Circular dichroism of cephalopod rhodopsin and its intermediates in the bleaching and photoregeneration process.

In the bleaching process of cephalopod rhodopsin, a new intermediate was found in the conversion process from lumirhodopsin to metarhodopsin. This intermediate of octopus has an absorption peak at about 475 nm and has been named as M475. The circular dichroism value of M475 is too small to be evaluated. On the other hand, lumirhodopsin shows a negative CD at 470 nm, a positive CD at 350 nm and a large positive CD band with three peaks at 280, 287 and 295 nm. Such a large CD band in the ultraviolet region is not observed in rhodopsin, M475 and metarhodopsin. This CD seems to be mainly due to tryptophan and tyrosine residues restricted in free rotation in the protein moiety of lumirhodopsin. The intermediate in the photoregeneration process of cephalopod rhodopsin, P380, has a positive CD band at the main peak, 380 nm, and also a large positive CD band in the ultraviolet region like lumirhodopsin.     

Photolysis intermediates of human rhodopsin.

Photochemical studies were conducted on human rhodopsin at 20 degrees C to characterize the intermediates which precede the formation of metarhodopsin II, the trigger for the enzyme cascade mechanism of visual transduction. Human rhodopsin was prepared from eyes which had previously been used for corneal donations. Time resolved absorption spectra collected from 10(-8) to 10(-6) s after photolysis of human rhodopsin in detergent suspensions displayed biexponential decay kinetics. The apparent lifetimes obtained from the data are 65 +/- 20 and 292 +/- 25 ns, almost a factor of 2 slower than the corresponding rates in bovine rhodopsin. The spectra can be fit well using a model in which human bathorhodopsin decays toward equilibrium with a blue-shifted intermediate (BSI) which then decays to lumirhodopsin. Spectra and kinetic rate constants were determined for all these intermediates using a global analysis which showed that the spectra of the human intermediates are remarkably similar to bovine intermediates. Microscopic rate constants derived from this model are 7.4 x 10(6) s-1 for bathorhodopsin decay and 7.5 x 10(6) s-1 and 4.6 x 10(6) s-1 for the forward and reverse reactions of BSI, respectively. Decay of lumirhodopsin to later intermediates was studied from 10(-6) to 10(-1) s after photolysis of rhodopsin in human disk membrane suspensions. The human metarhodopsin I in equilibrium metarhodopsin II equilibrium appears to be more forward shifted than in comparable bovine studies.     

The role of sulfhydryl groups in the bleaching and synthesis of rhodopsin

The condensation of retinene₁ with opsin to form rhodopsin is optimal at pH about 6, a pH which favors the condensation of retinene₁ with sulfhydryl rather than with amino groups. The synthesis of rhodopsin, though unaffected by the less powerful sulfhydryl reagents, monoiodoacetic acid and its amide, is inhibited completely by p-chloromercuribenzoate (PCMB). This inhibition is reversed in part by the addition of glutathione. PCMB does not attack rhodopsin itself, nor does it react with retinene₁. Its action in this system is confined to the —SH groups of opsin. Under some conditions the synthesis of rhodopsin is aided by the presence of such a sulfhydryl compound as glutathione, which helps to keep the —SH groups of opsin free and reduced. By means of the amperometric silver titration of Kolthoff and Harris, it is shown that sulfhydryl groups are liberated in the bleaching of rhodopsin, two such groups for each retinene₁ molecule that appears. This is true equally of rhodopsin from the retinas of cattle, frogs) and squid. The exposure of new sulfhydryl groups adds an important element to the growing evidence that relates the bleaching of rhodopsin to protein denaturation. The place of sulfhydryl groups in the structure of rhodopsin is still uncertain. They may be concerned directly in binding the chromophore to opsin; or alternatively they may furnish hydrogen atoms for some reductive change by which the chromophore is formed from retinene₁. In the amperometric silver titration, the bleaching of rhodopsin yields directly an electrical variation. This phenomenon may have some fundamental connection with the role of rhodopsin in visual excitation, and may provide a model of the excitation process in general.     

Pressure induced intermediates in the photochemical reaction of squid rhodopsin.

Studies of the pressure effect on the photochemical reaction of squid rhodopsin have been initiated. On irradiation of rhodopsin with blue light at 6 kb, an intermediate having absorption maximum at 502 nm appeared, which we call p-lumirhodopsin. Upon release of pressure, a new intermediate having absorption maximum at 472 nm, which we call p-LM-rhodopsin. Molar free volume change takes place in the transformations of p-lumirhodopsin → p-LM-rhodopsin and p-LM-rhodopsin → Metarhodopsin.     

New intermediates in the photochemical transformation of rhodopsin

The conditions of preferential accumulation of intermediates of the photochemical reaction cycle of bacteriorhodopsin (BR) P550 and P419 at low temperature are found. Upon illumination P550 and P419 undergo photochemical conversions into the light-adapted form of BR (P570), forming during this conversions a number of new intermediates: P550 leads to P560-- -- -- leads to P570; P419 leads to P421-- -- -- leads to P565-- -- -- leads to P585-- -- -- leads to P570; P419 leads to P470-- -- -- leads to P570. All intermediates are photoactive. All light reactions are photoreversible and give formation to the products with absorption maximum shifted to the red as compared to the initial state. The absorption spectra of intermediates are complex and include several bands which are more pronounced in the spectrum of P419 (maxima at 442, 419, 398 nm, a shoulder at 375 nm) and P421, less in the spectrum of P570 (maximum at 578 nm, shoulders at 540 and 608 nm) and others.     

Transition dipole orientations in the early photolysis intermediates of rhodopsin.

The linear dichroism spectrum of rhodopsin in sonicated bovine disk membranes was measured 30, 60, 170, and 600 ns after room temperature photolysis with a linearly polarized, 7-ns laser pulse (lambda = 355 or 477 nm). A global exponential fitting procedure based on singular value decomposition was used to fit the linear dichroism data to two exponential processes which differed spectrally from one another and whose lifetimes were 42 +/- 7 ns and 225 +/- 40 ns. These results are interpreted in terms of a sequential model where bathorhodopsin (BATHO, lambda max = 543 nm) decays toward equilibrium with a blue shifted intermediate (BSI, lambda max = 478 nm). BSI then decays to lumirhodopsin (LUMI, lambda max = 492 nm). It has been suggested that two bathorhodopsins decay in parallel to their products. However, a Monte Carlo simulation of partial photolysis of solid-state visual pigment samples shows that one mechanism which creates populations of BATHO having different photolysis rates at 77 K may not be responsible for the two decay rates reported here at room temperature. The angle between the cis band and 498-nm band transition dipoles of rhodopsin is determined to be 38 degrees. The angles between both these transition dipoles and those of the long-wave-length bands of BATHO, BSI, and LUMI are also determined. It is shown that when BATHO is formed its transition dipole moves away from the original cis band transition dipole direction. The transition dipole then moves roughly twice as much towards the original cis band direction when BSI appears. Production of LUMI is associated with return of the transition dipole almost to the original orientation relative to the cis band, but with some displacement normal to the plane which contains the previous motions. The correlation between the lambda max of an intermediate and its transition dipole direction is discussed.     

Transient spectra of intermediates in the photolytic sequence of octopus rhodopsin.

The intermediate photolytic sequence of octopus rhodopsin was studied at different temperatures and different pH values by means of a flash photolysis-rapid scan spectrophotometry near physiological temperature. The first photoproduct in the photolysis of rhodopsin was lumirhodopsin. Transformation of lumirhodopsin leads to mesorhodopsin took place independently of the pH of the solution. Mesorhodopsin was transformed to acid metarhodopsin in acid solution. In alkaline solution, mesorhodopsin was transformed to transient acid metarhodopsin whose absorption spectrum was similar to acid metarhodopsin. Transient acid metarhodopsin was then transformed to alkaline metarhodopsin reaching a tautomeric equilibrium which was determined by the pH of the solution.     

Identification of a rhodopsin photoreceptor in Euglena gracilis.

Visual pigments are a class of receptor proteins that absorb light and trigger sensory signals. Retinal-containing proteins are used in nature as photoreceptors mainly in animals vision. Mammalian rhodopsin is the best studied example of a light sensor which couples photon absorption to a cascade of biochemical reactions amplifying the input signal. A surprising discovery was to find rhodopsin also in Archaebacteria and in unicellular eukaryotes. On the basis of absorption microspectroscopic measurements and of inhibition experiments on pigment biosynthetic pathways, we have recently suggested that a rhodopsin could be the functional receptor of the visual process in Euglena gracilis, a flagellate which can use light directly to promote photosynthetic reactions, or as an incident flux of information to adjust its swimming orientation. We here report purification and identification of all-trans-retinal by column chromatography, HPLC and GC-MS in E. gracilis; these findings indicate with absolute certainty that rhodopsin is the photoreceptor molecule of this microorganism.     

Proton movement and photointermediate kinetics in rhodopsin mutants

The role of ionizable amino acid side chains in the bovine rhodopsin activation mechanism was studied in mutants E134Q, E134R/R135E, H211F, and E122Q. All mutants exhibited bathorhodopsin stability on the 30 ns to 1 micros time scale similar to that of the wild type. Lumirhodopsin decay was also similar to that of the wild type except for the H211F mutant where early decay (20 micros) to a second form of lumirhodopsin was seen, followed by formation of an extremely long-lived Meta I(480) product (34 ms), an intermediate which forms to a much reduced extent, if at all, in dodecyl maltoside suspensions of wild-type rhodopsin. A smaller amount of a similar long-lived Meta I(480) product was seen after photolysis of E122Q, but E134Q and E134R/R135Q displayed kinetics much more similar to those of the wild type under these conditions (i.e., no Meta I(480) product). These results support the idea that specific interaction of His211 and Glu122 plays a significant role in deprotonation of the retinylidene Schiff base and receptor activation. Proton uptake measurements using bromcresol purple showed that E122Q was qualitatively similar to wild-type rhodopsin, with at least one proton being released during lumirhodopsin decay per Meta I(380) intermediate formed, followed by uptake of at least two protons per rhodopsin bleached on a time scale of tens of milliseconds. Different results were obtained for H211F, E134Q, and E134R/R135E, which all released approximately two protons per rhodopsin bleached. These results show that several ionizable groups besides the Schiff base imine are affected by the structural changes involved in rhodopsin activation. At least two proton uptake groups and probably at least one proton release group in addition to the Schiff base are present in rhodopsin.     

Identification of the autophosphorylation sites in rhodopsin kinase.

Rhodopsin kinase (RK) is a second-messenger-independent protein kinase that is involved in deactivation of photolyzed rhodopsin (Rho*). We have developed a significantly improved method for isolation of RK based on the specific interactions of phosphorylated forms of the enzyme with heparin-Sepharose. Conversion of the dephosphorylated form of RK to the fully phosphorylated enzyme leads to specific elution of the kinase from the resin. Limited proteolysis of RK with endoproteinase Asp-N removes the phosphorylation sites. Peptides containing the autophosphorylation sites were isolated by reverse-phase high performance liquid chromatography and analyzed by Edman degradation and tandem mass spectrometry. The derived amino acid sequence of the peptide containing the major autophosphorylation site yielded the following sequence: DVGAFS488T489VKGVAFEK, where Ser488 and Thr489 are phosphorylated. Additionally, a minor autophosphorylation site was identified at Ser21. A 15-residue peptide (DVGAFSTVKGVAFEK) encompassing the major autophosphorylation site was synthesized and used for phosphorylation and inhibition studies. In contrast to many other protein kinases, the low catalytic activity of RK toward its autophosphorylation site peptide and the poor inhibitory properties of this peptide suggest unique properties of this member of the family of G protein-coupled receptor kinases.     

Radical intermediates involved in the bleaching of the carotenoid crocin. Hydroxyl radicals, superoxide anions and hydrated electrons

The participation of the primary radicals in the bleaching of aqueous solutions of the carotenoid crocin by ionizing radiation was investigated, employing both X-radiolysis and pulse radiolysis. The pulse-radiolytic data demonstrated a very rapid diffusion-controlled attack by both hydroxyl radicals (.OH) and hydrated electrons (eaq-), while superoxide anions (O2-) did not react at all. The site of the initial reaction of these radicals was not limited to the polyene chromophore. Slower secondary reactions involving crocin alkyl or peroxy radicals contribute mainly to the overall bleaching, in particular during steady-state irradiation.     

Transient spectra of intermediates in the photolytic sequence of octopus rhodopsin

The intermediate photolytic sequence of octopus rhodopsin was studied at different temperatures and different pH values by means of a flash photolysisrapid scan spectrophotometry near physiological temperature.The first photoproduct in the photolysis of rhodopsin was lumirhodopsin. Transformation of lumirhodopsin → mesorhodopsin took place independently of the pH of the solution. Mesorhodopsin was transformed to acid metarhodopsin in acid solution. In alkaline solution, mesorhodopsin was transformed to transient acid metarhodospsin whose absorption spectrum was similar to acid metarhodopsin. Transient acid metarhodopsin was then transformed to alkaline metarhodopsin reaching a tautomeric equilibrium which was determined by the pH of the solution.     

Two forms of intermediates of frog rhodopsin in rod outer segments

Using frog rod outer segments, we measured changes of the absorption spectrum during the conversion of rhodopsin to a photosteady-state mixture composed of rhodopsin, isorhodopsin and bathorhodopsin by irradiation with blue light (440 nm) at ? 190°C and during the reversion of bathorhodopsin to a mixture of rhodopsin and isorhodopsin by irradiation with red light (718 nm) at ? 190°C. The reaction kinetics was expressed by one exponential in the former case and by two exponentials in the latter. These results suggest that rhodopsin is composed of a single molecular species, while bathorhodopsin is composed of two kinds of molecular species designated as batho₁-rhodopsin and batho₂-rhodopsin. On warming the two forms of bathorhodopsin, each bathorhodopsin converted to its own lumirhodopsin, metarhodopsin I and finally a free all-trans-retinal plus opsin. The absorption spectra of the two forms of bathorhodopsin, lumirhodopsin and metarhodopsin I were measured at ? 190°C. We infer that a rhodopsin molecule in the excited state relaxes to either batho₁-rhodopsin or batho₂-rhodopsin, and then converts to its own intermediates through one of the two parallel pathways.     

Hybridization kinetics and thermodynamics of molecular beacons

Molecular beacons are increasingly being used in many applications involving nucleic acid detection and quantification. The stem–loop structure of molecular beacons provides a competing reaction for probe–target hybridization that serves to increase probe specificity, which is particularly useful when single-base discrimination is desired. To fully realize the potential of molecular beacons, it is necessary to optimize their structure. Here we report a systematic study of the thermodynamic and kinetic parameters that describe the molecular beacon structure–function relationship. Both probe and stem lengths are shown to have a significant impact on the binding specificity and hybridization kinetic rates of molecular beacons. Specifically, molecular beacons with longer stem lengths have an improved ability to discriminate between targets over a broader range of temperatures. However, this is accompanied by a decrease in the rate of molecular beacon–target hybridization. Molecular beacons with longer probe lengths tend to have lower dissociation constants, increased kinetic rate constants, and decreased specificity. Molecular beacons with very short stems have a lower signal-to-background ratio than molecular beacons with longer stems. These features have significant implications for the design of molecular beacons for various applications.     

Nicotinamide-dependent one-electron and two-electron (flavin) oxidoreduction: thermodynamics, kinetics, and mechanism.

1. Biological nicotinamide-dependent oxidoreduction consists of reversible 2e- oxidoreduction of substrates. A mechanism involving subsequent 1e- steps is shown to be very unfavourable due to the high energy of the nicotinamide radical. 2. Free energy relationships provide a convenient tool, allowing one to differentiate between hydride transfer and hydrogen atom transfer. It is concluded that biological nicotinamide-dependent, as well as flavin-nicotinamide oxidoreduction, proceed via hydride transfer but not via hydrogen atom transfer. 3. In flavin-nicotinamide oxidoreduction, flavin-nicotinamide charge transfer complexes are very likely the catalytic intermediates, preceding transfer of hydride ion. The energy of the long-wavelength charge transfer transition of zwitterionic oxidized-nicotinamide/reduced-flavin complexes is strongly dependent on polarity. It is maximal in a highly polar environment. 4. 5-Deazaflavins show the high thermodynamic radical instability of nicotinamides. They have to be considered as nicotinamide analog 2e- oxidoreductants rather than flavin analogs, therefore, lacking the ability to catalyze reversible 1e- oxidoreduction, essential for many flavoenzymes.