Physiological and structural investigations of bacteriorhodopsin analogs

Experimental evidence for secondary protein-chromophore interactions at the Schiff base linkage in bacteriorhodopsin: Molecular mechanism for proton pumping

Resonance Raman spectroscopy of the retinylidene chromophore in various isotopically labeled membrane environments together with spectra of isotopically labeled model compounds demonstrates that a secondary protein interaction is present at the protonated Schiff base linkage in bacteriorhodopsin. The data indicate that although the interaction is present in all protonated bacteriorhodopsin species it is absent in unprotonated intermediates. Furthermore, kinetic resonance Raman spectroscopy has been used to monitor the dynamics of Schiff base deprotonation as a function of pH. All our results are consistent with lysine as the interacting group. A structure for the interaction is proposed in which the interacting protein group in an unprotonated configuration is complexed through the Schiff base proton to the Schiff base nitrogen. These data suggest a molecular mechanism for proton pumping and ion gate molecular regulation. In this mechanism, light causes electron redistribution in the retinylidene chromophore, which results in the deprotonation of an amino acid side chain with pK >10.2 +/- 0.3 (e.g., arginine). This induces subsequent retinal and protein conformational transitions which eventually lower the pK of the Schiff base complex from >12 before light absorption to 10.2 +/- 0.3 in microseconds after photon absorption. Finally, in this low pK state the complex can reprotonate the proton-deficient high pK group generated by light, and the complex is then reprotonated from the opposite side of the membrane.

Kinetics of photo-active bacteriorhodopsin analog 3,4-didehydroretinal

Kinetics of the photo-induced processes of the transient states of the 3,4-didehydroretinal (3,4-dhr) modified bacteriorhodopsin (bR) was studied by a flash photolysis method in a water suspension at room temperature. The excitation initiated a photocycle with several transient intermediates similar to the trans photocycle of native bR. The main observation of the study was that although major part (80%) of the population of the M state relaxed via the O intermediate as in natural bR, 20% relaxed directly to the bR ground state in 200 ms.

Bacteriorhodopsin oriented in polyvinyl alcohol films as an erasable optical storage medium

Films of oriented bacteriorhodopsin have been formed in polyvinyl alcohol with excellent optical quality. Images with high contrast have been impressed and erased on these films. Second-harmonic microscopy has been used to read the image on a bacteriorhodopsin-polyvinyl alcohol film without erasure. The potential of these films for molecular information storage and computation is discussed.

Orientation of the protonated retinal Schiff base group in bacteriorhodopsin from absorption linear dichroism

Linear dichroism experiments are performed on light-adapted bacteriorhodopsin (BR568) films containing native retinal (A1) and its 3,4-dehydroretinal (A2) analogue to measure the angle between the chromophore transition dipole moment and the membrane normal. QCFF/pi calculations show that the angle between the transition moment and the long axis of the polyene is changed by 3.4 degrees when the C3-C4 bond is unsaturated. The difference vector between the two transition moments points in the same direction as the Schiff base (N----H) bond for the all-trans BR568 chromophore. Because the plane of the chromophore is perpendicular to the membrane plane, a comparison of the transition moment orientations in the A1- and A2-pigments enables us to determine the orientation of the N----H bond with respect to the absolute chromophore (N----C5 vector) orientation. The angles of the transition moments are 70.3 degrees +/- 0.4 degrees and 67.8 degrees +/- 0.4 degrees for the A1- and A2-pigments, respectively. The fact that the change in the transition moment angle (2.5 degrees) is close to the predicted 3.4 degrees supports the idea that the chromophore plane is nearly perpendicular to the membrane plane. The decreased transition moment angle in the A2-analogue requires that the N----H bond and the N----C5 vector point toward the same membrane surface. Available results indicate that the N----C5 vector points toward the exterior in BR568. With this assignment, we conclude that the N----H bond points toward the exterior surface and its most likely counterion Asp-212. This information makes possible the construction of a computer graphics model for the active site in BR568.

An investigation of the electrochemical cycle of bacteriorhodopsin analogs with the modified ring

5,6-Epoxy-, 4-methoxy-, 4-hydroxy-, and 3,4-dehydrobacteriorhodopsins can generate delta psi coupled to a photochemical cycle with intermediate M. The kinetics of delta psi comprises three main electrogenic phases: the fast small negative, the microsecond, and the millisecond positive phases. The photocycle efficiency is lower in all the analogs. The photocycle is modified insignificantly only in 3,4-dehydrobacteriorhodopsin. In the other pigments the decay of the flash-induced bleaching in the chromophore main absorption band is slower than the decay of M or long-wave intermediates, especially in the 4-hydroxy analog. In the latter analog, such distinctions, according to delta pH measurements, are partly due to deceleration of the decay of the novel intermediate (P). In 5,6-epoxybacteriorhodopsin, at all wavelengths, the decay of the intermediates takes seconds upon M formation. According to our and literature data, no bacteriorhodopsin analogs are known to have a cycle which preserves the M-intermediate and does not transport a proton.

The opsin family of proteins

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Interaction of aromatic retinal analogues with apopurple membranes of Halobacterium halobium

Absorption spectral properties of aromatic analogues of retinal with apopurple membrane of Halobacterium halobium were studied. The spectra of the all-trans forms were composed of two or more absorption bands. During incubation at 20 degrees C, an absorption band above 500 nm increased in intensity gradually at the expense of an absorption band in the shorter wavelength region with no isomerization of the chromophore. The longer wavelength species was shown to be the protonated form of the shorter wavelength species by changing the pH of the medium. Upon irradiation with blue light, the bandwidth of the spectrum became smaller with isomerization of the chromophore to its 13-cis form. Irreversible binding of protons on the membrane occurred during this process. The rate of the increase in the longer wavelength absorption band was especially low in the reaction with the all-trans form of retinal analogues having a bulky substituent at the para or meta positions of the phenyl ring. In contrast, the 13-cis isomer of aromatic retinal analogues gave a single absorption peak. The extent of the spectral shift upon binding to apopurple membranes was compared over a series of aromatic retinals, and the results were explained in terms of steric interactions of the chromophore with the protein.

Regeneration of rhodopsin and bacteriorhodopsin. The role of retinal analogues as inhibitors

The rate of regeneration of rhodopsin, from 11-cis-retinal and opsin, and bacteriorhodopsin from all-trans-retinal and bacterio-opsin, in the presence or absence of compounds whose structures partially resemble retinal were measured. Some of these compounds severely slowed down the regeneration process, but did not influence the extent of regeneration. In the case of compounds with a carbonyl functional group they were not joined to the active site of the apo-protein via a Schiff's base linkage since after treatment with NaBH4 an active apo-protein remained. The most effective inhibitors of rhodopsin regeneration were molecules whose structure could be superimposed on 9-cis or 11-cis retinal up to carbon atom 11. These C13 and C15 molecules were not distinguished between aldehyde, ketone or alcohol functional groups. The regeneration of bacteriorhodopsin was not inhibited by retinal analogues with short side chains. The most effective inhibitors were the all-trans C17-aldehyde (beta-ionylideneacetaldehyde) or C18-ketone (beta-ionylidenepent-3-ene-2-one) which, compared to retinal, lack two or three carbon atoms from the end of the poylene chain. The inhibition was very dependent upon the presence of the all-trans isomer and required aldehyde or ketone as functional group nitriles and alcohols were less effective. However, similarly to retinol, the all-trans C17 and C18 alcohols underwent a bathochromic shift and showed fine-structured spectra when mixed with bacterio-opsin.

Photochemical and functional properties of bacteriorhodopsins formed from 5,6-dihydro- and 5,6-dihydrodesmethylretinals

5,6-Dihydroretinal and 5,6-dihydro-1,1,5,9,13-desmethylretinal are synthesized, and their all-trans isomers are shown to form pigment analogues (lambda max at 475 and 460 nm, respectively) of bacteriorhodopsin (purple membrane protein). The shift of the absorption maximum od the pigment from that of the protonated Schiff base of the chromophore for 5,6-dihydrobacteriorhodopsin is small compared to that of the native pigment, suggesting that negative charges similar to those controlling the lambda max of visual pigment rhodopsin exist near the cyclohexyl ring. Both pigment analogues undergo reversible light-induced spectral shifts reflecting cyclic photoreactions of the pigments. These results indicate that the absence of the C-5--C-6 double bond and of the five methyl groups of retinal does not abolish the photochemistry of these pigment analogues and strongly suggest that these structural features are not directly required for the photoreactions of native bacteriorhodopsin. The apparent rates of the photochemical transformations of these artificial pigments are quite different from those of bacteriorhodopsin. A working hypothesis is proposed for the photocycle of the pigment analogues, which includes a slower light-induced cycling rate (for the light-adapted pigments) than that of native bacteriorhodopsin and an increased rate of dark adaptation. When incorporated into egg lecithin vesicles both pigment analogues show proton pumping ability, again indicating that the missing double bond and the methyl groups are not structurally required for the function of the pigments.

Resonance Raman spectroscopy of chemically modified and isotopically labelled purple membranes. I. A critical examination of the carbon-nitrogen vibrational modes

Resonance Raman spectra of bacteriorhodopsin are compared to the spectra of this protein modified in the following ways: (1) selective deuteration at the C-15 carbon atom of retinal, (2) full deuteration of the retinal, (3) the addition of a conjugated double bond in the beta-ionone ring (3-dehydroretinal), (4) full deuteration of the protein and lipid components, (5) 15N enrichment of the entire membrane and (6) deuteration of the entire membrane (including the retinal). A detailed comparison of the 15N-enriched membrane and naturally occurring purple membrane from 800 cm-1 to 1700 cm-1 reveals that 15N enrichment affects the frequency of only two vibrational modes. These occur at 1642 cm-1 and 1620 cm-1 in naturally occurring purple membrane and at 1628 cm-1 and 1615 cm-1 in the 15N-enriched samples. Therefore, this pair of bands reflects the states of protonation of the Schiff base. However, our data also indicate that neither of these modes are simple, localized C=N-H or C=N stretching vibrations. In the case of the 1642 cm-1 band motions of the retinal chain beyond C-15 are not significantly involved. On the other hand, in the 1620 cm-1 band atomic motions in the isoprenoid chain beyond C-15 are involved.