Kinetic isotope effects in the photochemical cycle of bacteriorhodopsin

Kinetics were determined for the four transients K₅₉₀, L₅₄₀, M₄₁₀, O₆₆₀ of the photochemical cycle of bacteriorhodopsin (BR₅₇₀) both in ¹H₂O and in ²H₂O over a wide temperature range. Breaks in the Arrhenius plots, observed at 25–32 for the longest-lived transients coincide with a transition point in the microviscosity of the membrane as measured by depolarization of an added fluorescent probe. The earliest isotope effect occurs in the decay of L₅₄₀, and is present in the subsequent formation and decay of M₄₁₀ and O₆₆₀. Thus in the light-driven proton pump of BR₅₇₀, proton ejection from the Schiff base correlates with decay of L₅₀₄ and reprotonation occurs with the decay of both M₄₁₀ and O₆₆₀ back to BR₅₇₀.     

The photochemical cycle of bacteriorhodopsin.

The reaction cycle of bacteriorhodopsin in the purple membrane isolated from Halobacterium halobium has been studied by optical absorption spectroscopy using low-temperature and flash kinetic techniques. After absorption of light, bacteriohodopsin passes through at least five distinct intermediates. The temperature and pH dependence of the absorbance changes suggests that branch points and/or reversible steps exist in this cycle. Flash spectroscopy in the presence of a pH-indicating dye shows that the transient release of a proton accompanies the photoreaction cycle. The proton release occurs from the exterior and the uptake is on the cytoplasmic side of the membrane, as required by the function of bacteriorhodopsin as a light-driven proton pump. Proton translocating steps connecting release and uptake are indicated by deuterium isotope effects on the kinetics of the cycle. The rapid decay of a light-induced linear dichroism shows that a chromophore orientation change occurs during the reaction cycle.     

Primary intermediates in the photochemical cycle of bacteriorhodopsin.

Picosecond studies of the primary photochemical events in the light-adapted bacteriorhodopsin, bR570, indicate that the first metastable intermediate K610 is formed with a rise time of 11 ps. Difference spectra obtained at 50 ps after excitation show that K610 is the same species as that trapped in low temperature glasses. A precursor species (S) of the K610 intermediate has been observed which is red shifted with respect to K610 and is formed within the 6-ps time width of the excitation pulse. The formation of the precursor has no observable thermal dependence between 298 degrees and 1.8 degrees K. The formation of K610 has a very low thermal barrier and at very low temperatures, the rate of formation becomes practically temperature independent which is characteristic of a tunneling process. The rate of formation becomes practically temperature independent which is characteristic of a tunneling process. The rate of formation of K610 has a moderate deuterium isotope effect of kH/kD approximately 1.6 at 298 degrees K and 2.4 at 4 degrees K. The mechanism for formation of K610 is found to involve a rate-limiting proton transfer which occurs by tunneling at low temperatures.     

Quantum efficiency of the photochemical cycle of bacteriorhodopsin

Values in the literature for the quantum efficiency of the photochemical cycle of bacteriorhodopsin (bR) range from 0.25 to 0.79 and the sum of the quantum yields of the forward and back photoreactions [Formula: see text] has been proposed to be 1. In the present work, low intensity laser flashes (532 nm) and kinetic spectroscopy were used to determine the quantum efficiency of bR photoconversion, [UNK]_bR, by measuring transient bleaching of bR at 610 nm in the millisecond time scale. Bovine rhodopsin (R) in 2% ammonyx LO was used as a photon counter. We find that the ratio of the quantum yields of bacteriorhodopsin photoconversion and bleaching of rhodopsin, [UNK]_bR/[UNK]_R, is 0.96 ± 0.04. Based on the quantum yield of the photobleaching of rhodopsin, 0.67, the quantum efficiency of bR photoconversion was determined to be 0.64 ± 0.04. The quantum yield of M formation was found to be 0.65 ± 0.06. From the transient bleaching of bR at 610 nm with a saturating laser flash (28 mJ/cm²) the maximum amount of bR cycling was estimated to be 47 ± 3%. From this value and the spectrum of K published in the literature, the ratio of the efficiencies of the forward and back light reactions, [UNK]₁/[UNK]₂, was estimated to be 0.67 ± 0.06 and so [UNK]₂ ≈ 1 (0.94 ± 0.06). The sum of [UNK]₁ + [UNK]₂ ≈ 1.6. It was found that repeated high-intensity laser flashes (>20 mJ/cm²) irreversibly transformed bR into two stable photoproducts. One has its absorption maximum at 605 nm and the other has a well-resolved vibronic spectrum with maxima at 342, 359 (main peak), and 379 nm. The quantum yield of the formation of the photoproducts is ≈ 10^-4.     

Flash photometric experiments on the photochemical cycle of bacteriorhodopsin

The photochemical reaction cycle of bacteriorhodopsin was investigated by means of flash photometric methods. Three different intermediates with absorption maxima at about 630 nm, 411 nm, and 646 nm could be detected. Kinetic data of the occurrence of these intermediates were obtained from isolated purple membrane in different mediums and from intact halobacteria. An activation energy of 14.1±0.4 kcal·mol⁻¹ and of about 19 kcal·mol⁻¹ for the formation of bacteriorhodopsin 411 and of bacteriorhodopsin 565, resp., was calculated. pH-changes in the medium caused by the reaction cycle of bacteriorhodopsin were detected by use of the pH-indicator bromocresol green.     

Substitution of amino acids in helix F of bacteriorhodopsin: effects on the photochemical cycle

The effects of amino acid substitutions in helix F of bacteriorhodopsin on the photocycle of this light-driven proton pump were studied. The photocycles of Ser-183----Ala and Glu-194----Gln mutants were qualitatively similar to that of wild-type bacteriorhodopsin produced in Escherichia coli and bacteriorhodopsin from Halobacterium halobium. The substitution of a Phe for either Trp-182 or Trp-189 significantly reduced the fraction of photocycling bacteriorhodopsin. The amino acid substitutions Tyr-185----Phe and Ser-193----Ala substantially increased the lifetime of the photocycle without substantially increasing the lifetime of the M photocycle intermediate. Similar results were also obtained with the Pro-186----Gly substitution. In contrast, replacing Pro-186 with the larger residue Leu inhibited the formation of the M photocycle intermediate. These results are consistent with a structural model of the retinal-binding pocket suggested by low-temperature UV/visible and Fourier transform infrared difference spectroscopies that has Trp-182, Tyr-185, Pro-186, and Trp-189 forming part of the binding pocket.     

Primary photochemical processes in bacteriorhodopsin.

Experiments in the picosecond range indicate that the rate of formation of the first intermediate in the photoreaction cycle of bacteriorhodopsin is approximately 10¹¹ sec^?1. A transient at 580 nm has been observed and is tentatively attributed to the excited singlet state.     

Quantum efficiencies of bacteriorhodopsin photochemical reactions.

Determination of quantum efficiencies of bacteriorhodopsin (bR) photoreactions is an essential step toward a full understanding of its light-driven proton-pumping mechanism. The bR molecules can be photoconverted into and from a K state, which is stable at 110 K. I measured the absorption spectra of pure bR, and the photoequilibrium states of bR and K generated with 420, 460, 500, 510, 520, 540, 560, 570, 580, 590, and 600 nm illumination at 110 K. The fraction of the K population in the photoequilibrium state, fk, is determined by AbR and AK the absorbances of the bR and K states at the excitation wavelengths, and also by phi 1 and phi 2, the quantum efficiencies for the bR to K and K to bR photoconversion: fK = phi 1 AbR/(phi 1AbR + phi 2Ak). By assuming that the ratio phi 1/phi 2 is the same at two different but close wavelengths, for example 570 and 580 nm, the value of phi 1/phi 2 at 570 and 580 nm was determined to be 0.55 +/- 0.02, and the spectrum of the K state was obtained with the peak absorbance at 607 nm. The values of phi 1/phi 2 at the other excitation wavelengths were then evaluated using the known K spectrum, and show almost no dependence on the excitation wavelength within the main band. The result phi 1/phi 2 = 0.55 +/- 0.02 disagrees with those of many other groups. The advantages of this method over others are its minimal assumptions and its straightforward procedure.     

Kinetic studies of phototransients in bacteriorhodopsin.

Aqueous suspensions of bacteriorhodopsin in purple membrane fragments from Halobacterium halobium have bben subjected to microsecond flash photometry utilizing both unpolarized and polarized light. Depletion of the ground state chromophore centered at 570 nm is accompanied by the formation of transients absorbing maximally at 410 nm and 660 nm with rise times of about 0.4 and 6 ms, respectively. Decay of both transients and reformation of the ground state chromophore occurs with identical first-order kinetics with a half life of about 6 ms. All three chromophores are polarized with dichroic ratios which remain constant throughout the transient lifetimes, indicating that Brownian rotation of the chromophore within the membrane is considerably restricted. Whereas agents which induce permeability of membranes to protons (2,4-dinitrophenol, carbonylcyanide-m-chlorophenylhydrazone) and non-specific univalent cations (gramicidin) or inhibit ATPase (ouabain) had no influence, the K+-specific ionophore valinomycin in the presence of K+ inhibited and quenched the formation of the 660 nm transient with concomitant increase in lifetime of the 410 nm transient and delay in recovery of the 570 nm chromophore. High concentrations of Na+ produced an effect similar to that of valinomycin. The relationship of these data to the mechanism of the proton pump in the intact bacterium is discussed, with the conclusion that the 410 nm transient performs a key role.     

Substitution of membrane-embedded aspartic acids in bacteriorhodopsin causes specific changes in different steps of the photochemical cycle

Millisecond photocycle kinetics were measured at room temperature for 13 site-specific bacteriorhodopsin mutants in which single aspartic acid residues were replaced by asparagine, glutamic acid, or alanine. Replacement of aspartic acid residues expected to be within the membrane-embedded region of the protein (Asp-85, -96, -115, or -212) produced large alterations in the photocycle. Substitution of Asp-85 or Asp-212 by Asn altered or blocked formation of the M410 photointermediate. Substitution of these two residues by Glu decreased the amount of M410 formed. Substitutions of Asp-96 slowed the decay rate of the M410 photointermediate, and substitutions of Asp-115 slowed the decay rate of the O640 photointermediate. Corresponding substitutions of aspartic acid residues expected to be in cytoplasmic loop regions of the protein (Asp-36, -38, -102, or -104) resulted in little or no alteration of the photocycle. Our results indicate that the defects in proton pumping which we have previously observed upon substitution of Asp-85, Asp-96, Asp-115, and Asp-212 [Mogi, T., Stern, L. J., Marti, T., Chao, B. H., & Khorana, H. G. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 4148-4152] are closely coupled to alterations in the photocycle. The photocycle alterations observed in these mutants are discussed in relation to the functional roles of specific aspartic acid residues at different stages of the bacteriorhodopsin photocycle and the proton pumping mechanism.     

Kinetic isotope effects on the catalytic activity of pig-plasma benzylamine oxidase.

1. Isotope effects on the catalytic activity of benzylamine oxidase at pH 7 and 9 have been studied by steady-state and transient-state kinetics methods, using [alpha,alpha-2H]benzylamine as the substrate. 2. Replacement of the alpha-hydrogen atoms in benzylamine by deuterium has no significant effect on substrate-binding to benzylamine oxidase, neither does it affect the rate of reoxidation of the reduced form of the enzyme. Conversion of the primarily formed enzyme-substrate complex into the reduced enzyme species, however, exhibits an isotope effect of about 3. 3. The data obtained are consistent with a mechanism in which reduction of benzylamine oxidase takes place by a rapid pre-equilibration between enzyme and substrate to form an amine-pyridoxal Schiff-base, which is then tautomerized by a comparatively slow prototropic shift to an amino aldehyde-pyridoxamine Schiff-base from which there is a rapid hydrolytic release of the aldehyde product corresponding to the amine substrate. Proton abstraction from the alpha-carbon of the amine moiety in the primary Schiff-base appears to be at least partially rate-limiting for the tautomerization step, and hence for the entire process of enzyme reduction.     

Kinetic studies of phototransients in bacteriorhodopsin

Aqueous suspensions of bacteriorhodopsin in purple membrane fragments from Halobacterium halobium have been subjected to microsecond flash photometry utilizing both unpolarized and polarized light. Depletion of the ground state chromophore centered at 570 nm is accompanied by the formation of transients absorbing maximally at 410 nm and 660 nm with rise times of about 0.4 and 6 ms, respectively. Decay of both transients and reformation of the ground state chromophore occurs with identical first-order kinetics with a half life of about 6 ms. All three chromophores are polarized with dichroic ratios which remain constant throughout the transient lifetimes, indicating that Brownian rotation of the chromophore within the membrane is considerably restricted. Whereas agents which induce permeability of membranes to protons (2,4-dinitrophenol, carbonylcyanide-m-chlorophenylhydrazone) and non-specific univalent cations (gramicidin) or inhibit ATPase (ouabain) had no influence, the K⁺-specific ionophore valinomycin in the presence of K⁺ inhibited and quenched the formation of the 660 nm transient with concomitant increase in lifetime of the 410 nm transient and delay in recovery of the 570 nm chromophore. High concentrations of Na⁺ produced an effect similar to that of valinomycin. The relationship of these data to the mechanism of the proton pump in the intact bacterium is discussed, with the conclusion that the 410 nm transient performs a key role.     

Origins of deuterium kinetic isotope effects on the proton transfers of the bacteriorhodopsin photocycle

Deuterium kinetic isotope effects (KIE) were measured, and proton inventory plots were constructed, for the rates of reactions in the photocycles of wild-type bacteriorhodopsin and several site-specific mutants. Consistent with earlier reports from many groups, very large KIEs were observed for the third (and largest) rise component for the M state and for the decay of the O state, processes both linked to proton transfers in the extracellular region. The proton inventory plots (ratio of reaction rates in mixtures of H(2)O and D(2)O to that in H(2)O vs mole fraction of D(2)O) were approximately linear for the first and second M rise components and for M decay, as well as for O decay, indicating that the rates of these reactions are limited by simple proton transfer. Uniquely, the third rise component of M (and in the D96N mutant also a fourth rise component) exhibited a strongly curved proton inventory plot, suggesting that its rate, which largely accounts for the rate of deprotonation of the retinal Schiff base, depends on a complex multiproton process. This curvature is observed also in the E194Q, E204Q, and Y57F mutants but not in the R82A mutant. From these findings, and from the locations of bound water in the extracellular region in the crystal structure of the protein [Luecke, Schobert, Richter, Cartailler, and Lanyi (1999) J. Mol. Biol. 291, 899-911], we suspect that the effects of deuterium substitution on the formation of the M state originate from cooperative rearrangements of the extensively hydrogen-bonded water molecules 401, 402, and 406 near Asp-85 and Arg-82.     

Electric field effects in bacteriorhodopsin.

Exposure of aqueous suspensions of fragments of the purple membrane of Halobacterium halobium to electric field pulses leads to transient linear dichroism phenomena. The effects are interpreted in terms of field-induced alignments of the bacteriorhodopsin chromophore. Two observed relaxation times (tau) are attributed to rotation of the whole membrane fragments (tau s approximately 100 ms), and to a much faster reorientation of the chromophore within membrane (tau f approximately 260 microns).     

Kinetic alpha-deuterium isotope effects for enzymatic and nonenzymatic hydrolysis of nicotinamide-beta-riboside.

The kinetic α-secondary deuterium isotope effect, $\text{k}{}_{\mathrm{H}}\text{k}{}_{\mathrm{D}}$, for the pH-independent hydrolysis of nicotinamide riboside, yielding nicotinamide and ribose, in water at 25 ° is 1.14, establishing that this reaction proceeds with unimolecular substrate decomposition to yield a carboxonium ion, or related species, in the rate-determining step. Surprisingly, the corresponding isotope effect for the base-catalyzed decomposition of the same substrate is 1.12, a value indicating considerable sp² character at the Cl′ position in the transition state for this reaction. A similar result, $\text{k}{}_{\mathrm{H}}\text{k}{}_{\mathrm{D}}\text{= 1.15}$, was obtained for base-catalyzed hydrolysis of NAD⁺. The kinetic alpha deuterium isotope effect for the pig brain NAD glycohydrolasecatalyzed hydrolysis of nicotinamide riboside is 1.08. This value suggests that CN bond cleavage to form an intermediate carboxonium ion, or structurally related species, is at least partially rate-determining. In contrast, the corresponding value for the hydrolysis of this substrate catalyzed by Escherichia coli nicotinamide ribonucleotide glycohydrolase is very near unity, a result consistent with several interpretations including a rate-determining enzyme isomerization reaction.     

Kinetic isotope effects of nucleoside hydrolase from Escherichia coli

rihC is one of a group of three ribonucleoside hydrolases found in Escherichia coli (E. coli). The enzyme catalyzes the hydrolysis of selected nucleosides to ribose and the corresponding base. A family of Vmax/Km kinetic isotope effects using uridine labeled with stable isotopes, such as 2H, 13C, and 15N, were determined by liquid chromatography/mass spectrometry (LC/MS). The kinetic isotope effects were 1.012+/-0.006, 1.027+/-0.005, 1.134+/-0.007, 1.122+/-0.008, and 1.002+/-0.004 for [1'-13C], [1-15N], [1'-2H], [2'-2H], and [5'-2H2] uridine, respectively. A transition state based upon a bond-energy bond-order vibrational analysis (BEBOVIB) of the observed kinetic isotope effects is proposed. The main features of this transition state are activation of the heterocyclic base by protonation of/or hydrogen bonding to O2, an extensively broken C-N glycosidic bond, formation of an oxocarbenium ion in the ribose ring, C3'-exo ribose ring conformation, and almost no bond formation to the attacking nucleophile. The proposed transition state for the prokaryotic E. coli nucleoside hydrolase is compared to that of a similar enzyme isolated from Crithidia fasciculata (C. fasciculata).     

Kinetic isotope effects in the oxidation of arachidonic acid by soybean lipoxygenase-1

The reaction of soybean lipoxygenase-1 with linoleic acid has been extensively studied and displays very large kinetic isotope effects. In this work, substrate and solvent kinetic isotope effects as well as the viscosity dependence of the oxidation of arachidonic acid were investigated. The hydrogen atom abstraction step was rate-determining at all temperatures, but was partially masked by a viscosity-dependent step at ambient temperatures. The observed KIEs on k(cat) were large ( approximately 100 at 25 degrees C).