The molar extinction coefficient of bacteriochlorophyll e and the pigment stoichiometry in Chlorobium phaeobacteroides

We have determined the molar extinction coefficient of bacteriochlorophyll (BChl) e, the main light-harvesting pigment from brown-coloured photosynthetic sulfur bacteria. The extinction coefficient was determined using pure [Pr,E]BChl e_F isolated by reversed-phase HPLC from crude pigment extracts of Chlorobium (Chl.) phaeobacteroides strain CL1401. The extinction coefficients at the Soret and Q_y bands were determined in four organic solvents. The extinction coefficient of BChl e differs from those of other related Chlorobium chlorophylls (BChl c and BChl d) but is similar to that of chlorophyll b. The determined extinction coefficient was used to calculate the stoichiometric BChl e to BChl a and BChl e to carotenoids ratios in whole cells and isolated chlorosomes from Chl. phaeobacteroides strain CL1401 using the spectrum-reconstruction method (SRCM) described by Naqvi et al. (1997) (Spectrochim Acta A Mol Biomol Spectrosc 53: 2229–2234) . In isolated chlorosomes, BChl a content was ca. 1% of the total BChl content and the stoichiometric ratio of BChl e to carotenoids was 6. In whole cells, however, BChl a content was 3–4%, owing to the presence of BChl a-containing elements, i.e. FMO protein and reaction centre. An average of 5 BChl e molecules per carotenoid was determined in whole cells.     

Experimental determination of the molar differential extinction coefficient of P700

The molar differential extinction coefficients of P700 at 435 and 703 nm have been determined by using a directly coupled reaction in the dark involving the reduction of photooxidized P700 and the oxidation of reduced cytochromes.From the coupled oxidation of mammalian cytochrome c by Anabaena high-P700 particles, the molar differential extinction coefficients of P700 at 435 and 703 nm are calculated to be 8.6·10⁴ and 1.20·10⁵ M⁻¹·cm⁻¹, respectively, and the ratio of the red to blue band heights is 1.4.From the coupled oxidation of Euglena cytochrome-552 by Triton-fractionated pigment system 1 subchloroplast particles enriched in P700, the calculated molar differential extinction coefficients of P700 at 435 and 703 nm are very close to the values given above.Using an absorbance decrease at 580 nm as a measure of the photoreduction of dichlorophenolindophenol by Triton-fractionated pigment system 1 subchloroplast particles enriched in P700 tends to yield a low extinction value because of other absorbance changes which occur at this wavelength and the non-reproducibility of the values obtained.Comparisons are made between the extinction values of P700 and the corresponding extinction values of the bacteriochlorophyll reaction centers in photosynthetic bacteria.     

A method for the determination of the molar extinction coefficient of structure-linked chromophores

Synopsis This paper describes a general method for the determination of the molar extinction ceefficient of a chromophore covalently bound to structure-linked groups, without isolating the compound formed. The method is illustrated by the determination of the molar extinction coefficient of the reaction product of 2,4-dinitro-1-fluorobenzene (DNFB) with films of aminoethyl-cellulose (AE-cellulose). The method is based on the relation between the decrease in extinction of a DNFB staining solution and the increase in extinction of the AE-cellulose after staining as measured in a film-spectrophotometer. In addition, the value of the molar extinction coefficient was used in establishing reaction conditions for a quantitative staining procedure for determining amino groups with DNFB and picric acid. Conditions of optimum DNFB staining were determined and the measured extinction was converted into concentration of amino groups using the molar extinction coefficient. The amino group concentration of the same batch of AE-cellulose was also determined, after finding the optimum reaction conditions, by staining with picric acid. The results, when compared, showed a linear relationship with a slope of unity for batches of AE-cellulose of varying amino group concentrations. This is consistent with the same stoichiometry in both cases and indicates that in both procedures one chromophore molecule has reacted with one amino group and that this reaction has proceeded to completion. The general applicability of the method is discussed.     

Determination of the molar extinction coefficient for the ferric reducing/antioxidant power assay

The FRAP reagent contains 2,4,6-tris(2-pyridyl)-s-triazine, which forms a blue–violet complex ion in the presence of ferrous ions. Although the FRAP (ferric reducing/antioxidant power) assay is popular and has been in use for many years, the correct molar extinction coefficient of this complex ion under FRAP assay conditions has never been published, casting doubt on the validity of previous calibrations. A previously reported value of 19,800 is an underestimate. We determined that the molar extinction coefficient was 21,140. The value of the molar extinction coefficient was also shown to depend on the type of assay and was found to be 22,230 under iron assay conditions, in good agreement with published data. Redox titration indicated that the ferrous sulfate heptahydrate calibrator recommended by Benzie and Strain, the FRAP assay inventors, is prone to efflorescence and, therefore, is unreliable. Ferrous ammonium sulfate hexahydrate in dilute sulfuric acid was a more stable alternative. Few authors publish their calibration data, and this makes comparative analyses impossible. A critical examination of the limited number of examples of calibration data in the published literature reveals only that Benzie and Strain obtained a satisfactory calibration using their method.     

The structure of bovine rhodopsin

We have isolated 16 peptides from a cyanogen bromide digest of rhodopsin. These cyanogen bromide peptides account for the complete composition of the protein. Methionine-containing peptides from other chemical and enzymatic digests of rhodopsin have allowed us to place the cyanogen bromide peptides in order, yielding the sequence of the protein. We have completed the sequence of most of the cyanogen bromide peptides. This information, in conjunction with that from other laboratories, forms the basis for our prediction of the secondary structure of the protein and how it may be arranged in the disk membrane.     

The signaling pathway of rhodopsin

The signal-transduction mechanism of rhodopsin was studied by molecular dynamics (MD) simulations of the high-resolution, inactive structure in an explicit membrane environment. The simulations were employed to calculate equal-time correlations of the fluctuating interaction energy of residue pairs. The resulting interaction-correlation matrix was used to determine a network that couples retinal to the cytoplasmic interface, where transducin binds. Two highly conserved motifs, D(E)RY and NPxxY, were found to have strong interaction correlation with retinal. MD simulations with restraints on each transmembrane helix indicated that the major signal-transduction pathway involves the interdigitating side chains of helices VI and VII. The functional roles of specific residues were elucidated by the calculated effect of retinal isomerization from 11-cis to all-trans on the residue-residue interaction pattern. It is suggested that Glu134 may act as a "signal amplifier" and that Asp83 may introduce a threshold to prevent background noise from activating rhodopsin.     

The active-site environment of rhodopsin

The 11-cis-retinal binding site of rhodopsin is of great interest because it is buried in the membrane but yet must provide an environment for charged amino acids. In addition, the active-site lysine residue must be able to engage in rapid Schiff base formation with 11-cis-retinal at neutral and lower pH values. This requires that this lysine be unprotonated. We have begun to study the environment of the active-site lysine using a reporter group adducted to it. Non-active-site permethylated opsin was reacted with 5-nitrosalicylaldehyde, and the resulting Schiff base was permanently fixed by borohydride reduction. The stoichiometry of incorporation was one. This chromophoric and pH-sensitive reporter group affords information on the active-site environment of rhodopsin by determining the ionization constants of its ionizable groups at different pH values. The pH titration of the modified protein showed a single pKa = 7.8 +/- 0.19 ascribable to the ionization of the phenol. The ionization of the modified lysine residue was not observed at all pH values studied. These studies are interpreted to mean that a negatively charged amino acid is propinquous to the active-site lysine residue and that this latter residue does not have an unusually low pKa.     

Spectrophotometric quantitation of protochlorophyll(ide): Specific absorption and molar extinction coefficients reconsidered

To allay doubt about how to calculate molar extinction eoeffieients from the specific absorption coefficients of protoehlorophyll(ide), dark-grown leaf segments and saponin protochlorophyll(ide) holochrome subunits frotn barley ( Hordeum vulgare L.) and cotyledons of cucumber ( Cucumis sativus L.) were extracted with acetone without or following prior, brief illumination. Absorbance data and eoeffieients of chlorophyll a were used to derive extinetion eoeffieients of protoehlorophyll(ide); 626 nm (range: 30 to 35 1 mmol^-1 cm^-1) without recourse to published coefficients c protochlorophyll(ide). These results combined with evaluation of how the origin; coefficients were obtained, argue for using the molecular weight of protochlorophy rather than protochlorophyllide to calculate molar extinction eoeffieients from th specific absorption coefficients.     

Pigment content and molar extinction coefficients of photochemical reaction centers from Rhodopseudomonas spheroides

Reaction center particles isolated from carotenoidless mutant Rhodopseudomonas spheroides were studied with the aim of determining the pigment composition and the molar extinction coefficients.

Two independent sets of measurements using a variety of methods show that a sample with A_{800 nm} = 1.00 contains 20.8 ± 0.8 μM tetrapyrrole and that the ratio of bacteriochlorophyll to bacteriopheophytin is 2:1.

Measurements were made of the absorption changes attending the oxidation of cytochrome c coupled to reduction of the photooxidized primary electron donor in reaction centers, using laser flash excitation. The ratio of the absorption change at 865 nm (due to the bleaching of P870) to that at 550 nm (oxidation of cytochrome) was found to be 5.77.

These results, combined with other data, yield a pigment composition of 4 bacteriochlorophyll and 2 bacteriopheophytin molecules in a reaction center. Based on this choice, extinction coefficients are determined for the 802- and 865-nm bands: _{802 nm} = 288 (± 14) mM⁻¹ · cm⁻¹ and _{865 nm} = 128 (± 6) mM⁻¹ · cm⁻¹. For reversible bleaching of the 865-nm band, Δ^{red - ox}_865nm = 112 (± 6) mM⁻¹ · cm⁻¹ (referred to the molarity of reaction centers). Earlier reported values of photochemical quantum efficiency are recomputed, and the revised values are shown to be compatible with those obtained from measurements of fluorescence transients.     

The causes of extinction

A species may go extinct either because it is unable to evolve rapidly enough to meet changing circumstances, or because its niche disappears and no capacity for rapid evolution could have saved it. Although recent extinctions can usually be interpreted as resulting from niche disappearance, the taxonomic distribution of parthenogens suggests that inability to evolve may also be important. A second distinction is between physical and biotic causes of extinction. Fossil evidence for constant taxonomic diversity, combined with species turnover, implies that biotic factors have been important. A similar conclusion emerges from studies of recent introductions of predators, competitors and parasites into new areas. The term 'species selection' should be confined to cases in which the outcome of selection is determined by properties of the population as a whole, rather than of individuals. The process has been of only trivial importance in producing complex adaptations, but of major importance in determining the distribution of different types of organisms. An adequate interpretation of the fossil record requires a theory of the coevolution of many interacting species. Such a theory is at present lacking, but various approaches to it are discussed.     

The nature of extinction

The phenomenon of species extinction raises more and more concern among ecologists facing the actual crisis of biodiversity. Scientific investigations of the causes and effects of extinction must be completed by a philosophical analysis of the concept of extinction that aims to clarify the meanings of the term 'extinction' and to analyse modalities, criteria and degrees of extinction. We will focus our attention on the apparent paradox of the possible 'resurrection' of species in the near future with the help of genetic biotechnology and cloning techniques. The ontological background of the extinction concept is analysed in relation to the idea of species as classes. We will also show that there is no simple analogy between death and species extinction, and develop a conceptualist and dualistic system of supra-individual entities (species vs. population), supported by an instrumentalist approach to genetic manipulations which transform species into interactive kinds, which can go extinct and be recreated.     

The rhodopsin system of the squid

Squid rhodopsin (λ_max 493 mµ)—like vertebrate rhodopsins—contains a retinene chromophore linked to a protein, opsin. Light transforms rhodopsin to lumi- and metarhodopsin. However, whereas vertebrate metarhodopsin at physiological temperatures decomposes into retinene and opsin, squid metarhodopsin is stable. Light also converts squid metarhodopsin to rhodopsin. Rhodopsin is therefore regenerated from metarhodopsin in the light. Irradiation of rhodopsin or metarhodopsin produces a steady state by promoting the reactions, See PDF for Equation Squid rhodopsin contains neo-b (11-cis) retinene; metarhodopsin all-trans retinene. The interconversion of rhodopsin and metarhodopsin involves only the stereoisomerization of their chromophores. Squid metarhodopsin is a pH indicator, red (λ_max 500 mµ) near neutrality, yellow (λ_max 380 mµ) in alkaline solution. The two forms—acid and alkaline metarhodopsin—are interconverted according to the equation, Alkaline metarhodopsin + H⁺ acid metarhodopsin, with pK 7.7. In both forms, retinene is attached to opsin at the same site as in rhodopsin. However, metarhodopsin decomposes more readily than rhodopsin into retinene and opsin. The opsins apparently fit the shape of the neo-b chromophore. When light isomerizes the chromophore to the all-trans configuration, squid opsin accepts the all-trans chromophore, while vertebrate opsins do not and hence release all-trans retinene. Light triggers vision by affecting directly the shape of the retinene chromophore. This changes its relationship with opsin, so initiating a train of chemical reactions.     

The action of enzymes on rhodopsin

The effects have been examined of chymotrypsin, pepsin, trypsin, and pancreatic lipase on cattle rhodopsin in digitonin solution. The digestion of rhodopsin by chymotrypsin was measured by the hydrolysis of peptide bonds (formol titration), changes in pH, and bleaching. The digestion proceeds in two stages: an initial rapid hydrolysis which exposes about 30 amino groups per molecule, without bleaching; superimposed on a slower hydrolysis which exposes about 50 additional amino groups, with proportionate bleaching. The chymotryptic action begins at pH about 6.0 and increases logarithmically in rate to pH 9.2. Trypsin and pepsin also bleach rhodopsin in solution. A preparation of pancreatic lipase bleached it slightly, but no more than could be explained by contamination with proteases. In digitonin solution each rhodopsin molecule is associated in a micelle with about 200 molecules of digitonin; yet the latter do not appear to hinder enzyme action. It is suggested that the digitonin sheath is sufficiently fluid to be penetrated on collision with an enzyme molecule; and that once together the enzyme and substrate are held together by intermolecular attractive forces, and by the "cage effect" of bombardment by surrounding solvent molecules. The two stages of chymotryptic digestion of rhodopsin may correspond to an initial rapid fragmentation, such as has been observed with many proteinases and substrates; superimposed upon a slower digestion of the fragments. Since the first phase involves no bleaching, this may mean that rhodopsin can be broken into considerably smaller fragments without loss of optical properties.     

Efficient sensitization of nanocrystalline TiO2 films with high molar extinction coefficient ruthenium complex

A novel heteroleptic polypyridine ruthenium complex, cis-Ru(L1)(L2)(NCS)₂, L1 = 4,4′-dicarboxylic acid-2,2′-bipyridine (dcbpy), L2 = 4,4′-bis[p-diethylamino]-α-styryl]-2,2′-bipyridine, was synthesized. The dye displays extremely high molar extinction coefficient, which is comparable with organic dye. Preliminary test shows the dye-sensitized TiO₂ solar cell gives high conversion efficiency up to 8.65% under 1 Sun, while 8.35% is given for N3 based DSCs under the same condition. The dye will be further employed in solid state DSCs with hole transport material.