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Organization of campsites construction for auto tourists in Russia is an effective means of ensuring their rest and sleep during travel. Formation of normative and methodological support of campsites fire safety should take into account not only security, but also meet consumers' motivation to visit them. The authors examine conditions and requirements for the infrastructure of campsites and their localization, as well as methods of fire risk assessment in camping. They propose camping localization techniques and expert evaluation of fire risk in them.

In this study, the vibrational characteristics of optically excited echinenone in various solvents and the Orange Carotenoid Protein (OCP) in red and orange states are systematically investigated through steady-state and time-resolved spectroscopy techniques. Time-resolved experiments, employing both Transient Absorption (TA) and Femtosecond Stimulated Raman Spectroscopy (FSRS), reveal different states in the OCP photoactivation process. The time-resolved studies indicate vibrational signatures of exited states positioned above the S 1 state during the initial 140 fs of carotenoid evolution in OCP, an absence of a vibrational signature for the relaxed S 1 state of echinenone in OCP, and more robust signatures of a highly excited ground state (GS) in OCP. Differences in S 1 state vibration population signatures between OCP and solvents are attributed to distinct conformations of echinenone in OCP and hydrogen bonds at the keto group forming a short-lived intramolecular charge transfer (ICT) state. The vibrational dynamics of the hot GS in OCP show a more pronounced red shift of ground state CC vibration compared to echinenone in solvents, thus suggesting an unusually hot form of GS. The study proposes a hypothesis for the photoactivation mechanism of OCP, emphasizing the high level of vibrational excitation in longitudinal stretching modes as a driving force. In conclusion, the comparison of vibrational signatures reveals unique dynamics of energy dissipation in OCP, providing insights into the photoactivation mechanism and highlighting the impact of the protein environment on carotenoid behavior. The study underscores the importance of vibrational analysis in understanding the intricate processes involved in early phase OCP photoactivation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Primary processes of light energy conversion by Photosystem II (PSII) were studied using femtosecond broadband pump-probe absorption difference spectroscopy. Transient absorption changes of core complexes isolated from the cyanobacterium Synechococcus sp. PCC 7335 grown under far-red light (FRL-PSII) were compared with the canonical Chl a containing spinach PSII core complexes upon excitation into the red edge of the Q y band. Absorption changes of FRL-PSII were monitored at 278 K in the 400-800 nm spectral range on a timescale of 0.1-500 ps upon selective excitation at 740 nm of four chlorophyll (Chl) f molecules in the light harvesting antenna, or of one Chl d molecule at the Chl D1 position in the reaction center (RC) upon pumping at 710 nm. Numerical analysis of absorption changes and assessment of the energy levels of the presumed ion-radical states made it possible to identify P D1 + Chl D1 - as the predominant primary charge-separated radical pair, the formation of which upon selective excitation of Chl d has an apparent time of ∼1.6 ps. Electron transfer to the secondary acceptor pheophytin Pheo D1 has an apparent time of ∼7 ps with a variety of excitation wavelengths. The energy redistribution between Chl a and Chl f in the antenna occurs within 1 ps, whereas the energy migration from Chl f to the RC occurs mostly with lifetimes of 60 and 400 ps. Potentiometric analysis suggests that in canonical PSII, P D1 + Chl D1 - can be partially formed from the excited (P D1 Chl D1 )* state., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Primary excitation energy transfer and charge separation in photosystem I (PSI) from the extremophile desert green alga Chlorella ohadii grown in low light were studied using broadband femtosecond pump-probe spectroscopy in the spectral range from 400 to 850 nm and in the time range from 50 fs to 500 ps. Photochemical reactions were induced by the excitation into the blue and red edges of the chlorophyll Qy absorption band and compared with similar processes in PSI from the cyanobacterium Synechocystis  sp. PCC 6803. When PSI from C. ohadii was excited at 660 nm, the processes of energy redistribution in the light-harvesting antenna complex were observed within a time interval of up to 25 ps, while formation of the stable radical ion pair P 700 + A 1 - was kinetically heterogeneous with characteristic times of 25 and 120 ps. When PSI was excited into the red edge of the Qy band at 715 nm, primary charge separation reactions occurred within the time range of 7 ps in half of the complexes. In the remaining complexes, formation of the radical ion pair P 700 + A 1 - was limited by the energy transfer and occurred with a characteristic time of 70 ps. Similar photochemical reactions in PSI from Synechocystis  6803 were significantly faster: upon excitation at 680 nm, formation of the primary radical ion pairs occurred with a time of 3 ps in ~30% complexes. Excitation at 720 nm resulted in kinetically unresolvable ultrafast primary charge separation in 50% complexes, and subsequent formation of P 700 + A 1 - was observed within 25 ps. The photodynamics of PSI from C. ohadii was noticeably similar to the excitation energy transfer and charge separation in PSI from the microalga Chlamydomonas reinhardtii ; however, the dynamics of energy transfer in C. ohadii PSI also included slower components.

The exciton interaction of four chlorophyll a (Chl a) molecules in a symmetrical tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP was analyzed in the pH range of 3-11. Exciton splitting ΔE = 232 ± 2 cm -1 of the Q y band of Chl a into two subcomponents with relative intensities of 78.1 ± 0.7 % and 21.9 ± 0.7 % was determined by a joint decomposition of the absorption and circular dichroism spectra into Gaussian functions. The exciton coupling parameters were calculated based on the BoWSCP atomic structure in three approximations: the point dipole model, the distributed atomic monopoles, and direct ab initio calculations in the TDDFT/PCM approximation. The Coulomb interactions of monomers were calculated within the continuum model using three values of optical permittivity. The models based on the properties of free Chl a in solution suffer from significant errors both in estimating the absolute value of the exciton interaction and in the relative intensity of exciton transitions. Calculations within the TDDFT/PCM approximation reproduce the experimentally determined parameters of the exciton splitting and the relative intensities of the exciton bands. The following factors of pigment-protein and pigment-pigment interactions were examined: deviation of the macrocycle geometry from the planar conformation of free Chl; the formation of hydrogen bonds between the macrocycle and water molecules; the overlap of wave functions of monomers at close distances. The most significant factor is the geometrical deformation of the porphyrin macrocycle, which leads to an increase in the dipole moment of Chl monomer from 5.5 to 6.9 D and to a rotation of the dipole moment by 15° towards the cyclopentane ring. The contributions of resonant charge-transfer states to the wave functions of the Chl dimer were determined and the transition dipole moments of the symmetric and antisymmetric charge-transfer states were estimated., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Phycobilisomes (PBSs) are giant water-soluble light-harvesting complexes of cyanobacteria and red algae, consisting of hundreds of phycobiliproteins precisely organized to deliver the energy of absorbed light to chlorophyll chromophores of the photosynthetic electron-transport chain. Quenching the excess of excitation energy is necessary for the photoprotection of photosynthetic apparatus. In cyanobacteria, quenching of PBS excitation is provided by the Orange Carotenoid Protein (OCP), which is activated under high light conditions. In this work, we describe parameters of anti-Stokes fluorescence of cyanobacterial PBSs in quenched and unquenched states. We compare the fluorescence readout from entire phycobilisomes and their fragments. The obtained results revealed the heterogeneity of conformations of chromophores in isolated phycobiliproteins, while such heterogeneity was not observed in the entire PBS. Under excitation by low-energy quanta, we did not detect a significant uphill energy transfer from the core to the peripheral rods of PBS, while the one from the terminal emitters to the bulk allophycocyanin chromophores is highly probable. We show that this direction of energy migration does not eliminate fluorescence quenching in the complex with OCP. Thus, long-wave excitation provides new insights into the pathways of energy conversion in the phycobilisome., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The paper reports on the absorption dynamics of chlorophyll a in a symmetric tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP. It was measured by a broadband femtosecond laser pump-probe spectroscopy within the range from 400 to 750 nm and with a time resolution of 20 fs-200 ps. When BoWSCP was excited in the region of the Soret band at a wavelength of 430 nm, nonradiative intramolecular conversion S 3 →S 1 was observed with a characteristic time of 83 ± 9 fs. When the complex was excited in the region of the Q y band at 670 nm, relaxation transition between two excitonic states of the chlorophyll dimer was observed in the range of 105 ± 10 fs. Absorption spectra of the excited singlet states S 1 and S 3 of chlorophyll a were obtained. The delocalization of the excited state between exciton-coupled Chl molecules in BoWSCP tetramer changed in time and depended on the excitation energy. When BoWSCP is excited in the Soret band region, an ultrafast photochemical reaction is observed. This could result from the reduction of tryptophan in the vicinity of chlorophyll.

Photosystem I (PSI) of the cyanobacterium Acaryochloris marina is capable of performing an efficient photoelectrochemical conversion of far-red light due to its unique suite of cofactors. Chlorophyll d (Chl-d) has been long known as the major antenna pigment in the PSI from A. marina, while the exact cofactor composition of the reaction centre (RC) was established only recently by cryo-electron microscopy. The RC consists of four Chl-d molecules, and, surprisingly, two molecules of pheophytin a (Pheo-a), which provide a unique opportunity to resolve, spectrally and kinetically, the primary electron transfer reactions. Femtosecond transient absorption spectroscopy was here employed to observe absorption changes in the 400-860 nm spectral window occurring in the 0.1-500 ps timescale upon unselective antenna excitation and selective excitation of the Chl-d special pair P 740 in the RC. A numerical decomposition of the absorption changes, including principal component analysis, allowed the identification of P 740 (+) Chl d2 (-) as the primary charge separated state and P 740 (+) Pheo a3 (-) as the successive, secondary, radical pair. A remarkable feature of the electron transfer reaction between Chl d2 and Pheo a3 is the fast, kinetically unresolved, equilibrium with an estimated ratio of 1:3. The energy level of the stabilised ion-radical state P 740 (+) Pheo a3 (-) was determined to be ~60 meV below that of the RC excited state. In this regard, the energetics and the structural implications of the presence of Pheo-a in the electron transfer chain of PSI from A. marina are discussed, also in comparison with those of the most diffused Chl-a binding RC., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Most cyanobacteria utilize a water-soluble Orange Carotenoid Protein (OCP) to protect their light-harvesting complexes from photodamage. The Fluorescence Recovery Protein (FRP) is used to restore photosynthetic activity by inactivating OCP via dynamic OCP-FRP interactions, a multistage process that remains underexplored. In this work, applying time-resolved spectroscopy, we demonstrate that the interaction of FRP with the photoactivated OCP begins early in the photocycle. Interacting with the compact OCP state, FRP completely prevents the possibility of OCP domain separation and formation of the signaling state capable of interacting with the antenna. The structural element that prevents FRP binding and formation of the complex is the short α-helix at the beginning of the N-terminal domain of OCP, which masks the primary site in the C-terminal domain of OCP. We determined the rate of opening of this site and show that it remains exposed long after the relaxation of the red OCP states. Observations of the OCP transitions on the ms time scale revealed that the relaxation of the orange photocycle intermediates is accompanied by an increase in the interaction of the carotenoid keto group with the hydrogen bond donor tyrosine-201. Our data refine the current model of photoinduced OCP transitions and the interaction of its intermediates with FRP.

Transient absorption dynamics of chlorophylls a and d dissolved in tetrahydrofuran was measured by the broadband femtosecond laser pump-probe spectroscopy in a spectral range from 400 to 870 nm. The absorption spectra of the excited S 1 singlet states of chlorophylls a and d were recorded, and the dynamics of the of the Q y band shift of the stimulated emission (Stokes shift of fluorescence) was determined in a time range from 60 fs to 4 ps. The kinetics of the intramolecular conversion Q x →Q y (electronic transition S 2 →S 1 ) was measured; the characteristic relaxation time was 54 ± 3 and 45 ± 9 fs for chlorophylls a and d, respectively.

This review analyzes new data on the mechanism of ultrafast reactions of primary charge separation in photosystem I (PS I) of cyanobacteria obtained in the last decade by methods of femtosecond absorption spectroscopy. Cyanobacterial PS I from many species harbours 96 chlorophyll a (Chl a ) molecules, including six specialized Chls denoted Chl 1A /Chl 1B (dimer P 700 , or P A P B ), Chl 2A /Chl 2B , and Chl 3A /Chl 3B arranged in two branches, which participate in electron transfer reactions. The current data indicate that the primary charge separation occurs in a symmetric exciplex, where the special pair P 700 is electronically coupled to the symmetrically located monomers Chl 2A and Chl 2B , which can be considered together as a symmetric exciplex Chl 2A P A P B Chl 2B with the mixed excited (Chl 2A P A P B Chl 2B ) * and two charge-transfer states P 700 + Chl 2A - and P 700 + Chl 2B - . The redistribution of electrons between the branches in favor of the A -branch occurs after reduction of the Chl 2A and Chl 2B monomers. The formation of charge-transfer states and the symmetry breaking mechanisms were clarified by measuring the electrochromic Stark shift of β-carotene and the absorption dynamics of PS I complexes with the genetically altered Chl 2B or Chl 2A monomers. The review gives a brief description of the main methods for analyzing data obtained using femtosecond absorption spectroscopy. The energy levels of excited and charge-transfer intermediates arising in the cyanobacterial PS I are critically analyzed., Competing Interests: Conflict of interestThe authors have no relevant financial or non-financial interests to disclose., (© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Femtosecond absorption spectroscopy of Photosystem I (PS I) complexes from the cyanobacterium Synechocystis sp. PCC 6803 was carried out on three pairs of complementary amino acid substitutions located near the second pair of chlorophyll molecules Chl 2A and Chl 2B (also termed A -1A and A -1B ). The absorption dynamics at delays of 0.1-500 ps were analyzed by decomposition into discrete decay-associated spectra and continuously distributed exponential components. The multi-exponential deconvolution of the absorption changes revealed that the electron transfer reactions in the PsaA-N600M, PsaA-N600H, and PsaA-N600L variants near the B-branch of cofactors are similar to those of the wild type, while the PsaB-N582M, PsaB-N582H, and PsaB-N582L variants near the A-branch of cofactors cause significant alterations of the photochemical processes, making them heterogeneous and poorly described by a discrete exponential kinetic model. A redistribution of the unpaired electron between the second and the third monomers Chl 2A /Chl 2B and Chl 3A /Chl 3B was identified in the time range of 9-20 ps, and the subsequent reduction of A 1 was identified in the time range of 24-70 ps. In the PsaA-N600L and PsaB-N582H/L variants, the reduction of A 1  occurred with a decreased quantum yield of charge separation. The decreased quantum yield correlates with a slowing of the phylloquinone A 0  → A 1 reduction, but not with the initial transient spectra measured at the shortest time delay. The results support a branch competition model, where the electron is sheared between Chl 2A -Chl 3A and Chl 2B -Chl 3B cofactors before its transfer to phylloquinone in either A 1A or A 1B sites., (© 2021. The Author(s), under exclusive licence to European Photochemistry Association, European Society for Photobiology.)

Despite the high level of symmetry between the PsaA and PsaB polypeptides in Photosystem I, some amino acids pairs are strikingly different, such as PsaA-Gly693 and PsaB-Trp673, which are located near a cluster of 11 water molecules between the A 1A and A 1B quinones and the F X iron-sulfur cluster. In this work, we changed PsaB-Trp673 to PsaB-Phe673 in Synechocystis sp. PCC 6803. The variant contains ~ 85% of wild-type (WT) levels of Photosystem I but is unable to grow photoautotrophically. Both time-resolved and steady-state optical measurements show that in the PsaB-W673F variant less than 50% of the electrons reach the terminal iron-sulfur clusters F A and F B ; the majority of the electrons recombine from A 1A - and A 1B - . However, in those reaction centers which pass electrons forward the transfer is heterogeneous: a minor population shows electron transfer rates from A 1A - and A 1B - to F X slightly slower than that of the WT, whereas a major population shows forward electron transfer rates to F X slowed to the ~ 10 µs time range. Competition between relatively similar forward and backward rates of electron transfer from the quinones to the F X cluster account for the relatively low yield of long-lived charge separation in the PsaB-W673F variant. A higher water content and its increased mobility observed in MD simulations in the interquinone cavity of the PsaB-W673F variant shifts the pK of PsaB-Asp575 and allows its deprotonation in situ. The heterogeneity found may be rooted in protonation state of PsaB-Asp575, which controls whether electron transfer can proceed beyond the phylloquinone cofactors., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion.

In Photosystem I (PS I), the role of the accessory chlorophyll (Chl) molecules, Chl 2A and Chl 2B (also termed A -1A and A -1B ), which are directly adjacent to the special pair P 700 and fork into the A- and B-branches of electron carriers, is incompletely understood. In this work, the Chl 2A and Chl 2B transient absorption ΔA 0 (λ) at a time delay of 100 fs was identified by ultrafast pump-probe spectroscopy in three pairs of PS I complexes from Synechocystis sp. PCC 6803 with residues PsaA-N600 or PsaB-N582 (which ligate Chl 2B or Chl 2A through a H 2 O molecule) substituted by Met, His, and Leu. The ΔA 0 (λ) spectra were quantified using principal component analysis, the main component of which was interpreted as a mutation-induced shift of the equilibrium between the excited state of primary donor P 700 ⁎ and the primary charge-separated state P 700 + Chl 2 - . This equilibrium is shifted to the charge-separated state in wild-type PS I and to the excited P 700 in the PS I complexes with the substituted ligands to the Chl 2A and Chl 2B monomers. The results can be rationalized within the framework of an adiabatic model in which the P 700 is electronically coupled with the symmetrically arranged monomers Chl 2A and Chl 2B ; such a structure can be considered a symmetric tetrameric exciplex Chl 2A P A P B Chl 2B , in which the excited state (Chl 2A P A P B Chl 2B )* is mixed with two charge-transfer states P 700 + Chl 2A - and P 700 + Chl 2B - . The electron redistribution between the two branches in favor of the A-branch apparently takes place in the picosecond time scale after reduction of the Chl 2A and Chl 2B monomers., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bR PM ) and in recombinant form (bR rec ). The primary intermediates of the ESR photocycle were similar to intermediates I , J , and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J , and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bR PM and 0.74 ps in bR rec . The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.

In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.

The energy and charge-transfer processes in photosystem I (PS I) complexes isolated from cyanobacteria Thermosynechococcus elongatus and Synechocystis sp. PCC 6803 were investigated by pump-to-probe femtosecond spectroscopy. The formation of charge-transfer (CT) states in excitonically coupled chlorophyll a complexes (exciplexes) was monitored by measuring the electrochromic shift of β-carotene in the spectral range 500-510 nm. The excitation of high-energy chlorophyll in light-harvesting antenna of both species was not accompanied by immediate appearance of an electrochromic shift. In PS I from T. elongatus, the excitation of long-wavelength chlorophyll (LWC) caused a pronounced electrochromic effect at 502 nm assigned to the appearance of CT states of chlorophyll exciplexes. The formation of ion-radical pair P 700 + A 1 - at 40 ps was limited by energy transfer from LWC to the primary donor P 700 and accompanied by carotenoid bleach at 498 nm. In PS I from Synechocystis 6803, the excitation at 720 nm produced an immediate bidentate bleach at 690/704 nm and synchronous carotenoid response at 508 nm. The bidentate bleach was assigned to the formation of primary ion-radical state P B + Chl 2B - , where negative charge is localized predominantly at the accessory chlorophyll molecule in the branch B, Chl 2B . The following decrease of carotenoid signal at ~ 5 ps was ascribed to electron transfer to the more distant molecule Chl 3B . The reduction of phylloquinone in the sites A 1A and A 1B was accompanied by a synchronous blue-shift of the carotenoid response to 498 nm, pointing to fast redistribution of unpaired electron between two branches in favor of the state P B + A 1A - .

Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.

The Photosystem I (PSI) reaction center in cyanobacteria is comprised of ~96 chlorophyll (Chl) molecules, including six specialized Chl molecules denoted Chl1A/Chl1B (P 700 ), Chl2A/Chl2B, and Chl3A/Chl3B that are arranged in two branches and function in primary charge separation. It has recently been proposed that PSI from Chroococcidiopsis thermalis (Nürnberg et al. (2018) Science 360, 1210-1213) and Fischerella thermalis PCC 7521 (Hastings et al. (2019) Biochim. Biophys. Acta 1860, 452-460) contain Chl f in the positions Chl2A/Chl2B. We tested this proposal by exciting RCs from white-light grown (WL-PSI) and far-red light grown (FRL-PSI) F. thermalis PCC 7521 with femtosecond pulses and analyzing the optical dynamics. If Chl f were in the position Chl2A/Chl2B in FRL-PSI, excitation at 740 nm should have produced the charge-separated state P 700 + A 0 - followed by electron transfer to A 1 with a τ of ≤25 ps. Instead, it takes ~230 ps for the charge-separated state to develop because the excitation migrates uphill from Chl f in the antenna to the trapping center. Further, we observe a strong electrochromic shift at 685 nm in the final P 700 + A 1 - spectrum that can only be explained if Chl a is in the positions Chl2A/Chl2B. Similar arguments rule out the presence of Chl f in the positions Chl3A/Chl3B; hence, Chl f is likely to function solely as an antenna pigment in FRL-PSI. We additionally report the presence of an excitonically coupled homo- or heterodimer of Chl f absorbing around 790 nm that is kinetically independent of the Chl f population that absorbs around 740 nm., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Cyanobacterial photosystem I (PSI) functions as a light-driven cyt c 6 -ferredoxin/oxidoreductase located in the thylakoid membrane. In this work, the energy and charge transfer processes in PSI complexes isolated from Thermosynechococcus elongatus via conventional n-dodecyl-β-D-maltoside solubilization (DM-PSI) and a, to our knowledge, new detergent-free method using styrene-maleic acid copolymers (SMA-PSI) have been investigated by pump-to-probe femtosecond laser spectroscopy. In DM-PSI preparations excited at 740 nm, the excitation remained localized on the long-wavelength chlorophyll forms within 0.1-20 ps and revealed little or no charge separation and oxidation of the special pair, P700. The formation of ion-radical pair P700 + A1 - occurred with a characteristic time of 36 ps, being kinetically controlled by energy transfer from the long-wavelength chlorophyll to P 700 . Quite surprisingly, the detergent-free SMA-PSI complexes upon excitation by these long-wave pulses undergo an ultrafast (<100 fs) charge separation in ∼45% of particles. In the remaining complexes (∼55%), the energy transfer to P 700 occurred at ∼36 ps, similar to the DM-PSI. Both isolation methods result in a trimeric form of PSI, yet the SMA-PSI complexes display a heterogenous kinetic behavior. The much faster rate of charge separation suggests the existence of an ultrafast pathway for charge separation in the SMA-PSI that may be disrupted during detergent isolation., (Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures reveal a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. This binding site contains a sodium ion in those GPCRs that are crystallized in their inactive conformations but does not in those GPCRs that are trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction have until now remained obscure. Here, by modeling the available experimental data, we show that the sodium gradient over the cell membrane increases the sensitivity of GPCRs if their activation is thermodynamically coupled to the sodium ion translocation into the cytoplasm but decreases it if the sodium ion retreats into the extracellular space upon receptor activation. The model quantitatively describes the available data on both activation and suppression of distinct GPCRs by membrane voltage. The model also predicts selective amplification of the signal from (endogenous) agonists if only they, but not their (partial) analogs, induce sodium translocation. Comparative structure and sequence analyses of sodium-binding GPCRs indicate a key role for the conserved leucine residue in the second transmembrane helix (Leu2.46) in coupling sodium translocation to receptor activation. Hence, class A GPCRs appear to harness the energy of the transmembrane sodium potential to increase their sensitivity and selectivity., (Copyright © 2019. Published by Elsevier B.V.)

Up to half of the cellular energy gets lost owing to membrane proton leakage. The permeability of lipid bilayers to protons is by several orders of magnitude higher than to other cations, which implies efficient proton-specific passages. The nature of these passages remains obscure. By combining experimental measurements of proton flow across phosphatidylcholine vesicles, steered molecular dynamics (MD) simulations of phosphatidylcholine bilayers and kinetic modelling, we have analyzed whether protons could pass between opposite phospholipid molecules when they sporadically converge. The MD simulations showed that each time, when the phosphorus atoms of the two phosphatidylcholine molecules got closer than 1.6 nm, the eight oxygen atoms of their ester linkages could form a transmembrane 'oxygen passage' along which several water molecules aligned into a water wire. Proton permeability along such water wires would be limited by rearrangement of oxygen atoms, which could explain the experimentally shown independence of the proton permeability of pH, H 2 O/D 2 O substitution, and membrane dipole potential. We suggest that protons can cross lipid bilayers by moving along short, self-sustaining water wires supported by oxygen atoms of lipid ester linkages., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Coherent phonon dynamics in CdSe quantum dots (QD) under an ultrafast electron transfer (ET) reaction of the (1S e -1S 3/2 ) exciton quenched by methyl viologen (MV 2+ ) adsorbed onto the QD surface was studied by ultrafast pump-probe spectroscopy. Frequency and amplitude modulations (FM, AM) of the transient absorption ΔA(ω probe ,t) in the pure CdSe and coupled CdSe/MV 2+ QDs were identified in the bleach band dynamics of the red-edge exciton. The fast Fourier transform (FFT) and continuous wavelet transform analysis of the FM and AM oscillations revealed peaks at 0.51-0.58 THz (17-19 cm -1 ) and 6.06-6.27 THz (202-209 cm -1 ) attributed to the longitudinal acoustic (LA) and longitudinal optical (LO) phonons, respectively. The electron transfer to MV 2+ proceeded non-exponentially with effective time constants of 164 fs (∼30%) and 540 fs (∼70%). The quantum yield of MV˙ + radical formation was 40 ± 5%. It implies a fast route for the electron-hole pair [h + …MV˙ + ] recombination that can be rationalized in accordance with the adiabatic ET mechanism at the semiconductor surface. In the coupled CdSe/MV 2+ QDs, the amplitude of the FM oscillations rose considerably with time despite the natural attenuation of the phonon amplitude due to decoherence processes. A kinetic model explaining the increase of FM oscillations is proposed. The surprising growth of FM oscillations is elucidated by the kinetic model taking into account the relatively slow damping of LO phonon oscillations (∼1.5 ps), the ultrafast ET to MV 2+ , and the quantum yield of charge separation [h + …MV˙ + ] (∼40%). The fast formation of the charge-separated pair [h + …MV˙ + ] suggests the appearance of an electric field F with a strength of ∼3 × 10 6 V cm -1 . The MV 2+ reduction substantially increased the magnitude of LA phonon oscillations. Since the ET time is shorter than the period of LA phonon oscillations (∼1.8 ps), the MV 2+ reduction substantially increased the magnitude of LA phonon oscillations due to the inverse piezoelectric effect. The CdSe nanocrystals exposed to the electric field F exhibit the quantum-confined Stark and Franz-Keldysh electro-absorption effects. The proposed kinetic model gives consideration to the dynamic Stark shift of the red-edge exciton and to the increased amplitude of LO phonon oscillations in the bleach band dynamics.

The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases., Competing Interests: DS, DC, MG, AG, AM No competing interests declared

This work aims to fully elucidate the effects of a trehalose glassy matrix on electron transfer reactions in cyanobacterial Photosystem I (PS I). Forward and backward electron transfer rates from A 1A - and A 1B - to F X, and charge recombination rates from A 0 - , A 1B - , A 1A - , F X - , and [F A /F B ] - to P 700 + were measured in P 700 -F A /F B complexes, P 700 -F X cores, and P 700 -A 1 cores, both in liquid and in a trehalose glassy matrix at 11% humidity. By comparing CONTIN-resolved kinetic events over 6 orders of time in increasingly simplified versions of PS I at 480 nm, a wavelength that reports primarily A 1A - /A 1B - oxidation, and over 9 orders of time at 830 nm, a wavelength that reports P 700 + reduction and A 0 - oxidation, assignments could be made for nearly all of the resolved kinetic phases. Trehalose-embedded PS I samples demonstrated partially arrested forward electron transfer. The fractions of complexes in which electron transfer did not proceed beyond A 0 , A 1 and F X were 53%, 16% and 22%, respectively, with only 10% of electrons reaching the terminal F A /F B clusters. The ~10 μs and ~150 μs components in both liquid and trehalose-embedded PS I were assigned to recombination between A 1B - and P 700 + and between A 1A - and P 700 + , respectively. The kinetics and amplitudes of these resolved kinetic phases in liquid and trehalose-embedded PS I samples could be well-fitted by a kinetic model that allowed us to calculate the asymmetrical contribution of the A 1A - and A 1B - quinones to the electrochromic signal at 480 nm. Possible reasons for these effects are discussed., (Copyright © 2018. Published by Elsevier B.V.)

One of the fundamental problems in biophysics is whether the protein medium at room temperature can be properly treated as a fluid dielectric or whether its dynamics is determined by a highly ordered molecular structure resembling the properties of crystalline and amorphous solids. Here, we measured the recombination between reduced A 1 and the oxidized chlorophyll special pair P 700 over a wide temperature range using preparations of photosystem I from the cyanobacterium Synechococcus sp. PCC 7002 depleted of the iron-sulfur clusters. We found that the dielectric properties of the protein matrix in early electron transfer reactions of photosystem I resemble the behavior of solids that require an implicit treatment of electron-phonon coupling even at ambient temperatures. The quantum effects of electron-phonon coupling in proteins could account for a variety of phenomena, such as the weak sensitivity of electron transfer in pigment-protein complexes to changing environmental conditions including temperature, driving force, polarity, and chemical composition.

This review considers the state-of-the-art on mechanisms and alternative pathways of electron transfer in photosynthetic electron transport chains of chloroplasts and cyanobacteria. The mechanisms of electron transport control between photosystems (PS) I and II and the Calvin-Benson cycle are considered. The redistribution of electron fluxes between the noncyclic, cyclic, and pseudocyclic pathways plays an important role in the regulation of photosynthesis. Mathematical modeling of light-induced electron transport processes is considered. Particular attention is given to the electron transfer reactions on the acceptor side of PS I and to interactions of PS I with exogenous acceptors, including molecular oxygen. A kinetic model of PS I and its interaction with exogenous electron acceptors has been developed. This model is based on experimental kinetics of charge recombination in isolated PS I. Kinetic and thermodynamic parameters of the electron transfer reactions in PS I are scrutinized. The free energies of electron transfer between quinone acceptors A 1A /A 1B in the symmetric redox cofactor branches of PS I and iron-sulfur clusters F X , F A , and F B have been estimated. The second-order rate constants of electron transfer from PS I to external acceptors have been determined. The data suggest that byproduct formation of superoxide radical in PS I due to the reduction of molecular oxygen in the A 1 site (Mehler reaction) can exceed 0.3% of the total electron flux in PS I.

The ultrafast primary charge separation in Photosystem I (PS I) excited by femtosecond pulses centered at 720 and 760nm was studied by pump-to-probe laser spectroscopy. The absorbance in the red edge of PS I absorption spectrum has an unusual exponential dependence on wavelength. The cutoff of short wavelength components of 760nm pulse allows direct excitation of reaction center chlorophyll molecules without involvement of light-harvesting antenna. The transient spectrum manifests the features of the primary ion-radical pair P 700 + A 0 - at time delay <180fs, followed by formation of the secondary pair P 700 + A 1 - with a characteristic time of 26ps. The obtained data are rationalized in the framework of adiabatic three-state model that includes the chlorophyll dimer P 700 and two symmetrically arranged nearest chlorophyll molecules of A 0 . The arrangement of chlorophylls results in strong electronic coupling between P 700 and A 0 . Excitation in the maximum of P 700 absorption generates electronic states with the highest contribution from P 700 *, whereas excitation in the far-red edge predominantly generates charge transfer state P 700 + A 0 - in both branches of redox-cofactors. The three-level model accounts for a flat-bottomed potential surface of the excited state and adiabatic character of electron transfer between P 700 and A 0 , providing a microscopic explanation of the ultrafast formation of P 700 + A 0 - and exponential decline of PS I absorption., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Interaction of photosystem I (PS I) complexes from cyanobacteria Synechocystis sp. PCC 6803 containing various quinones in the A 1 -site (phylloquinone PhQ in the wild-type strain (WT), and plastoquinone PQ or 2,3-dichloronaphthoquinone Cl 2 NQ in the menB deletion strain) and different numbers of Fe 4 S 4 clusters (intact WT and F X -core complexes depleted of F A /F B centers) with external acceptors has been studied. The efficiency of interaction was estimated by measuring the light-induced absorption changes at 820 nm due to the reduction of the special pair of chlorophylls (P 700 + ) by an external acceptor(s). It was shown that externally added Cl 2 NQ is able to effectively accept electrons from the terminal iron-sulfur clusters of PS I. Moreover, the efficiency of Cl 2 NQ as external acceptor was higher than the efficiency of the commonly used artificial electron acceptor, methylviologen (MV) for both the intact WT PS I and for the F X -core complexes. The comparison of the efficiency of MV interaction with different types of PS I complexes revealed gradual decrease in the following order: intact WT > menB > F X -core. The effect of MV on the recombination kinetics in menB complexes of PS I with Cl 2 NQ in the A 1 -site differed significantly from all other PS I samples. The obtained effects are considered in terms of kinetic efficiency of electron acceptors in relation to thermodynamic and structural characteristics of PS I complexes.

The reduction kinetics of the photo-oxidized primary electron donor P 700 in photosystem I (PS I) complexes from cyanobacteria Synechocystis sp. PCC 6803 were analyzed within the kinetic model, which considers electron transfer (ET) reactions between P 700 , secondary quinone acceptor A 1 , iron-sulfur clusters and external electron donor and acceptors - methylviologen (MV), 2,3-dichloro-naphthoquinone (Cl 2 NQ) and oxygen. PS I complexes containing various quinones in the A 1 -binding site (phylloquinone PhQ, plastoquinone-9 PQ and Cl 2 NQ) as well as F X -core complexes, depleted of terminal iron-sulfur F A /F B clusters, were studied. The acceleration of charge recombination in F X -core complexes by PhQ/PQ substitution indicates that backward ET from the iron-sulfur clusters involves quinone in the A 1 -binding site. The kinetic parameters of ET reactions were obtained by global fitting of the P 700 + reduction with the kinetic model. The free energy gap ΔG 0 between F X and F A /F B clusters was estimated as -130 meV. The driving force of ET from A 1 to F X was determined as -50 and -220 meV for PhQ in the A and B cofactor branches, respectively. For PQ in A 1A -site, this reaction was found to be endergonic (ΔG 0  = +75 meV). The interaction of PS I with external acceptors was quantitatively described in terms of Michaelis-Menten kinetics. The second-order rate constants of ET from F A /F B , F X and Cl 2 NQ in the A 1 -site of PS I to external acceptors were estimated. The side production of superoxide radical in the A 1 -site by oxygen reduction via the Mehler reaction might comprise ≥0.3% of the total electron flow in PS I.

Molecules of mitochondrial cardiolipin (CL) get selectively oxidized upon oxidative stress, which triggers the intrinsic apoptotic pathway. In a chemical model most closely resembling the mitochondrial membrane-liposomes of pure bovine heart CL-we compared ubiquinol-10, ubiquinol-6, and alpha-tocopherol, the most widespread naturally occurring antioxidants, with man-made, quinol-based amphiphilic antioxidants. Lipid peroxidation was induced by addition of an azo initiator in the absence and presence of diverse antioxidants, respectively. The kinetics of CL oxidation was monitored via formation of conjugated dienes at 234 nm. We found that natural ubiquinols and ubiquinol-based amphiphilic antioxidants were equally efficient in protecting CL liposomes from peroxidation; the chromanol-based antioxidants, including alpha-tocopherol, were 2-3 times less efficient. Amphiphilic antioxidants, but not natural ubiquinols and alpha-tocopherol, were able, additionally, to protect the CL bilayer from oxidation by acting from the water phase. We suggest that the previously reported therapeutic efficiency of mitochondrially targeted amphiphilic antioxidants is owing to their ability to protect those CL molecules that are inaccessible to natural hydrophobic antioxidants, being trapped within respiratory supercomplexes. The high susceptibility of such occluded CL molecules to oxidation may have prompted their recruitment as apoptotic signaling molecules by nature.

Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Primary electron transfer reactions in the bacterial reaction center are difficult for theoretical explication: the reaction kinetics, almost unalterable over a wide range of temperature and free energy changes, revealed oscillatory features observed initially by Shuvalov and coauthors (1997, 2002). Here the reaction mechanism was studied by molecular dynamics and analyzed within a phenomenological Langevin approach. The spectral function of polarization around the bacteriochlorophyll special pair PLPM and the dielectric response upon the formation of PL(+)PM(-) dipole within the special pair were calculated. The system response was approximated by Langevin oscillators; the respective frequencies, friction, and energy coupling coefficients were determined. The protein dynamics around PL and PM were distinctly asymmetric. The polarization around PL included slow modes with the frequency 30-80 cm(-1) and the total amplitude of 130 mV. Two main low-frequency modes of protein response around PM had frequencies of 95 and 155 cm(-1) and the total amplitude of 30 mV. In addition, a slowly damping mode with the frequency of 118 cm(-1) and the damping time >1.1 ps was coupled to the formation of PL(+)PM(-) dipole. It was attributed to elastic vibrations of α-helices in the vicinity of PLPM. The proposed trapping of P excitation energy in the form of the elastic vibrations can rationalize the observed properties of the primary electron transfer reactions, namely, the unusual temperature and ΔG dependences, the oscillating phenomena in kinetics, and the asymmetry of the charge separation reactions.

Cytochrome c oxidases (Coxs) are the basic energy transducers in the respiratory chain of the majority of aerobic organisms. Coxs studied to date are redox-driven proton-pumping enzymes belonging to one of three subfamilies: A-, B-, and C-type oxidases. The C-type oxidases (cbb3 cytochromes), which are widespread among pathogenic bacteria, are the least understood. In particular, the proton-pumping machinery of these Coxs has not yet been elucidated despite the availability of X-ray structure information. Here, we report the discovery of the first (to our knowledge) sodium-pumping Cox (Scox), a cbb3 cytochrome from the extremely alkaliphilic bacterium Thioalkalivibrio versutus. This finding offers clues to the previously unknown structure of the ion-pumping channel in the C-type Coxs and provides insight into the functional properties of this enzyme.

In mammalian mitochondria, cardiolipin molecules are the primary targets of oxidation by reactive oxygen species. The interaction of oxidized cardiolipin molecules with the constituents of the apoptotic cascade may lead to cell death. In the present study, we compared the effects of quinol-containing synthetic and natural amphiphilic antioxidants on cardiolipin peroxidation in a model system (liposomes of bovine cardiolipin). We found that both natural ubiquinol and synthetic antioxidants, even being introduced in micro- and submicromolar concentrations, fully protected the liposomal cardiolipin from peroxidation. The duration of their action, however, varied; it increased with the presence of either methoxy groups of ubiquinol or additional reduced redox groups (in the cases of rhodamine and berberine derivates). The concentration of ubiquinol in the mitochondrial membrane substantially exceeds the concentrations of antioxidants we used and would seem to fully prevent peroxidation of membrane cardiolipin. In fact, this does not happen: cardiolipin in mitochondria is oxidized, and this process can be blocked by amphiphilic cationic antioxidants (Y. N. Antonenko et al. (2008) Biochemistry (Moscow), 73, 1273-1287). We suppose that a fraction of mitochondrial cardiolipin could not be protected by natural ubiquinol; in vivo, peroxidation most likely threatens those cardiolipin molecules that, being bound within complexes of membrane proteins, are inaccessible to the bulky hydrophobic ubiquinol molecules diffusing in the lipid bilayer of the inner mitochondrial membrane. The ability to protect these occluded cardiolipin molecules from peroxidation may explain the beneficial therapeutic action of cationic antioxidants, which accumulate electrophoretically within mitochondria under the action of membrane potential.

Molecular dynamics (MD) calculations, a semi-continuum (SC) approach, and quantum chemistry (QC) calculations were employed together to investigate the molecular mechanics of ultrafast charge separation reactions in Photosystem I (PS I) of Thermosynechococcus elongatus. A molecular model of PS I was developed with the aim to relate the atomic structure with electron transfer events in the two branches of cofactors. A structural flexibility map of PS I was constructed based on MD simulations, which demonstrated its rigid hydrophobic core and more flexible peripheral regions. The MD model permitted the study of atomic movements (dielectric polarization) in response to primary and secondary charge separations, while QC calculations were used to estimate the direct chemical effect of the A(0A)/A(0B) ligands (Met or Asn in the 688/668 position) on the redox potential of chlorophylls A(0A)/A(0B) and phylloquinones A(1A)/A(1B). A combination of MD and SC approaches was used to estimate reorganization energies λ of the primary (λ₁) and secondary (λ₂ ) charge separation reactions, which were found to be independent of the active branch of electron transfer; in PS I from the wild type, λ₁ was estimated to be 390 ± 20mV, while λ₂ was estimated to be higher at 445 ± 15mV. MD and QC approaches were used to describe the effect of substituting Met688(PsaA)/Met668(PsaB) by Asn688(PsaA)/Asn668(PsaB) on the energetics of electron transfer. Unlike Met, which has limited degrees of freedom in the site, Asn was found to switch between two relatively stable conformations depending on cofactor charge. The introduction of Asn and its conformation flexibility significantly affected the reorganization energy of charge separation and the redox potentials of chlorophylls A(0A)/A(0B) and phylloquinones A(1A)/A(1B), which may explain the experimentally observed slowdown of secondary electron transfer in the M688N(PsaA) variant. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The mechanisms of the ultrafast charge separation in reaction centers of photosystem I (PS I) complexes are discussed. A kinetic model of the primary reactions in PS I complexes is presented. The model takes into account previously calculated values of redox potentials of cofactors, reorganization energies of the primary P700(+)A0(-) and secondary P700(+)A1(-) ion-radical pairs formation, and the possibility of electron transfer via both symmetric branches A and B of redox-cofactors. The model assumes that the primary electron acceptor A0 in PS I is represented by a dimer of chlorophyll molecules Chl2A/Chl3A and Chl2B/Chl3B in branches A and B of the cofactors. The characteristic times of formation of P700(+)A0(-) and P700(+)A1(-) calculated on the basis of the model are close to the experimental values obtained by pump-probe femtosecond absorption spectroscopy. It is demonstrated that a small difference in the values of redox potentials between the primary electron acceptors A0A and A0B in branches A and B leads to asymmetry of the electron transfer in a ratio of 70 : 30 in favor of branch A. The secondary charge separation is thermodynamically irreversible in the submicrosecond range and is accompanied by additional increase in asymmetry between the branches of cofactors of PS I.

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On the one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes., (© 2013.)

The effects of the mitochondria-targeted lipophilic cation dodecyltriphenylphosphonium (C12TPP, the charge is delocalized and screened by bulky hydrophobic residues) and those of lipophilic cations decyltriethylammonium bromide and cetyltrimethylammonium bromide (C10TEA and C16TMA, the charges are localized and screened by less bulky residues) on bilayer planar phospholipid membranes and tightly-coupled mitochondria from the yeast Yarrowia lipolytica have been compared. In planar membranes, C12TPP was found to generate a diffusion potential as if it easily penetrates these membranes. In the presence of palmitate, C12TPP induced H(+) permeability like plastoquinonyl decyltriphenilphosphonium that facilitates transfer of fatty acid anions (Severin et al., PNAS, 2010, 107, 663-668). C12TPP was shown to stimulate State 4 respiration of mitochondria and caused a mitochondrial membrane depolarization with a half-maximal effect at 6μM. Besides, C12TPP profoundly potentiated the uncoupling effect of endogenous or added fatty acids. C10TEA and C16TMA inhibited State 4 respiration and decreased the membrane potential, though at much higher concentrations than C12TPP, and they did not promote the uncoupling action of fatty acids. These relationships were modeled by molecular dynamics. They can be explained by different membrane permeabilities for studied cations, which in turn are due to different availabilities of the positive charge in these cations to water dipoles., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The permeability of a planar lipid membrane (composed of diphytanoylphosphatidylcholine) for tetraphenylphosphonium (TPP) was investigated. The observed level of the diffusion potential generated as a function of the TPP concentration gradient differed from the theoretically expected value, possibly due to proton leakage of the membrane mediated by the traces of fatty acids in the phospholipid forming the membrane. Using the molecular dynamics approach to study movement of TPP and dodecyltriphenylphosphonium (C(12)TPP) with different affinity to the lipid bilayer through a bilayer lipid membrane, it was found that C(12)TPP has a greater affinity to the membrane surface than TPP. However, the two cations have the same activation energy for transmembrane transfer. Interaction of TPP and C(12)TPP with tightly-coupled mitochondria from the yeast Yarrowia lipolytica was also investigated. At low, micromolar concentrations, both cations are "relatively weak, mild uncouplers", do not shunt electron transfer along the respiratory chain, do not disturb (damage) the inner mitochondrial membrane, and profoundly promote the uncoupling effect of fatty acids. At higher concentrations they inhibit respiration in state 3, and at much higher concentrations they induce swelling of mitochondria, possibly due to their detergent action.

Proton diffusion along membrane surfaces is thought to be essential for many cellular processes such as energy transduction. Commonly, it is treated as a succession of jumps between membrane-anchored proton-binding sites. Our experiments provide evidence for an alternative model. We released membrane-bound caged protons by UV flashes and monitored their arrival at distant sites by fluorescence measurements. The kinetics of the arrival is probed as a function of distance for different membranes and for different water isotopes. We found that proton diffusion along the membrane is fast even in the absence of ionizable groups in the membrane, and it decreases strongly in D(2)O as compared to H(2)O. We conclude that the fast proton transport along the membrane is dominated by diffusion via interfacial water, and not via ionizable lipid moieties.

Plastoquinone, a very effective electron carrier and antioxidant of chloroplasts, was conjugated with decyltriphenylphosphonium to obtain a cation easily penetrating through membranes. This cation, called SkQ1, is specifically targeted to mitochondria by electrophoresis in the electric field formed by the mitochondrial respiratory chain. The respiratory chain also regenerates reduced SkQ1H(2) from its oxidized form that appears as a result of the antioxidant activity of SkQ1H(2). SkQ1H(2) prevents oxidation of cardiolipin, a mitochondrial phospholipid that is especially sensitive to attack by reactive oxygen species (ROS). In cell cultures, SkQ1 and its analog plastoquinonyl decylrhodamine 19 (SkQR1) arrest H(2)O(2)-induced apoptosis. When tested in vivo, SkQs (i) prolong the lifespan of fungi, crustaceans, insects, fish, and mice, (ii) suppress appearance of a large number of traits typical for age-related senescence (cataract, retinopathies, achromotrichia, osteoporosis, lordokyphosis, decline of the immune system, myeloid shift of blood cells, activation of apoptosis, induction of β-galactosidase, phosphorylation of H2AX histones, etc.) and (iii) lower tissue damage and save the lives of young animals after treatments resulting in kidney ischemia, rhabdomyolysis, heart attack, arrhythmia, and stroke. We suggest that the SkQs reduce mitochondrial ROS and, as a consequence, inhibit mitochondria-mediated apoptosis, an obligatory step of execution of programs responsible for both senescence and fast "biochemical suicide" of an organism after a severe metabolic crisis.

A limited decrease in mitochondrial membrane potential can be beneficial for cells, especially under some pathological conditions, suggesting that mild uncouplers (protonophores) causing such an effect are promising candidates for therapeutic uses. The great majority of protonophores are weak acids capable of permeating across membranes in their neutral and anionic forms. In the present study, protonophorous activity of a series of derivatives of cationic rhodamine 19, including dodecylrhodamine (C(12)R1) and its conjugate with plastoquinone (SkQR1), was revealed using a variety of assays. Derivatives of rhodamine B, lacking dissociable protons, showed no protonophorous properties. In planar bilayer lipid membranes, separating two compartments differing in pH, diffusion potential of H(+) ions was generated in the presence of C(12)R1 and SkQR1. These compounds induced pH equilibration in liposomes loaded with the pH probe pyranine. C(12)R1 and SkQR1 partially stimulated respiration of rat liver mitochondria in State 4 and decreased their membrane potential. Also, C(12)R1 partially stimulated respiration of yeast cells but, unlike the anionic protonophore FCCP, did not suppress their growth. Loss of function of mitochondrial DNA in yeast (grande-petite transformation) is known to cause a major decrease in the mitochondrial membrane potential. We found that petite yeast cells are relatively more sensitive to the anionic uncouplers than to C(12)R1 compared with grande cells. Together, our data suggest that rhodamine 19-based cationic protonophores are self-limiting; their uncoupling activity is maximal at high membrane potential, but the activity decreases membrane potentials, which causes partial efflux of the uncouplers from mitochondria and, hence, prevents further membrane potential decrease., (© 2011 by The American Society for Biochemistry and Molecular Biology, Inc.)

The present state of the art in studies on the mechanisms of antioxidant activities of mitochondria-targeted cationic plastoquinone derivatives (SkQs) is reviewed. Our experiments showed that these compounds can operate as antioxidants in two quite different ways, i.e. (i) by preventing peroxidation of cardiolipin [Antonenko et al., Biochemistry (Moscow) 73 (2008) 1273-1287] and (ii) by fatty acid cycling resulting in mild uncoupling that inhibits the formation of reactive oxygen species (ROS) in mitochondrial State 4 [Severin et al. Proc. Natl. Acad. Sci. USA 107 (2009), 663-668]. The quinol and cationic moieties of SkQ are involved in cases (i) and (ii), respectively. In case (i) SkQH2 interrupts propagation of chain reactions involved in peroxidation of unsaturated fatty acid residues in cardiolipin, the formed SkQ- being reduced back to SkQH2 by heme bH of complex III in an antimycin-sensitive way. Molecular dynamics simulation showed that there are two stable conformations of SkQ1 with the quinol residue localized near peroxyl radicals at C9 or C13 of the linoleate residue in cardiolipin. In mechanism (ii), fatty acid cycling mediated by the cationic SkQ moiety is involved. It consists of (a) transmembrane movement of the fatty acid anion/SkQ cation pair and (b) back flows of free SkQ cation and protonated fatty acid. The cycling results in a protonophorous effect that was demonstrated in planar phospholipid membranes and liposomes. In mitochondria, the cycling gives rise to mild uncoupling, thereby decreasing membrane potential and ROS generation coupled to reverse electron transport in the respiratory chain. In yeast cells, dodecyltriphenylphosphonium (capital ES, Cyrillic12TPP), the cationic part of SkQ1, induces uncoupling that is mitochondria-targeted since capital ES, Cyrillic12TPP is specifically accumulated in mitochondria and increases the H+ conductance of their inner membrane. The conductance of the outer cell membrane is not affected by capital ES, Cyrillic12TPP., (Copyright © 2010 Elsevier B.V. All rights reserved.)

Photosystem II (PS II) is a biological energy transducer. The enzyme catalyses the light-driven oxidation of water and reduction of plastoquinone. The aim of this work was to review the mechanisms of electrical events in PS II. The major contribution to the total photoelectric response is due to the charge-separation between the primary chlorophyll donor P680 and quinone acceptor QA accompanied by re-reduction of P680+ by tyrosine residue YZ. The remaining part of the membrane potential is believed to be associated mainly with electron and proton transfer events due to the S-state transitions of the oxygen-evolving complex and proton uptake associated with protonation of the doubly reduced secondary quinone acceptor QB. Under certain non-physiological conditions, some other electrogenic reactions are observed, namely: proton-coupled electron transfer between QA and non-heme Fe3+ and electron transfer from the protein-water interface to the YZ radical in the presence of artificial electron donors. These data may provide a good platform for further development of artificial photosynthetic constructs and bio-inspired catalysts.

A unique phenomenon of mitochondria-targeted protonophores is described. It consists in a transmembrane H(+)-conducting fatty acid cycling mediated by penetrating cations such as 10-(6'-plastoquinonyl)decyltriphenylphosphonium (SkQ1) or dodecyltriphenylphosphonium (C(12)TPP). The phenomenon has been modeled by molecular dynamics and directly proved by experiments on bilayer planar phospholipid membrane, liposomes, isolated mitochondria, and yeast cells. In bilayer planar phospholipid membrane, the concerted action of penetrating cations and fatty acids is found to result in conversion of a pH gradient (DeltapH) to a membrane potential (Deltapsi) of the Nernstian value (about 60 mV Deltapsi at DeltapH = 1). A hydrophobic cation with localized charge (cetyltrimethylammonium) failed to substitute for hydrophobic cations with delocalized charge. In isolated mitochondria, SkQ1 and C(12)TPP, but not cetyltrimethylammonium, potentiated fatty acid-induced (i) uncoupling of respiration and phosphorylation, and (ii) inhibition of H(2)O(2) formation. In intact yeast cells, C(12)TPP stimulated respiration regardless of the extracellular pH value, whereas a nontargeted protonophorous uncoupler (trifluoromethoxycarbonylcyanide phenylhydrazone) stimulated respiration at pH 5 but not at pH 3. Hydrophobic penetrating cations might be promising to treat obesity, senescence, and some kinds of cancer that require mitochondrial hyperpolarization.

The midpoint redox potentials (E(m)) of all cofactors in photosystem I from Synechococcus elongatus as well as of the iron-sulfur (Fe(4)S(4)) clusters in two soluble ferredoxins from Azotobacter vinelandii and Clostridium acidiurici were calculated within the framework of a semi-continuum dielectric approach. The widely used treatment of proteins as uniform media with single dielectric permittivity is oversimplified, particularly, because permanent charges are considered both as a source for intraprotein electric field and as a part of dielectric polarizability. Our approach overcomes this inconsistency by using two dielectric constants: optical epsilon(o)=2.5 for permanent charges pre-existing in crystal structure, and static epsilon(s) for newly formed charges. We also take into account a substantial dielectric heterogeneity of photosystem I revealed by photoelectric measurements and a liquid junction potential correction for E(m) values of relevant redox cofactors measured in aprotic solvents. We show that calculations based on a single permittivity have the discrepancy with experimental data larger than 0.7 V, whereas E(m) values calculated within our approach fall in the range of experimental estimates. The electrostatic analysis combined with quantum chemistry calculations shows that (i) the energy decrease upon chlorophyll dimerization is essential for the downhill mode of primary charge separation between the special pair P(700) and the primary acceptor A(0); (ii) the primary donor is apparently P(700) but not a pair of accessory chlorophylls; (iii) the electron transfer from the A branch quinone Q(A) to the iron-sulfur cluster F(X) is most probably downhill, whereas that from the B branch quinone Q(B) to F(X) is essentially downhill.

Photosynthetic reaction centers of Blastochloris viridis require two quanta of light to catalyse a two-step reduction of their secondary ubiquinone Q(B) to ubiquinol. We employed capacitive potentiometry to follow the voltage changes that were caused by the accompanying transmembrane proton displacements. At pH 7.5 and 20 degrees C, the Q(B)-related voltage generation after the first flash was contributed by a fast, temperature-independent component with a time constant of approximately 30 micros and a slower component of approximately 200 micros with activation energy (E(a)) of 50 kJ/mol. The kinetics after the second flash featured temperature-independent components of 5 micros and 200 micros followed by a component of 600 micros with E(a) approximately 60 kJ/mol.

A number of the electrogenic reactions in photosystem I, photosystem II, and bacterial reaction centers (RC) were comparatively analyzed, and the variation of the dielectric permittivity (epsilon) in the vicinity of electron carriers along the membrane normal was calculated. The value of epsilon was minimal at the core of the complexes and gradually increased towards the periphery. We found that the rate of electron transfer (ET) correlated with the value of the dielectric permittivity: the fastest primary ET reactions occur in the low-polarity core of the complexes within the picosecond time range, whereas slower secondary reactions take place at the high-polarity periphery of the complexes within micro- to millisecond time range. The observed correlation was quantitatively interpreted in the framework of the Marcus theory. We calculated the reorganization energy of ET carriers using their van der Waals volumes and experimentally determined epsilon values. The electronic coupling was calculated by the empirical Moser-Dutton rule for the distance-dependent electron tunneling rate in nonadiabatic ET reactions. We concluded that the local dielectric permittivity inferred from the electrometric measurements could be quantitatively used to estimate the rate constant of ET reactions in membrane proteins with resolved atomic structure with the accuracy of less than one order of magnitude.