Reaction Centers Of Purple Bacteria Research Articles

Intraband Exciton Transitions in Photosynthetic Complexes Revealed by Novel Five-Wave-Mixing Spectroscopy.

We calculate the χ(4) optical response of an oriented photosystem II reaction center of purple bacteria described by the Frenkel exciton model using nonlinear exciton equations (NEE). This approach treats each chromophore as an anharmonic oscillator and provides an intuitive quasiparticle picture of nonlinear spectroscopic signals of interacting excitons. It provides a computationally powerful description of nonlinear spectroscopic signals that avoids complete diagonalization of the total Hamiltonian. Expressions for the second- and the fourth-order nonlinear signals are derived. The NEE have been successfully employed in the past to describe even-order-wave-mixing. Here, we extend them to aggregates with broken inversion symmetries. Even-order susceptibilities require the introduction of permanent dipoles, which allow to directly probe low-frequency intraband transitions of excitons.

Excited-State Dynamics of All the Mono-cis and the Major Di-cis Isomers of β-Apo-8'-Carotenal as Revealed by Femtosecond Time-Resolved Transient Absorption Spectroscopy.

Cis isomers of carotenoids play important roles in light harvesting and photoprotection in photosynthetic bacteria, such as the reaction center in purple bacteria and the photosynthetic apparatus in cyanobacteria. Carotenoids containing carbonyl groups are involved in efficient energy transfer to chlorophyll in light-harvesting complexes, and their intramolecular charge-transfer (ICT) excited states are known to be important for this process. Previous studies, using ultrafast laser spectroscopy, have focused on the central-cis isomer of carbonyl-containing carotenoids, revealing that the ICT excited state is stabilized in polar environments. However, the relationship between the cis isomer structure and the ICT excited state has remained unresolved. In this study, we performed steady-state absorption and femtosecond time-resolved absorption spectroscopy on nine geometric isomers (7-cis, 9-cis, 13-cis, 15-cis, 13'-cis, 9,13'-cis, 9,13-cis, 13,13'-cis, and all-trans) of β-apo-8'-carotenal, whose structures are well-defined, and discovered correlations between the decay rate constant of the S1 excited state and the S0-S1 energy gap, as well as between the position of the cis-bend and the degree of stabilization of the ICT excited state. Our results demonstrate that the ICT excited state is stabilized in polar environments in cis isomers of carbonyl-containing carotenoids and suggest that the position of the cis-bend plays an important role in the stabilization of the excited state.

Semi-continuous desulfurization of natural gas in photobioreactor by green sulfur-oxidizing bacterial consortia isolated from hot spring

Anoxygenic phototrophic bacteria are able to oxidize and remove hydrogen sulfide from natural sources by using inorganic substrates and light. In the present study, anoxygenic phototrophic bacteria were isolated from Vartoon hot spring (east of Isfahan Province, Iran) and used for removal of sulfide compounds from natural gas in a semi-continuous photobioreactor. Mat samples that obtained from the depth of spring were introduced into Winogradsky columns and kept in the presence of sunlight for 3–4 months until green and purple layers were composed. The layers were then transferred into mineral medium and incubated under anaerobic condition. The sequence of amplified 16S rDNA in green bacteria and an amplified sequence among the gene encoding photosynthetic reaction center in purple bacteria were used for molecular identification of bacteria. The bacterial growth based on the contents of bacteriochlorophylls and the extent of elemental sulfur production by the cells were measured after ethanol extraction. Molecular identification validated the presence of Chlorobium phaeobacteroides and Prosthecochloris vibrioformis from green sulfur bacteria in the consortium. The results indicated the most increase in bacteriochlorophylls c, d, and e content of mineral medium after bacterial growth. In addition, by releasing 62.4 mmol elemental sulfur, 79.30% increase was detected in sulfur content of the medium during 3 weeks. The consortium of sulfur-oxidizing phototrophic bacteria was potentially used for natural gas desulfurization in the semi-closed photobioreactor. This system is suggested as a replacement for chemoautotrophic systems in areas where there is sufficient access to sunlight.

Evolutionary Loss of the Ability of the Photosystem I Primary Electron Donor for the Redox Interaction with Mn-Bicarbonate Complexes

The structure and functional organization of the photosystem I (PSI) reaction center (RC) donor side has a significant similarity to the reaction centers of purple bacteria (bRCs), despite the fact that they belong to different types of RCs. Moreover, the redox potential values of their primary electron donors are identical (~0.5 V). In our earlier reports [Khorobrykh et al. (2008) Phylos. Trans. R. Soc. B., 363, 1245-1251; Terentyev et al. (2011) Biochemistry (Moscow), 76, 1360-1366; Khorobrykh et al. (2018) ChemBioChem, 14, 1725-1731], we have demonstrated redox interaction of low-potential Mn2+-bicarbonate complexes with bRCs, which might have been one of the first steps in the evolutionary origin of Mn-cluster of the photosystem II water-oxidizing complex that occurred in the Archean (over 3 billion years ago). In this study, we investigated redox interactions between Mn2+-bicarbonate complexes and PSI. Such interactions were almost absent in the original PSI preparations and emerged only in preoxidized PSI preparations containing ~50% oxidized RCs. The interaction between Mn2+-bicarbonate complexes and PSI required increased Mn2+ concentrations, while its dependence on the HCO3- concentration indicated involvement of electroneutral low-potential [Mn(HCO3)2] complex in the process. Analysis of the PSI crystal structure revealed steric hindrances on the RC donor side, which could block the redox interaction between Mn2+-bicarbonate complexes and oxidized primary electron donor. Comparison of structures of RCs from the PSI and ancient RCs from heliobacteria belonging to the same type of RCs suggested that such hindrances should be absent in the primitive PSI in the Archean and allowed to explain their evolutionary origin as a consequence of PSI RCs into the united electron transport chain (ETC) of the photosynthetic membrane that was accompanied by the evolutionary loss of PSI capacity for the redox interaction with Mn2+-bicarbonate complexes.

Features of Bacteriochlorophylls Axial Ligation in the Photosynthetic Reaction Center of Purple Bacteria.

This review focuses on recent experimental data obtained by site-directed mutagenesis of the reaction center in purple nonsulfur bacteria. The role of axial ligation of (bacterio)chlorophylls in the regulation of spectral and redox properties of these pigments, as well as correlation between the structure of chromophores and nature of their ligands, are discussed. Cofactor ligation in various types of reaction centers is compared, and possible reasons for observed differences are examined in the light of modern ideas on the evolution of photosynthesis.

Electrostatic interactions and covalent binding effects on the energy transfer between quantum dots and reaction centers of purple bacteria

The effect of electrostatic interaction and covalent binding on the energy transfer from negatively charged CdSe/CdS/ZnS-COО− and positively charged CdSe/CdS/ZnS-N H3+ quantum dots to reaction centers of Rb. sphaeroides bacteria (RC) in aqueous solutions is reported. The study was performed using optical absorption and steady-state and time resolved luminescence spectroscopies. The experiments were accompanied by theoretic modelling of charge distribution on the RC surface. More effective energy transfer from positively charged QD to RC, as compared with negatively charged QD, was observed. This effect was associated with the different localization of positively and negatively charged QD on the RC surface. The theoretic analysis has demonstrated that the periplasmic RC side is characterized by larger negative charge density as compared with the cytoplasmic side. Therefore, positively charged QD are localized mainly on periplasmic RC side while negatively charged QD are localized on the cytoplasmic RC side. In RC energy acceptors (porphyrins) are localized closer to the periplasmic side. Therefore, the energy transfer efficiency from positively charged QD is higher. The increase in ionic strength equalizes the charge distribution on both RC sides, thus levelling affinity of differently charged QD with RC. Equal energy transfer efficiency for both covalently bound and unbound QD is due to the fact of QD localization on the same RC side. This study demonstrates that for binding of charged QD with RC the electrostatic interaction is principal.

The nature of the lower excited state of the special pair of bacterial photosynthetic reaction center of Rhodobacter Sphaeroides and the dynamics of primary charge separation

Quantum-chemical calculations of the structure in the ground and lower singlet excited states and the vibrations (in the ground state) of special pair P of photosynthetic reaction center of purple bacteria (RCPb) Rhodobacter Sphaeroides, consisting of two bacteriochlorophyll molecules PA and PB, have been carried out. It is shown that excitation of the special pair is followed by fast relaxation dynamics, accompanied by the transformation of the initial P* state into the PAδ+PBδ- state (δ ~ 0.5) with charge separation. This behavior is due to the presence of several nonplanar vibrations with participation of the acetyl group of macrocycle PВ in the nuclear wave packet on the potential surface of the P* state; these vibrations facilitate destabilization of the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) of the macrocycle PA and formation of the PAδ+PBδ- state. The structural transformations in the P* state are due to its linking character in the contact region of the acetyl group-containing pyrrole rings of PA and PB. The transition from the P* state to specifically the PAδ+PBδ- state is related to the fact that the acetyl group PA is involved in the intermolecular hydrogen bond with amino acid residue HisL168; for this reason, this group and the pyrrole ring linked with it can hardly participate in structural transformations. The electronic matrix element Н12 of the electron transfer from the special pair in the PAδ+PBδ- state to a molecule of accessory bacteriochlorophyll ВА greatly exceeds that for the transfer to ВB. This circumstance and the fact that the PAδ+PBδ- state is energetically more favorable than the P* state facilitate the preferred directionality of the electron transfer in RCPb Rhodobacter Sphaeroides with participation of the cofactors located in its subunit L.

Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study.

Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.

The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria.

The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one—to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism.

A Model of Light-Activated Changes in Reaction Centers of Purple Bacteria

We have studied the slow dynamics of isolated complexes of chlorophyll-containing membrane proteins of photosynthetic Reaction Centers (RCs) of Rb. sphaeroides R-26 induced by light fluxes. The analysis of a variation of the absorption of a solution of RCs in the frame of the three-level model is carried out. The equation defining the ratio of the populations of the electron levels of the primary and secondary quinones is deduced. The solution of this equation has non-Boltzmann character even in the stationary case and depends on the exciting light intensity. A model of the dynamics of levels of RC which accounts the presence of polarization processes in the vicinity of the secondary quinone acceptor (QB) is proposed. It is assumed that all RCs have the same structure but can be in different states, whose characteristics depend on both the time interval having passed after the absorption of a light quantum and the local viscosity and elasticity of the environment of QB. The presence of deformational properties of the environment of QB yields the possibility for a configuration of RC to be changed, which agrees with the experimental data.

Non-Markov dissipative dynamics of electron transfer in a photosynthetic reaction center

We consider the dissipative dynamics of electron transfer in the photosynthetic reaction center of purple bacteria and propose a model where the transition between electron states arises only due to the interaction between a chromophore system and the protein environment and is not accompanied by the motion of nuclei of the reaction subsystem. We establish applicability conditions for the Markov approximation in the framework of this model and show that these conditions are not necessarily satisfied in the protein medium. We represent the spectral function of the “system+heat bath” interaction in the form of one or several Gaussian functions to study specific characteristics of non-Markov dynamics of the final state population, the presence of an induction period and vibrations. The consistency of the computational results obtained for non-Markov dynamics with experimental data confirms the correctness of the proposed approach.

The nonheme iron in photosystem II

Photosystem II (PSII), the light-driven water:plastoquinone (PQ) oxidoreductase of oxygenic photosynthesis, contains a nonheme iron (NHI) at its electron acceptor side. The NHI is situated between the two PQs QA and QB that serve as one-electron transmitter and substrate of the reductase part of PSII, respectively. Among the ligands of the NHI is a (bi)carbonate originating from CO2, the substrate of the dark reactions of oxygenic photosynthesis. Based on recent advances in the crystallography of PSII, we review the structure of the NHI in PSII and discuss ideas concerning its function and the role of bicarbonate along with a comparison to the reaction center of purple bacteria and other enzymes containing a mononuclear NHI site.

Calculated Molecular Structures Of Anion Ubiquinone In The Gas Phase, In Solvents And In The Qa Binding Site Of Purple Bacteria Reaction Centers

Structural properties of ubiquinone one anion radical (UQ1-) are studied in the gas phase and in QA binding site of purple bacteria reaction center using Gaussian 03. Polarizable continuum model (PCM) and Our own N-layered quantum mechanics + molecular mechanics (ONIOM) methods have been used to optimize the UQ1- molecule in solvent and in the QA binding site of purple bacteria Rhodobactor sphaeroides reaction centers. The UQ1- molecule exist four equivalent conformations of methoxy groups in the gas phase and solvents. However, all four conformations reduce to one in the QA binding site of the purple bacteria reaction centers. Both carbonyl (C=O) bond lengths are similar in all four conformations in the gas phase and in solvents. However, C4=O bond is slightly longer than C1=O bond in the QA binding site. This result infers that QA binding site impacts asymmetric interaction on the carbonyl groups of the quinone molecule.The Himalayan PhysicsVol. 3, No. 32012Page : 18-23

Quantum differences of ortho/para H2O spin-isomers as a factor of the femtosecond charge separation kinetics modulation in the reaction center of purple bacteria

We have proposed the mechanism of coherent modulations of the P* state in the transient absorption spectra of the reaction center isolated from purple bacteria. Two water molecules, located between special pair, Ba, Bb chlorophylls and histidine L173 and M202, are supposed to be ortho-H2O and para-H2O isomers with different magnetic properties. The distinctive modulation frequencies were labeling as rotational resonances of ortho-H2O. According to our assumption, the interaction of rotational modes of water isomers with the charge-transfer states is a reason of coherent modulations of kinetics. We have modified a Hamiltonian system in order to take into account the rotational modes of ortho-H2O. Evolution of the density matrix was calculated in Liouville space. The Redfield relaxation theory for molecular aggregates was used to model kinetics up to 3 ps.

H2O and D2O spin-isomers as a mediator of the electron transfer in the reaction center of purple bacteria

The dynamics of charge separation states has been numerically simulated in order to calculate the polarization (in the third order of the perturbation theory) and its evolution in a pulsed optical field. Time evolution of the rotational states of the ortho-D2O isomer with a nonzero magnetic momentum and mixed ortho/para-D2O states have been calculated on the basis of the Liouville equation for the density matrix and the Redfield relaxation model for molecular aggregates. Frequencies similar to the known experimental frequencies of the modulation of the kinetics (electron transfer) of the reaction centers special pair in purple bacteria are selected from the set of calculated rotational-resonance frequencies. This semiquantitative coincidence of frequencies (within the experimental error) confirms the previously stated hypothesis, according to which the ortho-H2 O( D 2O) spin isomer can play a role of mediator during electron transfer in the reaction centers of purple bacteria.

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a π-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.

Spectroscopic evidence for the effect of the ortho H2O spin on the electron transfer in photosynthesis

A spin mechanism for electron transfer control in the reaction center of purple bacteria in photosynthesis is proposed. Rotation and conversion of the ortho/para spin isomers of two H2O molecules located near the special pair of the reaction center are treated as the sources of the coherent modulations of transient kinetics. Modulation of the collective wave function of the reaction center electrons by the total proton spin of ortho H2O is a key feature allowing the molecule to play the role of a gate controlling the electron transfer. The iron atom in the reaction center with the gradient magnetic field is treated as a catalyst removing the strict forbiddenness of H2O ortho/para conversion. It is shown that the modulation of the reaction center stimulated emission kinetics observed in the field of femtosecond pulses coincides with the rotational transitions of ortho/para H2O. Influence of the effect of the electric field (Stark effect) on the level displacement and ortho/para conversion rate is discussed.

Diversity of Purple Phototrophic Bacteria, Inferred from <i>pufM</i> Gene, within Epilithic Biofilm in Tama River, Japan

The diversity of purple phototrophic bacteria in algae-dominated biofilm of a streambed in Tama River, Japan was investigated. Clone library analysis of the pufM gene encoding a subunit of the photochemical reaction center of purple bacteria detected 18 operational taxonomic units (OTUs) in several classes of Proteobacteria. Most of the OTUs showed less than 85% identity to the PufM amino acid sequences of known phototrophic bacteria. These results suggest that phylogenetically divergent and unknown purple phototrophic bacteria are present in the epilithic biofilm of the river.

Modeling of photosynthetic light-harvesting: From structure to function

In order to bridge the gap between the crystal structure of photosynthetic pigment-protein complexes and the data gathered in optical experiments, two essential problems need to be solved. On one hand, theories of optical spectra and excitation energy transfer have to be developed that take into account the pigment-pigment (excitonic) and the pigment-protein (exciton-vibrational) coupling on an equal footing. On the other hand, the parameters entering these theories need to be calculated from the structural data. Good agreement between simulations and experimental data then allows to draw conclusions on structure-function relationships of these complexes and to make predictions. In the development of theory, a delicate question is how to describe the interplay between the quantum dynamics of excitons and the dephasing of coherences by the coupling of excitons to protein vibrations. Quantum mechanic coherences are utilized for efficient light harvesting. In the reaction centers of purple bacteria an energy sink is created by a coherent coupling of exciton states to intermolecular charge transfer states. The dephasing of coherences can be monitored, e.g., by the temperature dependent shift of optical lines. In the Fenna-Matthews-Olson protein, which acts as an excitation energy wire between the outer chlorosome antenna and the reaction center complex, an energy funnel for efficient light-harvesting is formed by the pigment-protein coupling. The protein shifts the local transition energies of the pigments, the so-called site energies in a specific way, such that pigments facing the reaction center are redshifted with respect to those on the chlorosome side. In the light-harvesting complex of higher plants an excitation energy funnel is created by the use of two different types of chlorophyll (Chl) pigments, Chla and Chlb and by the pigment-protein coupling that creates an energy sink at Chla 610 located in the stromal layer at the periphery of the complex. The close contact between Chla and Chlb gives rise to ultrafast subpicosecond exciton transfer, whereas dynamic localization effects are inferred to lead to long ps relaxation times between the majority of Chla pigments.

Conformational control of cofactors in nature—functional tetrapyrrole conformations in the photosynthetic reaction centers of purple bacteria

Chemically identical tetrapyrrole cofactors such as hemes and chlorophylls participate in functionally diverse biological roles. An analysis of the available protein structural data for the bacteriochlorophylls in the photosynthetic reaction center gives statistically reliable evidence of the hypothesis that the protein induced cofactor conformation is a modulator of the bio-molecular function of each reaction center. The results serve as a general model to illustrate conformational control of tetrapyrrole cofactors in other proteins.