[Photochemical Processes of Cell DNA Damage by UV Radiation of Various Wavelengths: Biological Consequences].

Photochemical reactions in cell DNA are induced in various organisms by solar UV radiation and may lead to a series of biological responses to DNA damage, including apoptosis, mutagenesis, and carcinogenesis. The chemical nature and the amount of DNA lesions depend on the wavelength of UV radiation. UV type B (UVB, 290-320 nm) causes two main lesions, cyclobutane pyrimidine dimers (CPDs) and, with a lower yield, pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). Their formation is a result of direct UVB photon absorption by DNA bases. UV type A (UVA, 320-400 nm) induces only cyclobutane dimers, which most likely arise via triplet-triplet energy transfer (TTET) from cell chromophores to DNA thymine bases. UVA is much more effective than UVB in inducing sensitized oxidative DNA lesions, such as single-strand breaks and oxidized bases. Of the latter, 8-oxo-dihydroguanine (8-oxodG) is the most frequent, being produced in several oxidation processes. Many recent studies reported novel, more detailed information about the molecular mechanisms of the photochemical reactions that underlie the formation of various DNA lesions. The information is mostly summarized and analyzed in the review. Special attention is paid to the oxidation reactions that are initiated by reactive oxygen species (ROS) and radicals generated by potential endogenous photosensitizers, such as pterins, riboflavin, protoporphyrin IX, NADH, and melanin. The review discusses the role that specific DNA photoproducts play in genotoxic processes induced in living systems by UV radiation of various wavelengths, including human skin carcinogenesis.

Temperature Dependence of Tryptophan Fluorescence Lifetime as an Indicator of Its Microenvironment Dynamics.

The spectral-kinetic characteristics of the fluorescence of the tryptophan molecule in an aqueous solution and in the composition of a protein (albumin) were studied in the temperature range from -170 to 25°C. To explain the observed changes in the spectra and the tryptophan fluorescence lifetime with temperature, a model of transitions between the excited and ground states involving a charge-transfer state was used, which takes into account the nonlinear nature of the dynamics of these transitions. In these processes, an important role is played by the interaction of tryptophan molecules with its microenvironment, as well as rearrangements in the system of hydrogen bonds of the water-protein matrix surrounding the tryptophan molecule.

Model quantification of the light-induced thylakoid membrane processes in Synechocystis sp. PCC 6803 in vivo and after exposure to radioactive irradiation.

Measurements of OJIP-SMT patterns of fluorescence induction (FI) in Synechocystis sp. PCC 6803 (Synechocystis) cells on a time scale up to several minutes were mathematically treated within the framework of thylakoid membrane (T-M) model (Belyaeva et al., Photosynth Res 140:1-19, 2019) that was renewed to account for the state transitions effects. Principles of describing electron transfer in reaction centers of photosystems II and I (PSII and PSI) and cytochrome b6f complex remained unchanged, whereas parameters for dissipative reactions of non-radiative charge recombination were altered depending on the oxidation state of QB-site (neutral, reduced by one electron, empty, reduced by two electrons). According to our calculations, the initial content of plastoquinol (PQH2) in the total quinone pool of Synechocystis cells adapted to darkness for 10 min ranged between 20 and 40%. The results imply that the PQ pool mediates photosynthetic and respiratory charge flows. The redistribution of PBS antenna units responsible for the increase of Chl fluorescence in cyanobacteria (qT2 → 1) upon state 2 → 1 transition or the fluorescence lowering (qT1 → 2) due to state 1 → 2 transition were described in the model by exponential functions. Parameters of dynamically changed effective cross section were found by means of simulations of OJIP-SMT patterns observed on Synechocystis cells upon strong (3000 µmol photons m-2s-1) and moderate (1000 µmol photons m-2s-1) actinic light intensities. The corresponding light constant values kLΣAnt = 1.2 ms-1 and 0.4 ms-1 define the excitation of total antenna pool dynamically redistributed between PSII and PSI reaction centers. Although the OCP-induced quenching of antenna excitation is not involved in the model, the main features of the induction signals have been satisfactorily explained. In the case of strong illumination, the effective cross section decreases by approximately 33% for irradiated Synechocystis cells as compared to untreated cells. Under moderate light, the irradiated Synechocystis cells showed in simulations the same cross section as the untreated cells. The thylakoid model renewed with state transitions description allowed simulation of fluorescence induction OJIP-SMT curves detected on time scale from microseconds to minutes.

Effect of sucrose-bound polynuclear iron oxyhydroxide nanoparticles on the efficiency of electron transport in the photosystem II membranes.

Effect of water-soluble and stable sucrose-bound iron oxyhydroxide nanoparticles [Fe[III] sucrose complex (FSC)] on the efficiency of electron transport in the photosystem II membranes was studied. FSC significantly increases (by a factor 1.5) the rate of light-induced oxygen evolution in the presence of alternative electron acceptor 2,6-dichloro-p-benzoquinone (DCBQ). Without DCBQ, FSC only slightly (5%) provides the oxygen evolution. Electron transport supported by pair DCBQ + FSC is inhibited by diuron. Maximum of stimulating effect was recorded at Fe(III) concentration 5 µM. In the case of another benzoquinone electron acceptor (2-phenyl-p-benzoquinone and 2,3-dimethyl-p-benzoquinone) and 2,6-dichlorophenolindophenol, stimulating effect of FSC was not observed. Incubation of PSII membranes at different concentrations with FSC is accompanied by binding of Fe(III) by membrane components but only about 50% of iron can be extracted by membranes from Fe(III) solution at pH 6.5. This result implies the heterogeneity of FSC solution in a buffer. The heterogeneity depends on pH and decreases with its rising. At pH around 9.0 Fe(III), sucrose solution is homogeneous. The study of pH effect has shown that stimulation of electron transport is induced only by iron cations which can be bound by membranes. Not extractable iron pool cannot activate electron transfer from oxygen-evolving complex to DCBQ.

Analyzing both the fast and the slow phases of chlorophyll a fluorescence and P700 absorbance changes in dark-adapted and preilluminated pea leaves using a Thylakoid Membrane model.

The dark-to-light transitions enable energization of the thylakoid membrane (TM), which is reflected in fast and slow (OJIPSMT or OABCDE) stages of fluorescence induction (FI) and P700 oxidoreduction changes (ΔA810). A Thylakoid Membrane model (T-M model), in which special emphasis has been placed on ferredoxin-NADP+-oxidoreductase (FNR) activation and energy-dependent qE quenching, was applied for quantifying the kinetics of FI and ΔA810. Pea leaves were kept in darkness for 15 min and then the FI and ΔA810 signals were measured upon actinic illumination, applied either directly or after a 10-s light pulse coupled with a subsequent 10-s dark interval. On the time scale from 40 µs to 30 s, the parallel T-M model fittings to both FI and ΔA810 signals were obtained. The parameters of FNR activation and the buildup of qE quenching were found to differ for dark-adapted and preilluminated leaves. At the onset of actinic light, photosystem II (PSII) acceptors were oxidized (neutral) after dark adaptation, while the redox states with closed and/or semiquinone QA(-)QB(-) forms were supposedly generated after preillumination, and did not relax within the 10 s dark interval. In qE simulations, a pH-dependent Hill relationship was used. The rate constant of heat losses in PSII antenna kD(t) was found to increase from the basic value kDconst, at the onset of illumination, to its maximal level kDvar due to lumenal acidification. In dark-adapted leaves, a low value of kDconst of ∼ 2 × 106 s-1 was found. Simulations on the microsecond to 30 s time scale revealed that the slow P-S-M-T phases of the fluorescence induction were sensitive to light-induced FNR activation and high-energy qE quenching. Thus, the corresponding time-dependent rate constants kD(t) and kFNR(t) change substantially upon the release of electron transport on the acceptor side of PSI and during the NPQ development. The transitions between the cyclic and linear electron transport modes have also been quantified in this paper.

Intramolecular Mobility Affects the Energy Migration from Quantum Dots to Reaction Centers of Photosynthesizing Bacterium Rb. sphaeroides.

The temperature dependence of the efficiency of energy migration from the CdSe/CdS/ZnS quantum dots (QDs) with a fluorescence maximum at 580 nm to the reaction centers (RCs) of the bacteria Rb. sphaeroides is practically constant over the temperature range from 100 to ~230-240 K but then decreases 2.5-3 times as temperature further increases to 310 K. The analysis on this dependence on the basis of Förster's theory showed that the major changes in the energy transfer efficiency are associated with the temperature change in the quantum yield of QD fluorescence, which is due to the activation of intramolecular mobility in the RC structure.

Simulation of chlorophyll fluorescence rise and decay kinetics, and P700-related absorbance changes by using a rule-based kinetic Monte-Carlo method.

A model of primary photosynthetic reactions in the thylakoid membrane was developed and its validity was tested by simulating three types of experimental kinetic curves: (1) the light-induced chlorophyll a fluorescence rise (OJIP transients) reflecting the stepwise transition of the photosynthetic electron transport chain from the oxidized to the fully reduced state; (2) the dark relaxation of the flash-induced fluorescence yield attributed to the QA- oxidation kinetics in PSII; and (3) the light-induced absorbance changes near 820 or 705 nm assigned to the redox transitions of P700 in PSI. A model was implemented by using a rule-based kinetic Monte-Carlo method and verified by simulating experimental curves under different treatments including photosynthetic inhibitors, heat stress, anaerobic conditions, and very high light intensity.

Generation of radical form of dipyridamole at illumination of photosynthetic reaction centers of Rb. sphaeroides.

The study of the effect of vasodilator, antiplatelet agent, and inhibitor P-glycoprotein dipyridamole (DIP) on the functioning of the transmembrane protein of the reaction center (RC) of Rb. sphaeroides showed that the activation of RC by constant light generates the DIP radical cation, which significantly affects the kinetics of recombination of charges divided between photoactive bacteriochlorophyll and quinone acceptors. Thus, the antioxidant properties of DIP may affect the functional activity of membrane proteins, and this apparently should be taken into account in the studies of the mechanisms of therapeutic action of this drug.

Influence of trehalose on high-temperature stability of the photosynthetic reaction centers.

The effect of heating at 65°C for 20 min on the absorption spectra and kinetics of the dark recombination of charges separated between photoactive bacteriochlorophyll and quinone acceptors was studied in dry films of bacterial photosynthetic reaction centers (RCs), RC films in polyvinyl alcohol, and trehalose. A pronounced protective effect of trehalose against pheophytinizaiton of molecules bacteriochlorophylls in RC structure and in maintaining their higher photochemical activity was found.

Thylakoid membrane model of the Chl a fluorescence transient and P700 induction kinetics in plant leaves.

A new Thylakoid model is presented, which describes in detail the electron/proton transfer reactions between membrane protein complexes including photosystems II and I (PSII, PSI), cytochrome (Cyt) b 6 f, mobile plastoquinone PQ pool in the thylakoid membrane, plastocyanin in lumen and ferredoxin in stroma, reduction of NADP via FNR and cyclic electron transfer. The Thylakoid model parameters were fitted both to Chl fluorescence induction data (FI) and oxido-reductions of P700 (ΔA 810) measured from 20 µs up to 20 s in pea leaves. The two-wave kinetics of FI and ΔA 810 (O(JI)PSM and OABCDE) were described quantitatively, provided that the values of membrane electrochemical potential components ΔΨ(t), pHL(t)/pHS(t) are in physiologically relevant ranges. The time courses on the time scale from nanoseconds to tens of seconds of oxido-reduction changes of ET components as well as concentrations of proton/ions (K+, Cl-) were calculated. We assume a low constant FNR activity over this period. Charge movements across the thylakoid membrane by passive leakage and active ATPase transport and proton buffer reactions are simulated. The dynamics of charge fluxes during photosynthetic induction under low light (PFD 200 µmol photons m-2 s-1) were analyzed. The initial wave of P700 oxidation within 20 ms during independent operation of PSI and PSII was followed after 50 ms by PSI donor-side reduction from reduced PQ pool via Cyt b 6 f site. The Cyt b 6 f reactions contribute to the stabilization of fluxes in the time range 1 s < t < 10 s. The detailed analysis of Chl a fluorescence at the PSM stage (t > 10 s) would need the investigation of FNR activation effect in order to explain the transitions between cyclic and linear electron transport.

A comparative study of three signaling forms of the orange carotenoid protein.

Orange carotenoid protein (OCP) is a water-soluble photoactive protein responsible for a photoprotective mechanism of nonphotochemical quenching in cyanobacteria. Under blue-green illumination, OCP converts from the stable orange into the signaling red quenching form; however, the latter form could also be obtained by chemical activation with high concentrations of sodium thiocyanate (NaSCN) or point mutations. In this work, we show that a single replacement of tryptophan-288, normally involved in protein-chromophore interactions, by alanine, results in formation of a new protein form, hereinafter referred to as purple carotenoid protein (PCP). Comparison of resonance Raman spectra of the native photoactivated red form, chemically activated OCP, and PCP reveals that carotenoid conformation is sensitive to the structure of the C-domain, implicating that the chromophore retains some interactions with this part of the protein in the active red form. Combination of differential scanning fluorimetry and picosecond time-resolved fluorescence anisotropy measurements allowed us to compare the stability of different OCP forms and to estimate relative differences in protein rotation rates. These results were corroborated by hydrodynamic analysis of proteins by dynamic light scattering and analytical size-exclusion chromatography, indicating that the light-induced conversion of the protein is accompanied by a significant increase in its size. On the whole, our data support the idea that the red form of OCP is a molten globule-like protein in which, however, interactions between the carotenoid and the C-terminal domain are preserved.

Influence of pH and ionic strength on electrostatic properties of ferredoxin, FNR, and hydrogenase and the rate constants of their interaction.

Ferredoxin (Fd) protein transfers electrons from photosystem I (PSI) to ferredoxin:NADP+-reductase (FNR) in the photosynthetic electron transport chain, as well as other metabolic pathways. In some photosynthetic organisms including cyanobacteria and green unicellular algae under anaerobic conditions Fd transfers electrons not only to FNR but also to hydrogenase-an enzyme which catalyzes reduction of atomic hydrogen to H2. One of the questions posed by this competitive relationship between proteins is which characteristics of thylakoid stroma media allow switching of the electron flow between the linear path PSI-Fd-FNR-NADP+ and the path PSI-Fd-hydrogenase-H2. The study was conducted using direct multiparticle simulation approach. In this method protein molecules are considered as individual objects that experience Brownian motion and electrostatic interaction with the surrounding media and each other. Using the model we studied the effects of pH and ionic strength (I) upon complex formation between ferredoxin and FNR and ferredoxin and hydrogenase. We showed that the rate constant of Fd-FNR complex formation is constant in a wide range of physiologically significant pH values. Therefore it can be argued that regulation of FNR activity doesn't involve pH changes in stroma. On the other hand, in the model rate constant of Fd-hydrogenase interaction dramatically depends upon pH: in the range 7-9 it increases threefold. It may seem that because hydrogenase reduces protons it should be more active when pH is acidic. Apparently, regulation of hydrogenase's affinity to both her reaction partners (H+ and Fd) is carried out by changes in its electrostatic properties. In the dark, the protein is inactive and in the light it is activated and starts to interact with both Fd and H+. Therefore, we can conclude that in chloroplasts the rate of hydrogen production is regulated by pH through the changes in the affinity between hydrogenase and ferredoxin.

The role of electrostatic interactions in the process of diffusional encounter and docking of electron transport proteins.

Electrostatic interaction of plastocyanin and cytochrome f in the process of protein-protein complex formation was investigated by computer simulation methods. It was shown that long-range electrostatic interaction promotes energetically favorable mutual orientation of protein molecules at distances between their cofactors shorter than 5 nm. At distances shorter than 3 nm, these electrostatic interactions lead to a significantly detectable increase in the rate of convergence of the cofactors.

Temperature dependence of protein fluorescence in Rb. sphaeroides reaction centers frozen to 80 K in the dark or on the actinic light as the indicator of protein conformational dynamics.

The differences in the average fluorescence lifetime (τav) of tryptophanyls in photosynthetic reaction center (RC) of the purple bacteria Rb. sphaeroides frozen to 80 K in the dark or on the actinic light was found. This difference disappeared during subsequent heating at the temperatures above 250 K. The computer-based calculation of vibration spectra of the tryptophan molecule was performed. As a result, the normal vibrational modes associated with deformational vibrations of the aromatic ring of the tryptophan molecule were found. These deformational vibrations may be active during the nonradiative transition of the molecule from the excited to the ground state. We assume that the differences in τav may be associated with the change in the activity of these vibration modes due to local variations in the microenvironment of tryptophanyls during the light activation.

The time course of non-photochemical quenching in phycobilisomes of Synechocystis sp. PCC6803 as revealed by picosecond time-resolved fluorimetry.

As high-intensity solar radiation can lead to extensive damage of the photosynthetic apparatus, cyanobacteria have developed various protection mechanisms to reduce the effective excitation energy transfer (EET) from the antenna complexes to the reaction center. One of them is non-photochemical quenching (NPQ) of the phycobilisome (PB) fluorescence. In Synechocystis sp. PCC6803 this role is carried by the orange carotenoid protein (OCP), which reacts to high-intensity light by a series of conformational changes, enabling the binding of OCP to the PBs reducing the flow of energy into the photosystems. In this paper the mechanisms of energy migration in two mutant PB complexes of Synechocystis sp. were investigated and compared. The mutant CK is lacking phycocyanin in the PBs while the mutant ΔPSI/PSII does not contain both photosystems. Fluorescence decay spectra with picosecond time resolution were registered using a single photon counting technique. The studies were performed in a wide range of temperatures - from 4 to 300 K. The time course of NPQ and fluorescence recovery in darkness was studied at room temperature using both steady-state and time-resolved fluorescence measurements. The OCP induced NPQ has been shown to be due to EET from PB cores to the red form of OCP under photon flux densities up to 1000 µmolphotonsm⁻²s⁻¹. The gradual changes of the energy transfer rate from allophycocyanin to OCP were observed during the irradiation of the sample with blue light and consequent adaptation to darkness. This fact was interpreted as the revelation of intermolecular interaction between OCP and PB binding site. At low temperatures a significantly enhanced EET from allophycocyanin to terminal emitters has been shown, due to the decreased back transfer from terminal emitter to APC. The activation of OCP not only leads to fluorescence quenching, but also affects the rate constants of energy transfer as shown by model based analysis of the decay associated spectra. The results indicate that the ability of OCP to quench the fluorescence is strongly temperature dependent. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

Modeling of the redox state dynamics in photosystem II of Chlorella pyrenoidosa Chick cells and leaves of spinach and Arabidopsis thaliana from single flash-induced fluorescence quantum yield changes on the 100 ns-10 s time scale.

The time courses of the photosystem II (PSII) redox states were analyzed with a model scheme supposing a fraction of 11-25 % semiquinone (with reduced [Formula: see text]) RCs in the dark. Patterns of single flash-induced transient fluorescence yield (SFITFY) measured for leaves (spinach and Arabidopsis (A.) thaliana) and the thermophilic alga Chlorella (C.) pyrenoidosa Chick (Steffen et al. Biochemistry 44:3123-3132, 2005; Belyaeva et al. Photosynth Res 98:105-119, 2008, Plant Physiol Biochem 77:49-59, 2014) were fitted with the PSII model. The simulations show that at high-light conditions the flash generated triplet carotenoid (3)Car(t) population is the main NPQ regulator decaying in the time interval of 6-8 µs. So the SFITFY increase up to the maximum level [Formula: see text]/F 0 (at ~50 µs) depends mainly on the flash energy. Transient electron redistributions on the RC redox cofactors were displayed to explain the SFITFY measured by weak light pulses during the PSII relaxation by electron transfer (ET) steps and coupled proton transfer on both the donor and the acceptor side of the PSII. The contribution of non-radiative charge recombination was taken into account. Analytical expressions for the laser flash, the (3)Car(t) decay and the work of the water-oxidizing complex (WOC) were used to improve the modeled P680(+) reduction by YZ in the state S 1 of the WOC. All parameter values were compared between spinach, A. thaliana leaves and C. pyrenoidosa alga cells and at different laser flash energies. ET from [Formula: see text] slower in alga as compared to leaf samples was elucidated by the dynamics of [Formula: see text] fractions to fit SFITFY data. Low membrane energization after the 10 ns single turnover flash was modeled: the ∆Ψ(t) amplitude (20 mV) is found to be about 5-fold smaller than under the continuous light induction; the time-independent lumen pHL, stroma pHS are fitted close to dark estimates. Depending on the flash energy used at 1.4, 4, 100 % the pHS in stroma is fitted to 7.3, 7.4, and 7.7, respectively. The biggest ∆pH difference between stroma and lumen was found to be 1.2, thus pH- dependent NPQ was not considered.

ESR - a retinal protein with unusual properties from Exiguobacterium sibiricum.

This review covers the properties of a retinal protein (ESR) from the psychrotrophic bacterium Exiguobacterium sibiricum that functions as a light-driven proton pump. The presence of a lysine residue at the position corresponding to intramolecular proton donor for the Schiff base represents a unique structural feature of ESR. We have shown that Lys96 successfully facilitates delivery of protons from the cytoplasmic surface to the Schiff base, thus acting as a proton donor in ESR. Since proton uptake during the photocycle precedes Schiff base reprotonation, we conclude that this residue is initially in the uncharged state and acquires a proton for a short time after Schiff base deprotonation and M intermediate formation. Involvement of Lys as a proton donor distinguishes ESR from the related retinal proteins - bacteriorhodopsin (BR), proteorhodopsin (PR), and xanthorhodopsin (XR), in which the donor function is performed by residues with a carboxyl side chain. Like other eubacterial proton pumps (PR and XR), ESR contains a histidine residue interacting with the proton acceptor Asp85. In contrast to PR, this interaction leads to shift of the acceptor's pKa to more acidic pH, thus providing its ability to function over a wide pH range. The presence of a strong H-bond between Asp85 and His57, the structure of the proton-conducting pathways from cytoplasmic surface to the Schiff base and to extracellular surface, and other properties of ESR were demonstrated by solving its three-dimensional structure, which revealed several differences from known structures of BR and XR. The structure of ESR, its photocycle, and proton transfer reactions are discussed in comparison with homologous retinal proteins.

[Analysis of Chlorophyll Fluorescence Transient by Spectral Multi-exponential Approximation].

The method for analysis of chlorophyll fluorescence transient using approximation of measured signal by multi-exponential series is described. Visualization of partial sums of this series allows us to find amplitudes and characteristic times of individual phases of fluorescence induction curve. This method gives more rigid criteria of phase identification instead of semi-empirical approach currently used. Applied to Chlamidomonas reinhardtii sulfur deprivation case, it shows efficiency in finding visually undistinguishable phases of fluorescence transient for early detection of stress.

[Identification of Intermediate States of Electron Transfer Proteins Plastocyanin and Cytochrome f in the Process of Diffusional Encounter].

The Brownian dynamics method is used for qualitative analysis of events leading to formation of a functionally active plastocyanin-cytochrome f complex. Intermediate states of this process are identified by density-based hierarchical clustering. Diffusive entrapment of plastocyanin by cytochrome f is a key point of the suggested putative scenario of protein-protein approaching. Mobility of plastocyanin is characterized for different values of protein-protein electrostatic interaction energy.

[Brownian dynamics simulations of protein-protein interactions in photosynthetic electron transport chain].

The application of Brownian dynamics for simulation of transient protein-protein interactions is reviewed. The review focuses on theoretical basics of Brownian dynamics method, its particular implementations, advantages and drawbacks of the method. The outlook for future development of Brownian dynamics-based simulation techniques is discussed. Special attention is given to analysis of Brownian dynamics trajectories. The second part of the review is dedicated to the role of Brownian dynamics simulations in studying photosynthetic electron transport. Interactions of mobile electron carriers (plastocyanin, cytochrome c6, and ferredoxin) with their reaction partners (cytochrome b6f complex, photosystem I, ferredoxin:NADP-reductase, and hydrogenase) are considered.