrane and water soluble proteins are not simply reversed, however. The hydrophobicities of interior residues of both membrane and water-soluble proteins are comparable, whereas the bilayer-exposed residues of membrane proteins are more hydrophobic than the interior residues, and the aqueous-exposed residues of water-soluble proteins are more hydrophilic than the interior residues. A method of sequence analysis is described, based on the periodicity of residue replacement in homologous sequences, that extends conclusions derived from the known atomic structure of the reaction center to the more extensive database of putative transmembrane helical sequences.

Applications of ultrafast laser spectroscopy for the study of biological systems

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.

Linear dichroism of single crystals of the reaction center from Rhodobacter sphaeroides wild type strain 2.4.1

The linear dichroism of single crystals of the photochemical reaction center from Rhodobacter sphaeroides 2.4.1, expressed as the anisotropy (or polarization) ratio, p = (A ‖ - A ⊥)/A ‖ + A ⊥, relative to the long morphological axis of the crystals, has been measured to be -0.12±0.03 for the primary donor Q y and -0.15±0.8 for the carotenoid. These dichroic effects can be predicted using data obtained from magnetophotoselection (Frank et al. 1979, McGann and Frank 1985) and electron spin resonance (ESR)(Frank et al. 1988a, Budil et al. 1988) experiments. Magnetophotoselection data yield the projections of the transition moments onto the primary donor triplet state principal magnetic axis system. The single crystal triplet state ESR experiments provide the Euler matrix for the transformation from the principal magnetic axis system to the crystal unit cell axis system. Thus, the projections of the transition moments (site 1) onto the crystal units cell axes (a, b, c) are determined to be-0.39, 0.90 and 0.18, respectively. The projections of the carotenoid transition moment (site 1) onto the crystal unit cell axes (a, b, c) are determined to be -0.60, 0.02 and 0.80, respectively. This information used in conjunction with the crystalline space group symmetry (P212121) and the morphology of the crystals allows one to predict the observed anisotropy ratios.

An analysis of the periodicity of conserved residues in sequence alignments of G-protein coupled receptors. Implications for the three-dimensional structure

Twenty-three sequences from the family of G-protein coupled receptors have been aligned according to the 'historical alignment' procedure of Feng and Doolittle. Fourier transform analysis of this reveals that parts of five of the seven putative membrane-spanning regions exhibit a periodicity of conserved/nonconserved residues which is compatible with the periodicity of the alpha-helix. This would place the conserved residues on one side of the helix, which may face the inside of the proposed seven membered helical bundle.

Correlation of paramagnetic states and molecular structure in bacterial photosynthetic reaction centers: the symmetry of the primary electron donor in Rhodopseudomonas viridis and Rhodobacter sphaeroides R-26

The orientation of the principal axes of the primary electron donor triplet state measured in single crystals of photosynthetic reaction centers is compared to the x-ray structures of the bacteria Rhodobacter (Rb.) sphaeroides R-26 and Rhodopseudomonas (Rps.) viridis. The primary donor of Rps. viridis is significantly different from that of Rb. sphaeroides. The measured directions of the axes indicate that triplet excitation is almost completely localized on the L-subunit half of the dimer in Rps. viridis but is more symmetrically distributed (approximately 63% on the L half of the special pair and approximately 37% on the M half) on the dimeric donor in Rb. sphaeroides R-26. The large reduction of the zero field splitting parameters relative to monomeric bacteriochlorophyll triplet in vitro suggests significant participation of asymmetrical charge transfer electronic configurations in the special pair triplet state of both organisms (approximately 23% in Rps. viridis and approximately 13% in Rb. sphaeroides).

The primary structure of the Chloroflexus aurantiacus reaction-center polypeptides

The complete nucleotide sequence of two Chloroflexus aurantiacus reaction-center genes has been obtained. The amino acid sequence deduced from the first gene showed 40% similarity to the L subunit of the Rhodobacter sphaeroides reaction center. This L subunit was 310 amino acids long and had an approximate molecular mass of 35 kDa. The second gene began 17 bases downstream from the first gene. The amino acid sequence deduced from it (307 amino acids; 34950 Da) was 42% similar to the M subunit of the Rhodobacter sphaeroides reaction center. 20% of the deduced primary structure were confirmed through automated Edman degradation of cyanogen bromide peptide fragments or N-chlorosuccinimide peptide fragments isolated from the purified reaction-center complex or from the individual subunits. The peptides were isolated by preparative gel electrophoresis combined with molecular sieve chromatography in the presence of a mixture of formic acid, acetonitrile, 2-propanol and water. This method appeared to be applicable to the isolation of other hydrophobic proteins and their peptides.

Measurement of the extent of electron transfer to the bacteriopheophytin in the M-subunit in reaction centers of Rhodopseudomonas viridis

We have measured the extent of flash-induced electron transfer from the bacteriochlorophyll dimer, P, to the bacteriopheophytin in the M-subunit, HM, in reaction centers of Rhodopseudomonas viridis. This has been done by measuring the transient states produced by excitation of reaction centers trapped in the PHL (-)HM state at 90 K. Under these conditions the normal forward electron transfer to the bacteriopheophytin in the L-subunit, HL, is blocked and the yield of transient P(+)HM (-) can be estimated with respect to the lifetime of P(*). Under these conditions flash induced absorbance decreases of the bacteriochlorophyll dimer 990 nm band suggest that a transient P(+) state is formed with a quantum yield of 0.09±0.06 compared to that formed during normal photochemistry. These transient measurements provide an upper limited on the yield of a transient P(+) HM (-) state. An estimate of 0.09 as the yield of the P(+) HM (-) state is consistent with all current observations. This estimate and the lifetime of P(*) suggest that the electron transfer rate from P(*) to HM, kM, is about 5 × 10(9) sec(-1) (τM = 200ps). These measurements suggest that the a branching ratio kL/kM is on the order of 200. The large value of the branching ratio is remarkable in view of the structural symmetry of the reaction center. This measurement should be useful for electron transfer calculations based upon the reaction center structure.

Microscopic simulation of quantum dynamics and nuclear tunneling in bacterial reaction centers

The "dispersed polaron" version of the semiclassical trajectory approach is used to evaluate the quantum mechanical nuclear tunneling effects in the charge recombination reaction, P(+)Q(-)→PQ, in photosynthetic bacterial reaction centers, The cclculations are based on the crystallographic structure of reaction centers from Rhodopseudomonas viridis. They succeed in capturing the temperature dependence of the rate constant without using adjustable parameters. This provides the first example of a microscopic simulation of quantum mechanical nuclear tunneling in a biological system.

Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: symmetry relations and sequence comparisons between different species

Photosynthetic reaction centers from purple bacteria exhibit an approximate twofold symmetry axis, which relates both the cofactors and the L and M subunits. For the reaction center from Rhodobacter sphaeroides, deviations from this twofold symmetry axis have been quantitated by superposing, by a 180 degrees rotation, the cofactors of the B branch onto the A branch and the M subunit onto the L subunit. An alignment of the sequences of the L and M subunits from four purple bacteria, one green bacterium, and the D1 and D2 subunits of a photosystem II-containing green alga is presented. The residues that are conserved in all six species are shown in relation to the structure of Rb. sphaeroides and their possible role in the function of the reaction center is discussed. A method is presented for characterizing the exposure of alpha-helices to the membrane based on the periodicity of conserved residues. This method may prove useful for modeling the three-dimensional structures of membrane proteins.

Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions

The three-dimensional structures of the cofactors and protein subunits of the reaction center (RC) from the carotenoidless mutant strain of Rhodobacter sphaeroides R-26 and the wild-type strain 2.4.1 have been determined by x-ray diffraction to resolutions of 2.8 A and 3.0 A with R values of 24% and 26%, respectively. The bacteriochlorophyll dimer (D), bacteriochlorophyll monomers (B), and bacteriopheophytin monomers (phi) form two branches, A and B, that are approximately related by a twofold symmetry axis. The cofactors are located in hydrophobic environments formed by the L and M subunits. Differences in the cofactor-protein interactions between the A and B cofactors, as well as between the corresponding cofactors of Rb, sphaeroides and Rhodopseudomonas viridis [Michel, H., Epp, O. & Deisenhofer, J. (1986) EMBO J. 3, 2445-2451], are delineated. The roles of several structural features in the preferential electron transfer along the A branch are discussed. Two bound detergent molecules of beta-octyl glucoside have been located near BA and BB. The environment of the carotenoid, C, that is present in RCs from Rb. sphaeroides 2.4.1 consists largely of aromatic residues of the M subunit. A role of BB in the triplet energy transfer from D to C and the reason for the preferential ease of removal of BB from the RC is proposed.

Three-dimensional crystallization of membrane proteins

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres ofRhodopseudomonas viridis(Deisenhoferet al.1984, 1985) and ofRhodobacter sphaeroides(Allenet al.1986, 1987a, 6; Changet al.1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

Structure of the reaction center from Rhodobacter sphaeroides R-26: protein-cofactor (quinones and Fe2+) interactions

The three-dimensional structure of the reaction center (RC) from Rhodobacter sphaeroides has been determined by x-ray diffraction to a resolution of 2.8 A with an R value of 24%. The interactions of the protein with the primary quinone, QA, secondary quinone, QB, and the nonheme iron are described and compared to those of RCs from Rhodopseudomonas viridis. Structural differences between the QA and QB environments that contribute to the function of the quinones (the electron transfer from QA- to QB and the charge recombination of QA-, QB- with the primary donor) are delineated. The protein residues that may be involved in the protonation of QB are identified. A pathway for the doubly reduced QB to dissociate from the RC is proposed. The interactions between QB and the residues that have been changed in herbicide-resistant mutants are described. The environment of the nonheme iron is compared to the environments of metal ions in other proteins.