QUANTUM YIELD RATIO OF THE FORWARD and BACK LIGHT REACTIONS OF BACTERIORHODOPSIN T LOW TEMPERATURE and PHOTOSTEADY-STATE CONCENTRATION OF THE BATHOPRODUCT K*

The maximum photosteady state fraction of K, x_K^max, and the ratio of the quantum yields of the forward and back light reactions, trans-bacteriorhodopsin (bR) hArr; K, φ_bR/φ_K, were obtained by measuring the absorption changes produced by illumination of frozen water-glycerol (1:2) suspensions of light-adapted purple membrane at different wavelengths at -165°C. An independent method based on the second derivative of the absorption spectrum in the region of the β-bands was also used. It was found that The quantum yield ratio (0.66 ± 0.06) was found to be independent of excitation wavelength within experimental error in the range510–610 nm. The calculated absorption spectrum of K has its maximum at603–606 nm and an extinction 0.85 ± 0.03 that of bR. At shorter wavelengths there are P-bands at 410, 354 and 336 rim. Using the data of Hurley et al. (Nature 270,540–542, 1977) on relative rates of rhodopsin bleaching and K formation, the quantum yield of K formation was determined to be 0.66 ± 0.04 at low temperature. The quantum efficiency of the back reaction was estimated to be 0.93 ± 0.07. These values of quantum efficiencies of the forward and back light reactions of bR at - 165°C coincide with those recently obtained at room temperature. This indicates that the quantum efficiencies of both forward and back light reactions of bacteriorhodopsin are temperature independent down to -165°C.     

Solving generalized complex-symmetric eigenvalue problems arising from resonant MEMS simulations with PETSc

In the operation of high frequency resonators in micro electromechanical systems(MEMS), there is a strong need to be able to accurately determine the energy loss rates or alternatively the quality of resonance. The resonance quality is directly related to a designers ability to assemble a high fidelity system response for signal filtering, for example. This has implications on robustness and quality of electronic communication and also strongly influences overall rates of power consumption in such devices – i.e. battery life. An index of the quality of resonance Q is inversely proportional to the amount of energy loss existing in the system, and can be defined in terms of the complex-valued eigenvalues ω of the system as, . In this presentation, we examine methods for accurately simulating energy loss using the direct modeling of acoustic radiation via perfectly matched layer (PML) technology for 3-D structures, which results in complex-symmetric mass and stiffness matrices. Thus it is crucial that one is able to accurately compute eigenvalues of a complex-symmetric system. 3-D modeling increases the number of degrees of freedom and complexity in obtaining the solution, resulting in a requirement for more computing power and memory which can only be supplied by parallel computing methods. The simulations are conducted through the MEMS simulation software HiQLab in combination with the parallel numerical libraries PETSc and Trilinos. A modified smoothed aggregation algebraic multigrid method for solving a linear system of equations is combined with a Jacobi-Davidson method to solve for desired eigenvalues. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Oxygen evolving complex in photosystem II: better than excellent

The Oxygen Evolving Complex in photosystem II, which is responsible for the oxidation of water to oxygen in plants, algae and cyanobacteria, contains a cluster of one calcium and four manganese atoms. This cluster serves as a model for the splitting of water by energy obtained from sunlight. The recent published data on the mechanism and the structure of photosystem II provide a detailed architecture of the oxygen-evolving complex and the surrounding amino acids. Biomimetically, we expect to learn some strategies from this natural system to synthesize an efficient catalyst for water oxidation, that is necessary for artificial photosynthesis.     

A manganese oxide with phenol groups as a promising structural model for water oxidizing complex in Photosystem II: a 'golden fish'

We describe here the ability of manganese oxide monosheets to aggregate to form layered structures with 4-aminophenol molecules. These aggregated monosheets could be considered as the first step to synthesize a self-assembled layered hybrid of phenol-manganese ions with phenol and manganese(III) and (IV) as exists in the water oxidizing complex of Photosystem II.     

PHOTOCHEMISTRY OF METHYLATED RHODOPSINS

Abstract— Rhodopsin, in which the active-site Schiff-base lysine has been chemically modified by monomethylation, is unable to form the deprotonated Schiff base bleaching intermediate, rnetarhodop-sin II. The photochemistry of the methylated Schiff base rhodopsin stops at the metarhodopsin I stage, which then slowly decays to all-trans retinal and opsin. Methylation of the non active-site lysines does not block the photochemical transformation but does speed up the formation and decay of the metarhodopsins.     

pH DEPENDENCE OF THE ABSORPTION SPECTRA AND PHOTOCHEMICAL TRANSFORMATIONS OF THE ARCHAERHODOPSINS

Abstract —Two strains of archaebacteria have been found to contain light-driven proton pumping pigments analogous to bacteriorhodopsin (bR) in Halobacterium salinarium . These proteins are called archaerhodopsin-1 (aR-1) and archaerhodopsin-2 (aR-2). Their high degree of sequence identity with bR within the putative proton channel enables us to draw some conclusions about the roles of regions where differences in amino acids exist, and in particular the surface residues, on the structure and function of retinal-based proton pumps. We have characterized the spectral and photochemical properties of these two proteins and compared them to the corresponding properties of bR. While there are some differences in absorbance maxima and kinetics of the photocycle, most of the properties of aR-1 and aR-2 are similar to those of bR. The most striking differences of these proteins with bR are the lack of an alkaline-induced red-shifted absorption species and a dramatic (apparent) decrease in the light-induced transient proton release. In membrane sheet suspensions of aR-1 at 0.15 M KCI, the order of proton release and uptake appears opposite that of bR, in which proton release precedes uptake. The nature of this behavior appears to be due to differences in the amino acid sequence at the surfaces of the proteins. In particular, the residue corresponding to the lysine at position 129 of the extracellular loop region of bR is a histidine in aR-1 and could regulate the efficient release of protons into solution in bR.     

PROPERTIES OF SYNTHETIC BACTERIORHODOPSIN PIGMENTS. FURTHER PROBES OF THE CHROMOPHORE BINDING SITE

Abstract— A series of retinals with specific structural alterations have been synthesized to probe the bacteriorhodopsin binding site. The 4-chloro-, 4-bromo- and 4-iodoretinals all form pigments with bacterioopsin but undergo an in situ displacement of the allylic halogen to form the 4-hydroxyretinal pigment. Several naphthyl retinals were prepared which effectively extend the polyene chain and/or add bulk to the ring portion of the chromophore. All the naphthyl retinals form pigments with bacterioopsin but only the pigment containing the derivative with a polyene side chain identical to that of retinal pumps protons efficiently. The 12-butyl-13-desmethylretinal was also synthesized but this analogue did not form a pigment with bacterioopsin. These results confirm the nonspecificity at the ring portion of the chromophore binding site and the importance of the role of the polyene chain in the proton pumping function of bacteriorhodopsin.     

CHLOROPHYLL a FLUORESCENCE OF GONYAULAX POLYEDRA GROWN ON A LIGHT-DARK CYCLE AND AFTER TRANSFER TO CONSTANT LIGHT

Abstract— The chlorophyll a fluorescence properties of Gonyaulax polyedra cells before and after transfer from a lightdark cycle (LD) to constant dim light (LL) were investigated. The latter display a faster fluorescence transient from the level ‘I’ (intermediary peak) to ‘D’ (dip) to ‘P’ (peak) than the former (3 s as compared to 10 s), and a different pattern of decline in fluorescence from ‘I’ to ‘D’ and from ‘P’ to the steady state level with no clearly separable second wave of slow fluorescence change, referred to as ‘s' (quasi steady state)→‘M’ (maximum) →‘T’ (terminal steady state). The above differences are constant features of cells in LD and LL, and are not dependent on the time of day. They are interpreted as evidence for a greater ratio of photosystem II/photosystem I activity in cells in LL. After an initial photoadaptive response following transfer from LD to LL, the cell absorbance at room temperature and fluorescence emission spectra at 77 K for cells in LL and LD are comparable. The major emission peak is at 685–688 nm (from an antenna Chl a 680, perhaps Chl a-c complex), but, unlike higher plants and other algae, the emission bands at 696–698 nm (from Chl a_II complex, Chl a 685, close to reaction center II) and 710–720 nm (from Chl a₁, complexes, Chl a 695, close to reaction center I) are very minor and could be observed only in the fluorescence emission difference spectra of LL minus LD cells and in the ratio spectra of DCMU-treated to non-treated cells. Comparison of emission spectra of cells in LL and LD suggested that, in LL, there is a slightly greater net excitation energy transfer from the light-harvesting peridinin-Chl a (Chl a 670) complex, fluorescing at 675 nm, to the other antenna chlorophyll a complex fluorescing at 685–688 nm, and from the Chl a., complex to the reaction center II. Comparison of excitation spectra of fluorescence of LL and LD cells, in the presence of DCMU, confirmed that cells in LL transfer energy more extensively from the peridinin-Chl a complex to other Chl a complexes than do cells in LD.     

TEMPERATURE DEPENDENCE OF DELAYED LIGHT EMISSION IN THE 6 to 340 MICROSECOND RANGE AFTER A SINGLE FLASH IN CHLOROPLASTS

Abstract. The delayed light emission decay rate (up to 120 μs) and the rise in chlorophyll a fluorescence yield (from 3 to 35 μs) in isolated chloroplasts from several species, following a saturating 10 ns flash, are temperature independent in the 0–35°C range. However, delayed light in the 120–340 μs range is temperature dependent. Arrhenius plots of the exponential decay constants are: (a) linear for lettuce and pea chloroplasts but discontinuous for bush bean (12–17°C) and spinach (12–20°C) chloroplasts; (b) unaffected by 3-(3,4 dichlorophenyl)-1,1-dimethylurea (inhibitor of electron flow), gramicidin D (which eliminates light-induced membrane potential) and glutaraldehyde fixation (which stops gross structural changes).
The discontinuities, noted above for bush bean and spinach chloroplasts, are correlated with abrupt changes in (a) the thylakoid membrane lipid fluidity (monitored by EPR spectra of 12 nixtroxide stearate, 12NS) and (b) the fluidity of extracted lipids (monitored by differential calorimetry and EPR spectra of 12 NS). However, no such discontinuity was observed in (a) chlorophyll a fluorescence intensity of thylakoids and (b) fluorescence of tryptophan residues of delipidated chloroplasts.
Microsecond delayed light is linearly dependent on light intensity at flash intensities as low as one quantum per 2 times 10⁴ chlorophyll molecules. We suggest that this delayed light could originate from a one quantum process in agreement with the hypothesis that recombination of primary charges leads to this light emission. A working hypothesis for the energy levels of Photosystem II components is proposed involving a charge stabilization step on the primary acceptor side, which is in a lipid environment.
Finally, the redox potential of P680 (the reaction center for chlorophyll of system II) is calculated to be close to 1.0–1.3 V.