Kinetic model of primary energy transfer and trapping in photosynthetic membranes

The picosecond time-domain incoherent singlet excitation transfer and trapping kinetics in core antenna of photosynthetic bacteria are studied in case of low excitation intensities by numerical integration of the appropriate master equation in a wide temperature range of 4-300 K. The essential features of our two-dimensional-lattice model are as follows: Förster excitation transfer theory, spectral heterogeneity of both the light-harvesting antenna and the reaction center, treatment of temperature effects through temperature dependence of spectral bands, inclusion of inner structure of the trap, and transition dipole moment orientation. The fluorescence kinetics is analyzed in terms of distributions of various kinetic components, and the influence of different inhomogeneities (orientational, spectral) is studied.

A reasonably good agreement between theoretical and experimental fluorescence decay kinetics for purple photosynthetic bacterium Rhodospirillum rubrum is achieved at high temperatures by assuming relatively large antenna spectral inhomogeneity: 20 nm at the whole bandwidth of 40 nm. The mean residence time in the antenna lattice site (it is assumed to be the aggregate of four bacteriochlorophyll a molecules bound to proteins) is estimated to be ~12 ps. At 4 K only qualitative agreement between model and experiment is gained. The failure of quantitative fitting is perhaps due to the lack of knowledge about the real structure of antenna or local heating and cooling effects not taken into account.

     

Energy transfer in a model of the photosynthetic unit of green plants

A model array is set up to represent a photosynthetic unit of 344 chlorophyll molecules of seven different spectral varieties and in definite orientations. The array is provided with two traps, representing the reaction centers of photosystems I and II. The number of jumps required to obtain a high probability of trapping is lower than on a similar array of undifferentiated chlorophylls by a factor of 15. Most of the molecules fall into two groups which transfer their energy predominantly into one or the other trap, and which may be regarded as functional photosystems I and II. The rate of transfer between these two functional photosystems can be controlled by redirecting the orientation of only six of the molecules, which occupy a key position in the array. The effect on trapping rates of reorientation of these molecules is especially pronounced when one of the traps is closed. This constitutes a model for the control of energy distribution between the two photosystems, as indicated in recent years through fluorescence studies.     

Characterization of excitation energy trapping in photosynthetic purple bacteria at 77 K

We have studied the energy-transfer dynamics in chromatophores of Rhodobacter sphaeroides and Rhodospirillum rubrum at 77 K, with functional charge separation. Using low-intensity picosecond absorption recovery, we determined that transfer between the energetically low-lying antenna component BChl896 and the special pair of the reaction center occurs with a time constant of 37 ps in Rb. sphaeroides and 75 ps in R. rubrum. Assuming that a Förster energy-transfer mechanism applies to the process, this allows us to estimate the distance between BChl896 in the B875 complex and the special pair P870 in the reaction center to range between 26 and 39 Å in Rb. sphaeroides. Such a distance indicates that the BChl896 pigment and the special pair of the reaction center are at the minimum separation allowed by the size and shape of the reaction center and the light-harvesting polypeptides.     

Efficiency of excitation energy trapping in the green photosynthetic bacterium Chlorobaculum tepidum

During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations. Therefore a compromise between photon capture efficiency and excitation trapping efficiency needs to be found. Here we report results on the whole cells of the green sulfur bacterium Chlorobaculum tepidum. Its efficiency of excitation energy transfer and charge separation enables the organism to live in environments with very low illumination. Using fluorescence measurements with picosecond resolution, we estimate that despite a rather large size and complex composition of its light-harvesting apparatus, the quantum efficiency of its photochemistry is around ~87% at 20?°C, ~83% at 45?°C, and about ~81% at 77?K when part of the excitation energy is trapped by low-energy bacteriochlorophyll a molecules. The data are evaluated using target analysis, which provides further insight into the functional organization of the low-light adapted photosynthetic apparatus.     

Excitation energy transfer and trapping dynamics in the core complex of the filamentous photosynthetic bacterium Roseiflexus castenholzii

The light-harvesting core complex of the thermophilic filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii is intrinsic to the cytoplasmic membrane and intimately bound to the reaction center (RC). Using ultrafast transient absorption and time-resolved fluorescence spectroscopy with selective excitation, energy transfer, and trapping dynamics in the core complex have been investigated at room temperature in both open and closed RCs. Results presented in this report revealed that the excited energy transfer from the BChl 800 to the BChl 880 band of the antenna takes about 2?ps independent of the trapping by the RC. The time constants for excitation quenching in the core antenna BChl 880 by open and closed RCs were found to be 60 and 210?ps, respectively. Assuming that the light harvesting complex is generally similar to LH1 of purple bacteria, the possible structural and functional aspects of this unique antenna complex are discussed. The results show that the core complex of Roseiflexus castenholzii contains characteristics of both purple bacteria and Chloroflexus aurantiacus.     

鸢尾(Iris L.)叶片取向与其光合特性及光抑制的关系

通过气体交换、叶绿素荧光、反射光谱等方法,研究了鸢尾叶片取向对植株光合特性及光抑制的影响.自然状态下,鸢尾的叶片不同取向影响植株对光能的截获;叶片净光合速率Pn与光合有效辐射PAR呈极显著相关;东西取向叶片的Pn要大于南北取向.南北取向的植株中叶片叶绿素(Chl a和Chl b),类胡萝卜素(Car)含量略高于东西取向.日进程中,各取向的叶片在一天中均没有发生明显的光抑制.相对于东西取向的植株,南北取向植株发生了明显的倾斜;在两种取向的植株中,叶片东侧和南侧的光化学反射指数(PRI)下调幅度较大;PRI的变化量(△PRI)大小依次为:东侧>南侧>西侧>北侧.鸢尾植株取向改变了叶片倾斜角度,两者共同导致光能截获减小;同时,叶片光能利用效率下调和叶黄素循环增强,这可能是不同取向植株均未发生严重光抑制的原因.     

Influence of energy flux and quality of light on the molecular organization of the photosynthetic apparatus in Scenedesmus

The photosynthetic apparatus of the unicellular green alga Scenedesmus obliquus adapts to different levels and qualities of light as documented by the fluence-rate curves of photosynthetic oxygen evolution. Cultures adapted to low fluence rates of white light (5W·m^-2) have more chlorophyll (Chl) per cell mass, a higher chlorophyll to carotenoid ratio and a doubling of the chlorophyll to cytochrome f ratio compared with cells adapted to high fluence rates of white light (20W·m^-2). Only small differences can be observed in the halfrise time of fluorescence induction, the electrophoretic profile of the pigment-protein complexes and the Chl a/Chl b-ratio. Scenedesmus cells adapted to blue light of high spectral purity demonstrate, in comparison with those adapted to red light, a higher chlorophyll content, a higher ratio of chlorophyll to carotenoid and a much higher ratio of chlorophyll to cytochrome f. Regarding these parameters and the fluence-rate curves of photosynthesis, the blue light causes the same effects as low levels of white light. In contrast, the action of red light resembles rather that of high levels of white light. Blue-light-adapted Scenedesmus cells have a smaller Chl a to Chl b ratio, a faster half-rise time of fluorescence induction and more chlorophyll in the light-harvesting system than red-light-adapted cells, as shown in the electrophoretic profile of the pigment-protein complexes. Based on these results we propose a model for the adaptation of the photosynthetic apparatus of Scenedesmus to different levels and qualities of light. In this model low as compared with high levels of white light result in an increase in the number of photosystems per electron-transport chain, but not in an increase in the size of these photosystems. The same result is obtained by adaptation to blue light. The lack of sufficient Chl b formation in red-light-adapted cells results in a decrease in the light harvesting chlorophyll-protein complexes and a photosynthetic response like that found in cells adapted to high light levels. The findings reported here confirm our earlier results in comparing blue-and red-light adaptation of the photosynthetic apparatus with adaptation to low and high levels of white light, respectively.Abbreviations Chl chlorophyll - CP chlorophyll-protein complex - DCMU 3-(3,4-dichlorophenyl)-1,1 dimethyl-urea - LHCP light harvesting chlorophyll-protein complex - LiDS lithium dodecyl sulfate - PAGE polyacrylamide gel electrophoresis - PS photosystem     

Incorporation of measured photosynthetic rate in a mathematical model for calculation of non-structural saccharide concentration

A simple mathematical model for calculating the concentration of mobile carbon skeletons in the shoot of soya bean plants [Glycine max (L.) Merrill cv. Ransom] was built to examine the suitability of measured net photosynthetic rates (PN) for calculation of saccharide flux into the plant. The results suggest that either measurement of instantaneous PN overestimated saccharide influx or respiration rates utilized in the model were underestimated. If neither of these is the case, end-product inhibition of photosynthesis or waste respiration through the alternative pathway should be included in modelling of CH2O influx or efflux; and even if either of these is the case, the model output at a low coefficient of leaf activity indicates that PN still may be controlled by either end-product inhibition or alternative respiration.     

Means of optimizing conversion of light energy in the primary stages of photosynthesis. I. The need for optimizing the structure of a photosynthetic unit and calculation of its efficiency

It is shown, that the photosynthetic unit structure is to be strongly optimized in vivo to operate with a 90% quantum yield of primary charge separation in reaction centers, which means that a macroscopic photosynthetic unit is neither uniform nor isotropic. Some requirements for optimization of photosynthetic unit structure are determined. The modified probability matrix method to simulate the excitation energy transfer in photosynthesis is proposed. The method is adapted to excitation trapping time (but not to excitation jumps number) calculation. The calculations assume a F?rster inductive resonance mechanism for energy transfer within light-harvesting antenna and pairwise dipolar interactions.     

Celestial orientation in bees: the use of spectral cues

Summary The spectral cues used in the bee's celestial compass are investigated by presenting bees dancing on a horizontal comb with unpolarized (or polarized) spectral stimuli. Where appropriate, the use of e-vector information is prevented by painting out the specialized dorsal margin of the bee's eye (POL area, Fig. 1). This area has been shown to mediate e-vector information (Fig. 3; Wehner 1982), whereas the remainder of the dorsal retina is sufficient for mediating spectral information (Fig. 4).Spectral cues are used by the bees to discriminate between sun and sky (Fig. 4). According to physical reality (Fig. 2), a long-wavelength stimulus is taken as the sun, whereas a short-wavelength stimulus is expected by the bee to lie anywhere within the antisolar half of the sky (Figs. 5 and 6). This is in accord with the bee's e-vector compass in which e-vectors are confined to the antisolar half of the sky (Fig. 9).In general, spectral cues do not provide precise compass information except when a full celestial colour gradient is available including the solar and the antisolar meridian (Figs. 7 and 8).     

State transitions--the molecular remodeling of photosynthetic supercomplexes that controls energy flow in the chloroplast

In oxygen-evolving photosynthesis, the two photosystems-photosystem I and photosystem II-function in parallel, and their excitation levels must be balanced to maintain an optimal photosynthetic rate under natural light conditions. State transitions in photosynthetic organisms balance the absorbed light energy between the two photosystems in a short time by relocating light-harvesting complex II proteins. For over a decade, the understanding of the physiological consequences, the molecular mechanism, and its regulation has increased considerably. After providing an overview of the general understanding of state transitions, this review focuses on the recent advances of the molecular aspects of state transitions with a particular emphasis on the studies using the green alga Chlamydomonas reinhardtii. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.     

Magnetic resonance imaging: calculation of rates of energy absorption by a human-torso model

The three-dimensional impedance method was used to estimate specific absorption rate (SAR) in a human-torso model during exposure to the time-varying and static magnetic fields used in magnetic resonance imaging (MRI). Analytical data for discrete tissues as well as the entire torso are presented. Generalized equations were derived that enable calculation of whole-torso SAR over a broad range of conditions. In addition, the impedance method can generate data about internal distributions of SAR, which are needed to predict critical organs that might undergo excessive elevations of temperature. Fair to good agreement was found between impedance-method SAR and those predicted by simple phenomenological models.     

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation

Molecular dynamics simulations and free energy calculation have been performed to study how the single-chain variable fragment (scFv) binds methamphetamine (METH) and amphetamine (AMP). The structures of the scFv:METH and the scFv:AMP complexes are analyzed by examining the time-dependence of their RMSDs, by analyzing the distance between some key atoms of the selected residues, and by comparing the averaged structures with their corresponding crystallographic structures. It is observed that binding an AMP to the scFv does not cause significant changes to the binding pocket of the scFv:ligand complex. The binding free energy of scFv:AMP without introducing an extra water into the binding pocket is much stronger than scFv:METH. This is against the first of the two scenarios postulated in the experimental work of Celikel et al. (Protein Science 18, 2336 (2009)). However, adding a water to the AMP (at the position of the methyl group of METH), the binding free energy of the scFv:AMP-H2O complex, is found to be significantly weaker than scFv:METH. This is consistent with the second of the two scenarios given by Celikel et al. Decomposition of the binding energy into ligand-residue pair interactions shows that two residues (Tyr175 and Tyr177) have nearly-zero interactions with AMP in the scFv:AMP-H2O complex, whereas their interactions with METH in the scFv:METH complex are as large as -0.8 and -0.74 kcal mol^-1. The insights gained from this study may be helpful in designing more potent antibodies in treating METH abuse.     

Description of energy migration and trapping in photosystem I by a model with two distance scaling parameters

The energy transfer and trapping kinetics in the core antenna of Photosystem I are described in a new model in which the distance between the core antenna chlorophylls and P700 is proposed to be considerably longer than the distance between the chlorophylls within the antenna. Structurally, the model describes the Photosystem I core antenna as a regular sphere around P700, while energetically it consists of three levels representing the bulk antenna, P700 and the red-shifted antenna pigments absorbing at longer wavelength than P700, respectively. It is shown that the model explains experimental results obtained from the Photosystem I complex of the cyanobacterium Synechococcus sp. (A.R. Holzwarth, G. Schatz, H Brock, and E. Bittersman (1993) Biophys. J. 64: 1813–1826) quite well, and that no unrealistic charge separation rate and organization of the long-wavelength pigments has to be assumed. We suggest that excitation energy transfer and trapping in Photosystem I should be described as a ‘transfer-to-the-trap’-limited process     

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge‐based potential. Proteins 2017; 85:1046–1055. © 2017 Wiley Periodicals, Inc.     

Quantification of excitation energy distribution between photosystems based on a mechanistic model of photosynthetic electron transport

Absorbed light energy is converted into excitation energy. The excitation energy is distributed to photosystems depending on the wavelength and drives photochemical reactions. A non‐destructive, mechanistic and quantitative method for estimating the fraction of the excitation energy distributed to photosystem II (f) was developed. For the f values for two simultaneously provided actinic lights (ALs) with different spectral distributions to be estimated, photochemical yields of the photosystems were measured under the ALs and were then fitted to an electron transport model assuming the balance between the electron transport rates through the photosystems. For the method to be tested using leaves with different properties in terms of the long‐term and short‐term acclimation (adjustment of photosystem stoichiometry and state transition, respectively), the f values for red and far‐red light (R and FR) were estimated in leaves grown (~1 week) under white light without and with supplemental FR and adapted (~10 min) to R without and with supplemental FR. The f values for R were clearly greater than those for FR and those of leaves grown with and adapted to supplemental FR tended to be higher than the controls. These results are consistent with previous studies and therefore support the validity of the proposed method.     

Distribution and orientation of hydrogenase in various photosynthetic bacteria

All of the tested photosynthetic bacteria possessed hydrogenase activity. Cell membranes of representatives of the Chromatiaceae, Rhodospirillaceae, and Chlorobiaceae families were found to be impermeable to the oxidized redox dyes methyl viologen and benzyl viologen, whereas the reduced forms could easily penetrate the membranes. This permeability difference made possible the localization of the hydrogenase enzyme. Members of the Chromatiaceae and the Rhodospirillaceae contained a predominantly or exclusively membranebound enzyme. In contrast, the majority of hydrogenase activity was in the cytoplasm ofChlorobium limicola f. thiosulfatophilum. Hydrogenase, or at least its active center, was oriented toward the outer surface of the cell membrane in purple bacteria.