PEPTIDE MODELS FOR THE BACTERIORHODOPSIN CHROMOPHORE. RETINYLIDENE-LYSINE SYSTEMS CONTAINING ASPARTIC ACID AND SERINE RESIDUES

Abstract— The retinylidene Schiff base derivative of seven lysine containing peptides have been prepared in order to investigate solvent and neighboring group effects, on the absorption maximum of the protonated Schiff base chromophore. The peptides studied are Boc-Aib-Lys-Aib-OMe ( 1 ), Boc-Ala-Aib-Lys-OMe ( 2 ), Boc-Ala-Aib-Lys-Aib-OMe ( 3 ), Boc-Aib-Asp-Aib-Aib-Lys-Aib-OMe ( 4 ), Boc-Aib-Asp-Aib-Ala-Aib-Lys-Aib-OMe ( 5 ), Boc-Lys-Val-Gly-Phe-OMe ( 6 ) and Boc-Ser-Ala-Lys-Val-Gly-Phe-OMe ( 7 ). In all cases protonation shifts the absorption maxima to the red by 3150–8450 cm^-1. For peptides 1–3 the protonation shifts are significantly larger in nonhydrogen bonding solvents like CHCl₃ or CH₂Cl₂ as compared to hydrogen bonding solvents like CH₃OH. The presence of a proximal Asp residue in 4 and 5 results in pronounced blue shift of the absorption maximum of the protonated Schiff base in CHCl₃, relative to peptides lacking this residue. Peptides 6 and 7 represent small segments of the bacteriorhodopsin sequence in the vicinity of Lys-216. The presence of Ser reduces the magnitude of the protonation shift.     

SPECTROSCOPIC STUDIES ON A RETINYLIDENE-IMINE-TETRAFLUOROBORATE

Abstract— N -retinylidene-butyl-l-aminium tetrafluoroborate (NRBH+BF₄^-) was used to determine the frequencies of the free (non-hydrogen-bonded) v (N+-H) and v (C=NH+) vibrations and their anharmon-icity constants. For this purpose the Fourier-transform IR and near-IR (overtone) spectra were recorded. The visible-UV spectra were also taken. The results locate the free v (N+-H) band at about 3250 ± 50 cm^-1; the vibration has normal anharmonicity while v (C=NH+) is very nearly harmonic. The UV and IR spectra show that the Schiff base is protonated, but that the proton is only very weakly hydrogen-bonded to the anion. Therefore, in this respect, NRBH+BF₄^- is a good model for the hydrogen-bonding environment of the region around the nitrogen of rhodopsin chromophores.     

EXPERIMENTAL and THEORETICAL STUDIES OF SCHIFF BASE CHLOROPHYLLS

Abstract— A protonated Schiff base of Ni (II)-pyrochlorophyll a has been synthesized which exhibits a reversible bathochromic shift of 504 cm^-1 relative to Ni (II)-pyrochlorophyll a. The magnitude of this shift lies between those observed for P700 and P680, the photoactive pigments of photosystems I and II in plants. Cyclic voltammetric measurements show that the protonated Schiff base is about 0.2 V more difficult to oxidize than its unprotonated form. These results suggest that a protonated Schiff base may be a better model for P680 than, as was originally assumed, for P700. In addition, the results of solvent and counterion effect studies show that microenvironmental perturbations in the neighborhood of the protonated Schiff base moiety are unlikely to induce further spectral shifts. Ab initio quantum mechanical calculations show a small hypsochromic shift rather than the observed bathochromic one, and the reasons for this discrepancy are discussed.     

PROTONATED SCHIFFS BASE CHLOROPHYLL: A MODEL FOR P700?

Abstract— A Schiff's base of the Ni(II) analog of pyrochlorophyll a (PChl a) has been synthesized which exhibits a reversible bathochromic shift relative to Ni-PChl a of 504 cm^-1. The shift approaches that observed between Chi a and P700, the photoactive pigment of photosystem I in plants, and suggests that the protonated Schiff s base may be an appropriate model for P700.     

RESONANCE RAMAN SPECTRA OF THE Pr-FORM OF PHYTOCHROME

Abstract— Resonance Raman spectra of the P_r-form of oat phytochrome have been obtained at 77 K. Interference from phytochrome fluorescence is avoided by employing far-red 752 nm excitation. Vibrational assignments are suggested for the tetrapyrrole chromophore in phytochrome by comparison with previously published model compound spectra and by examining the characteristic shifts induced by deuteration of the pyrrole nitrogens. The lack of carbonyl intensity, the frequencies of the 1626 and 1644 cm^-1 C=C stretching modes, and the presence of an intense mode at 1326 cm^-1 are all consistent with a protonated structure for the tetrapyrrole chromophore in P_r. This suggests that the -50 nm red-shift of the protein-bound chromophore absorption compared to the chromophore in vitro is caused by protonation of the pyrrole nitrogen.     

TIME-RESOLVED RESONANCE RAMAN SPECTRA OF THE PHOTOCYCLE INTERMEDIATES OF ACID AND DEIONIZED BACTERIORHODOPSIN

Abstract— The photocycle of bacteriorhodopsin (bR) and its perturbed forms are investigated by a time-resolved resonance Raman study. These experiments were performed in the C=C stretching and in the fingerprint spectral regions for the acid blue, acid purple and deionized forms of bR.
The main observations are as follows: (1) isomerization of the retinal, from all- trans to 13- cis , occurs in native bR and in all of the acid and deionized perturbed bR species; (2) formation of the early intermediates (the K₆₁₀ and L₅₅₀ analogues) also occur in native bR and in all of the perturbed species; and (3) deprotonation of the protonated Schiff base (PSB), to give the M₄₁₂ type intermediate, occurs in native bR, but is inhibited in all of the perturbed bR species on the time-scale of the native bR photocycle.
The results show that isomerization alone is not a prerequisite for the PSB deprotonation process. The observed photocycle, initiated with retinal isomerization, is found to occur from all- trans to 13- cis in all of the perturbed forms of bR. In addition, the results imply that removal of the cations, of an increase in the hydrogen ion concentration, prevent only the PSB deprotonation process and not the formation of earlier cycle intermediates. Some attention is focused on the two blue forms of bR (acid and deionized) due to the fact that their ground-state absorption maximum, unphotolyzed Raman spectra, and Raman spectra changes during the photocycle are all very similar. The similarities between the acid blue and deionized blue forms in the fingerprint region support previous suggestions that both blue species have nearly the same retinal active site.     

THE 'OPSIN SHIFT' IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS

Abstract— The difference (in cm⁻¹) in absorption maxima between the protonated Schiff base of retinals and the pigment derived therefrom has been defined as the opsin shift. It represents the influence of the opsin binding site on the chromophore. The analysis of the opsin shifts of a series of dihydrobacteriorhodopsins has led to the external point-charge model, which in addition to a counter anion near the Schiff base ammonium, carries another negative charge in the vicinity of the β-ionone ring. This is in striking contrast to the external point-charge model proposed earlier for the bovine visual pigment. The absorption maxima of rhodopsins formed from bromo- and phenyl retinals support the two models. A retinal carrying a photoaffinity label has yielded a nonbleachable bacteriorhodopsin.     

SPECTROSCOPY OF POLYENES–III. ABSORPTION AND EMISSION SPECTRAL INVESTIGATION OF POLYENE SCHIFF BASES AND PROTONATED SCHIFF BASES RELATED TO VISUAL PIGMENTS

Abstract— A number of n -butylamine Schiff bases of polyenals related to retinals as homologues and analogues, and their protonated forms, have been studied for absorption and emission spectral properties. The polyene Schiff bases exhibit the same general features in their absorption spectra as those of the parallel polyenals except that the ^lB_u←¹A_g and π*← n singlet transitions are at substantially higher energy in the Schiff bases (the shift being larger for the π *← n transition). The Schiff bases with short polyene chainlength ( n = 2, 3 where n is the number of double bonds including C=N) do not fluoresce or phosphoresce in 3-methylpentane in the temperature range 298–77 K. The Schiff bases with intermediate chainlength ( n = 4, 5) show fluorescence at 77 K with intensity strongly dependent on the nature of solvent. The Schiff bases with relatively long chainlength ( n = 5–7) show strong or moderately strong fluorescence at 77 K and very weak fluorescence at 298 K ( n = 7) with intrinsic radiative lifetimes much longer than those estimated from the oscillator strength of the low-energy, strong absorption band (¹B_u←¹ A_g ). A discussion on the possible state order and nature of the fluorescing state of the various polyene Schiff base systems is presented.     

THE EFFECT OF ACIDS ON THE INFRARED SPECTRA OF SCHIFF BASES—II. IMINES CONTAINING THE C=C-C=N AND C=C-C=C-C=N UNITS

Abstract— The Fourier-transform infrared spectra of chloroform-d solutions of conjugated imines CH₃CH=CHCH=NCH(CH₃)₂ and CH₃CH₂CH=CHCH=CHCH=NCH(CH₃)₂ and the related protonated species with HCl, HBr, HI, trichloro, dichloro, monobromo and monochloroacetic acids or propionic acid are presented. The effects of conjugation and protonation are examined. The results show that conjugation slightly increases the basicity of the Schiff bases. HCl, HBr and HI protonate the Schiff bases completely. The carboxylic acids protonate partially depending on their p K _a, values. When the Schiff base contains two (or more) C=C bonds conjugated with C=N, the main C=C stretching band undergoes a strong intensification showing that sizeable dipole moment variations occur along the conjugated chain.     

RESONANCE RAMAN SPECTRA OF BACTERIORHODOPSIN MUTANTS WITH SUBSTITUTIONS AT ASP-85, ASP-96, AND ARG-82

Detergent solubilized bacteriorhodopsin (BR) proteins which contain alterations made by site-directed mutagenesis (Asp-96----Asn, D96N; Asp-85----Asn, D85N; and Arg-82----Gln, R82Q) have been studied with resonance Raman spectroscopy. Raman spectra of the light-adapted (BRLA) and M species in D96N are identical to those of native BR, indicating that this residue is not located near the chromophore. The BRLA states of D85N and especially R82Q contain more of the 13-cis, C = N syn (BR555) species under ambient illumination compared to solubilized native BR. Replacement of Asp-85 with Asn causes a 25 nm red-shift of the absorption maximum and a frequency decrease in both the ethylenic (-7 cm-1) and the Schiff base C = NH+ (-3 cm-1) stretching modes of BRLA. These changes indicate that Asp-85 is located close to the protonated retinal Schiff base. The BRLA spectrum of R82Q exhibits a slight perturbation of the C = NH+ band, but its M spectrum is unperturbed. The Raman spectra and the absorption properties of D85N and R82Q suggest that the protein counterion environment involves the residues Asp-85-, Arg-82+ and presumably Asp-212-. These data are consistent with a model where the strength of the protein-chromophore interaction and hence the absorption maximum depends on the overall charge of the Schiff base counterion environment.     

THE PHOTOCHEMICAL INTERACTION BETWEEN THE TRIPLET STATE OF 8-METHOXYPSORALEN AND THE MELANIN PRECURSORL–3, 4 DIHYDROXYPHENYLALANINE

Abstract— The photochemical interaction between 8-methoxypsoralen (8-MOP) and the melanin precursorL–3,4-dihydroxyphenylalanine(dopaH₂) has been studied using laser flash photolysis. Triplet excited 8-MOP was thus found to abstract electrons from dopaH₂ ( k ∼ 2 × 10⁹ dm³ mol^-1 s^-1) to form semireduced 8-MOP and semioxidised dopaH₂.The technique of pulse radiolysis was used to establish separately the spectra of (a) the semi-reduced form of 8-MOP at pH 6.5 and (b) the semioxidised forms of dopaH₂ at pH 6.5, 5.8, 4.6 and 3.3. The corresponding λ_max and extinction coefficients found were: for 8-MOP at pH 6.5, λ_max= 350 nm (= 9050 dm³ mol^-1 cm^-1); for dopa at pH 6.5, λ_max= 305 nm (ε= 12000 dm³ mol^-1 cm^-1) and for dopaH at pH 3.3, λ= 305 nm (ε= 5900 dm³ mol^-1 cm^-1).     

THEORY OF THE OPTICAL ABSORPTION OF LIGHT-ADAPTED BACTERIORHODOPSIN AND ITS ACIDIFIED FORMS

Abstract— We assume a model for bacteriorhodopsin chromophore such that the protonated retinal Schiff-base (PRSB) interacts with two anions in the case of light-adapted bacteriorhodopsin (bR^L), while it does with one anion in the case of the acidified form of bacteriorhodopsin (bR^acid₆₀₀). On the basis of this model, the π-electronic states of all- trans -PRSB are calculated according to our LCAO-ASMO-SCF-CI method, the anions being approximated by negative point-charges in the plane of PRSB π-system. A possible distribution of the negative point-charges around PRSB is proposed for the chromophores of bR^L, bR^acid₆₀₀, and the two irradiated forms of bR^acid₆₀₀ (the one at 3°C containing 9- cis -PRSB, and the other at — 72°C all- trans -PRSB). It is shown that the wavelength λ_max of absorption maximum observed for each form of bacteriorhodopsin can be explained reasonably well by the suggested charge distribution. Furthermore, a model for the structure of the active site of bR^L is proposed, considering that two COO⁻ groups form the anions that interact with PRSB. The calculated optical absorption of all- trans -PRSB at such a site is shown to be consistent with the observed absorption spectrum of bR^L.     

Effects of Substitutions D73E, D73N, D103N and V106M on Signaling and pH Titration of Sensory Rhodopsin II

Abstract— Several mutations in the repellent phototaxis receptor sensory rhodopsin II (SRII), in residues homologous to residues important in the related proton pump bacteriorhodopsin, were expressed in Pho81Wr^–, a Halobacterium salinarum strain deficient in production of SRII and its transducer protein HtrII. The lack of production of SRII and HtrII is shown to be due to insertion of an ISH2 transposon into the promoter region upstream of the htrII - sopH gene pair. Near wild-type phototaxis responses are rescued in Pho81Wr^– by expression of HtrII with D73E, D103N or V106M receptors. Partial responses are restored by the HtrII-D73N pair. From absorption spectroscopy of his-tag-purified receptor protein from mutants D73N and D73E we conclude that Asp73 is the primary counterion to the protonated Schiff base in SRII, like the corresponding Asp85 in bacteriorhodopsin. The absorption maximum of SRII (487 nm) is shifted to 514 nm in mutant D73N, a 1080 cm⁻¹ shift identical to that caused by D85N in bacteriorhodopsin. Acid titration of SRII also induces the red shift with a pK of 3.0 in wild type. The absorption shift and the pK are nearly the same in V106M and D103N, but the pK is raised to 5.1 in D73E, confirming that Asp73 is the residue responsible for this spectral transition.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

THE ORIGIN OF THE RED-SHIFTED ABSORPTION MAXIMUM OF THE M412 INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE

The factors that red shift the absorption maximum of the retinal Schiff base chromophore in the M₄₁₂ intermediate of bacteriorhodopsin photocycle relative to absorption in solution were investigated using a series of artificial pigments and studies of model compounds in solution. The artificial pigments derived from retinal analogs that perturb chromophore-protein interactions in the vicinity of the ring moiety indicate that a considerable part of the red shift may originate from interactions in the vicinity of the Schiff base linkage. Studies with model compounds revealed that hydrogen bonding to the Schiff base moiety can significantly red shift the absorption maximum. Furthermore, it was demonstrated that although s-trans ring-chain planarity prevails in the M₄₁₂ intermediate it does not contribute significantly (only ca 750 cm⁻¹) to the opsin shift observed in M₄₁₂. It is suggested that in M₄₁₂, the Schiff base linkage is hydrogen bonded to bound water and/or protein residues inducing a considerable red shift in the absorption maximum of the retinal chromophore.     

A Resonance Raman Study Of the C=C Stretch Modes in Bovine and Octopus Visual Pigments with Isotopically Labeled Retinal Chromophores

Abstract— Previous resonance Raman spectroscopic studies of bovine and octopus rhodopsin and bathorhodopsin in the C–C stretch fingerprint region have shown drastically different spectral patterns, which suggest different chromophore-protein interactions. We have extended our resonance Raman studies of bovine and octopus pigments to the C=C stretch region in order to reveal a more detailed picture about the difference in retinal-protein interactions between these two pigments. The C=C stretch motions of the protonated retinal Schiff base are strongly coupled to form highly delocalized ethylenic modes located in the 1500 to 1650 cm⁻¹ spectral region. In order to decouple these vibrations, a series of 11,12-D₂-labeled retinals, with additional 13C labeling at C₈, C₁₀, C₁₁ and C₁₄, respectively, are used to determine the difference of specific C=C stretch modes between bovine and octopus pigments. Our results show that the C₉=C₁₀ and C₁₃=C₁₄ stretch mode are about 20 cm⁻¹ lower in the Raman spectrum of octopus bathorhodopsin than in bovine bathorhodopsin, while the other C=C stretch modes in these two bathorhodopsins are similar. In contrast, only the C₉=C₁₀ stretch mode in octopus rhodopsin is about 10 cm⁻¹ lower than in bovine rhodopsin, while other C=C stretches are similar.     

THE EFFECT OF IONIC STRENGTH AND pH ON THE PROTONATED SCHIFF BASE AND TYROSINE DEPROTONATION KINETICS DURING THE BACTERIORHODOPSIN PHOTOCYCLE

Abstract— The deprotonation kinetics of tyrosine and the protonated Schiff base during the bacteriorho-dopsin photocycle were studied under different perturbations by transient absorption spectroscop Native purple membrane, as well as samples which were deionized (blue) then restored with Na⁺ or La³⁺ were used at pH's ranging from 7 to 10 at very low salt concentrations. The results were compared with previous studies at higher ionic strength. The important conclusions can be summarized as follows: (a) The rate constants of both the Schiff base and tyrosine deprotonation are not very sensitive to the changes of conditions. (b) An almost linear relationship is observed between the relative amplitudes of the tyrosine deprotonated during the cycle and the slow component of the Schiff base deprotonation under the different perturbations studied. This was taken to support the two site model for the protonated Schiff base, one near tyrosine and the other near its ionized form. (c) The pK_a value determined from the ratio of the amplitude of the fast to the slow component of the Schiff base deprotonation is found to decrease with increasing ionic strength of the medium. At extremely low ionic strength, it was found to equal that of the tyrosine phenolic group in solution.     

PICOSECOND TRANSIENT BEHAVIOR OF REACTION-CENTER PARTICLES OF PHOTOSYSTEM I ISOLATED FROM SPINACH CHLOROPLASTS. ENERGY AND ELECTRON TRANSFER UPON SINGLE AND MULTIPLE PHOTON EXCITATION

Abstract— Both [15-¹³C] and [14-¹³C] all-trans-retinals were synthesized. Bacteriorhodopsin containing [14-¹³C]retinal as a chromophore, when solubilized with octyl-β-D-glucoside, showed characteristic resonances at 125 and 118 ppm from tetramethyl silane. The former was assigned to the signal from free retinal and the latter from protonated Sehiff base. When the bacteriorhodopsin was denatured in sodium dodecyl sulfate, the signal at 118 ppm disappeared, while the signal at 125 ppm rather increased.
In the case of bacteriorhodopsin containing [15-¹³C]retinal, when solubilized with Triton X-100, a characteristic resonance at 169 ppm was distinguishable as a shoulder peak superimposed on the broad signal of carbonyl carbons and it was assigned to the signal from the protonated Sehiff base. The other signal observed at 191 ppm was from free retinal.
These results suggested that the Sehiff base of bacteriorhodopsin is protonated in the dark.     

NEAR-INFRARED FOURIER-TRANSFORM RAMAN STUDY OF CHLOROPHYLL a IN SOLUTIONS

Abstract— The 1064 nm excited Fourier-transform (FT) Raman spectra have been measured for chlorophyll a (Chl- a ) in various solutions. Features of the obtained spectra are largely different from those of Soret-resonant Raman spectra of Chl- a . For example, a band due to the C=0 stretching mode of the 13-keto group is much stronger in the former than in the latter. Although the excitation wavelength is rather far from that of the Qy absorption of Chl- a , notable enhancements of bands due to the C=O stretching mode of the 13¹-keto group and to the C=C stretching mode of the vinyl group and those in the 1250–600 cm^-1 region suggest that the 1064 nm-excited Raman spectra of Chl- a are preresonance enhanced via the Qy band. Some of the marker bands for the coordination number of the central Mg atom, which have been used in the visible-excited resonance Raman spectra, are not valid in the 1064 nm-excited Raman spectra. Instead, new marker bands are found in the latter. The 1064-nm excited Raman spectra of Chl- a in a hydrated hexane solution reveal that the dehydrated oligomer of Chl- a as well as Chl- a -water micelles coexist in the solution. They also suggest that the size of the oligomer is considerably larger and the hydrogen bonding of the 13¹-keto group in the oligomer is weaker than that in the micelles.     

REEVALUATION OF THE SPECTRAL AND KINETIC PROPERTIES OF HO2 AND O2- FREE RADICALS

Abstract— The spectra and molar absorbances of the HO₂ and O₂^- free radicals have been redetermined in aqueous formate solutions by pulse and stopped-flow radiolysis as well as by ⁶⁰Co gamma-ray studies. The extinction coefficients at the corresponding maxima and 23°C are ²²⁵= 1400 ± 80 M ^-1 cm^-1 and ²²⁵= 2350 ± 120 M ^-1 cm^-1 respectively. Reevaluation of earlier published rate data in terms of the new extinction coefficients yielded the following rate constants for the spontaneous decay of HO₂ and O₂^-: K _Ho2+HO2= (8.60 ± 0.62) × 10⁵ M ^-1 s^-1; K _Ho2+O2-= (1.02 ± 0.49) × 10⁸ M ^-1 s^-1; K _Ho2+O2- < 0.35 M ^-1 s^-1. For the equilibrium HO₂→ O₂^-+ H⁺ the dissociation constant is K _Ho2= (2.05 ± 0.39) × 10^-5 M or p K _HO2= 4.69 ± 0.08. G (O₂^-) has been evaluated as a function of formate concentration.