Sensitive light scattering probe of enzymatic processes in retinal rod photoreceptor membranes

Light excitation of as little as 0.05% of the rhodopsin in a retinal rod membrane suspension reduces the near-IR optical transmission by 25%. This transmission decrease requires the presence of guanosine triphosphate, is opposite in sign and 25 times larger in amplitude than a GTP-dependent light-scattering signal previously reported in rod outer segment suspensions [Kuhn, H., Bennett, N., Michel-Vallez, M. & Chabre, M. (1981) Proc. Natl. Acad. Sci. USA, 78, 6873-6877], and is kinetically complex. The initial phase of the optical transmission decrease begins after about a 50-ms lag (at 0.05% bleach) and has a first-order time constant of 300-500 ms. The scattering signal returns to the preactinic baseline in a time dependent on the amount of GTP added. A nonhydrolyzable GTP analogue, guanylyl imidodiphosphate, produces a scattering signal that does not return to the preactinic baseline. Adenosine triphosphate strongly inhibits the return of the GTP-dependent transmission decrease to the preactinic baseline. This effect of ATP on the GTP signal apparently requires ATP hydrolysis because it is inhibited by the simultaneous presence of adenylyl imidodiphosphate, a nonhydrolyzable analogue of ATP. The light-scattering signal and the velocity of the activation of a rod outer segment phosphodiesterase saturate when >0.05% of the rhodopsin is bleached and both show nearly identical dependence on light stimulus. It is suggested that these nucleotide-dependent light-scattering signals arise from changes in the state of membrane aggregation that are controlled by enzymatic processes. This hypothesis is supported by the large amplitude of the signals, sedimentation experiments, and a strong membrane concentration dependence. The ATP effects can be rationalized within the above hypothesis as being due to ATP-dependent rhodopsin phosphorylation that adds negative charges to the membrane surface and tends to keep the membranes disaggregated. An additional signal, which increases light transmission, is produced by a second, much more intense flash. The latter signal is interpreted as the result of proton binding by bleached rhodopsin molecules that decreases the negative charge repulsion between the membranes and allows increased aggregation.

The effect of water on the rate of conformational change in protein allostery

The influence of solvation on the rate of quaternary structural change is investigated in human hemoglobin, an allosteric protein in which reduced water activity destabilizes the R state relative to T. Nanosecond absorption spectroscopy of the heme Soret band was used to monitor protein relaxation after photodissociation of aqueous HbCO complex under osmotic stress induced by the nonbinding cosolute poly(ethylene glycol) (PEG). Photolysis data were analyzed globally for six exponential time constants and amplitudes as a function of osmotic stress and viscosity. Increases in time constants associated with geminate rebinding, tertiary relaxation, and quaternary relaxation were observed in the presence of PEG, along with a decrease in the fraction of hemes rebinding CO with the slow rate constant characteristic of the T state. An analysis of these results along with those obtained by others for small cosolutes showed that both osmotic stress and solvent viscosity are important determinants of the microscopic R --> T rate constant. The size and direction of the osmotic stress effect suggests that at least nine additional water molecules are required to solvate the allosteric transition state relative to the R-state hydration, implying that the transition state has a greater solvent-exposed area than either end state.

Steric barrier to bathorhodopsin decay in 5-demethyl and mesityl analogues of rhodopsin

Absorbance difference spectra were recorded from 20 ns to 1 micros after 20 degrees C photoexcitation of artificial visual pigments derived either from 5-demethylretinal or from a mesityl analogue of retinal. Both pigments produced an early photointermediate similar to bovine bathorhodopsin (Batho). In both cases the Batho analogue decayed to a lumirhodopsin (Lumi) analogue via a blue-shifted intermediate, BSI, which formed an equilibrium with the Batho analogue. The stability of 5-demethyl Batho, even though the C8-hydrogen of the polyene chain cannot interact with a ring C5-methyl group to provide a barrier to Batho decay, raises the possibility that the 5-demethylretinal ring binds oppositely from normal to form a pigment with a 6-s-trans ring-chain conformation. If 6-s-trans binding occurred, the ring C1-methyls could replace the C5-methyl in its interaction with the chain C8-hydrogen to preserve the steric barrier to Batho decay, consistent with the kinetic results. The possibility of 6-s-trans binding for 5-demethylretinal also could account for the unexpected blue shift of 5-demethyl visual pigments and could explain why 5-demethyl artificial pigments regenerate so slowly. Although the mesityl analogue BSI's absorption spectrum was blue-shifted relative to its pigment spectrum, the blue shift was much smaller than for rhodopsin's or 5-demethylisorhodopsin's BSI. This suggests that increased C6-C7 torsion may be responsible for some of BSI's blue shift, which is not the case for mesityl analogue BSI either because of reduced spectral sensitivity to C6-C7 torsion or because the symmetry of the mesityl retinal analogue precludes having 6-s-cis and 6-s-trans conformers. The similarity of the mesityl analogue BSI and native BSI lambda(max) values supports the idea that BSI has a 6-s angle near 90 degrees, a condition which could disconnect the chain (and BSI's spectrum) from the double bond specifics of the ring.

Effect of NADPH on formation and decay of human metarhodopsin III at physiological temperatures

Difference absorption spectra were recorded during the formation and decay of metarhodopsin III after sonicated membrane suspensions of rhodopsin were bleached at 37 degrees C. The data were analyzed using SVD, spectral decomposition and global exponential fitting. By comparison of the results in the presence or absence of 70 microM NADPH and those for bovine or human rhodopsin, a single comprehensive scheme was fit to all the data, including reduction of retinal to retinol by the intrinsic retinol dehydrogenase. On the time scale studied the mechanism involves two 382 nm absorbing species and two 468 nm, absorbing species, supporting the notion that human metarhodopsin III is not a homogeneous species. The results confirm that metarhodopsin III forms and persists sufficiently long in the human retina under physiological conditions that it could undergo secondary photoisomerization.

Structural constraints imposed by a non-native disulfide cause reversible changes in rhodopsin photointermediate kinetics

Suspensions of bovine rhodopsin in 2% lauryl maltoside detergent were treated with Cu(phen)(3)(2+) to form a disulfide bridge between cysteines 140 and 222 which occur naturally in the bovine rhodopsin sequence. Absorption difference spectra were collected after excitation with a pulse of 477 nm light on the time scale from 1 micros to 690 ms, and the results were analyzed using global exponential fitting. Only two exponentials could be fit to data from the Cu(phen)(3)(2+)-treated rhodopsin, while three exponentials were needed to fit data either from untreated rhodopsin or from Cu(phen)(3)(2+)-oxidized rhodopsin after further dithiothreitol reduction. Dithiothreitol treatment of rhodopsin which had not been previously oxidized with Cu(phen)(3)(2+) had no effect on the observed kinetics. Since the 140-222 disulfide has previously been shown to block transducin activation, its effects on rhodopsin activation are of considerable interest. Cu(phen)(3)(2+) treatment favors formation of the meta I(380) intermediate relative to meta I(480) and slows formation of meta II from meta I(380). This suggests that the protein change involved in meta I(380) formation is similar to the structural constraint introduced by the 140-222 disulfide. These results show that formation of disulfides in rhodopsin has potential as a tool for discriminating between the three isochromic, 380 nm absorbing intermediates involved in rhodopsin activation and for gaining insight into how their structures differ.

Near-ultraviolet magnetic circular dichroism spectroscopy of protein conformational states: correlation of tryptophan band position and intensity with hemoglobin allostery

The near-UV magnetic circular dichroism spectroscopy of the aromatic amino acid bands of hemoglobin was investigated as a potential probe of structural changes at the alpha(1)beta(2) interface during the allosteric transition. Allosteric effectors were used to direct carp and chemically modified human hemoglobins into the R (relaxed) or T (tense) state in order to determine the heme-ligation-independent spectral characteristics of the quaternary states. The tryptophan magnetic circular dichroism (MCD) peak observed at 293 nm in the R state of N-ethylsuccinimide- (NES-) des-Arg-modified human hemoglobin (Hb) was shifted to a slightly longer wavelength in the T state, consistent with the shift expected for tryptophan acting as a proton donor in a T-state hydrogen bond. Moreover, the increase observed in the T-state MCD intensity of this band relative to the R-state intensity was consistent with the effect expected for proton donation by tryptophan on the basis of the Michl perimeter model of aromatic MCD. The peak-to-trough magnitude of the R - T MCD difference spectrum is equal to 30% of the total R-state peak intensity contributed by all six tryptophans present in the human tetramer; the relative magnitude specific to the two beta37 tryptophans undergoing conformational change is estimated accordingly to be 3 times larger. The Trp-beta37 spectral shift, about 200 cm(-)(1), is in good agreement with the shifts observed in other H-bonded proton donors and provides corroborating spectral evidence for the formation in solution of a T-state Trp beta37-Asp alpha94 hydrogen bond observed in X-ray diffraction studies of deoxyHb crystals.

Multiple geminate ligand recombinations in human hemoglobin

The geminate ligand recombination reactions of photolyzed carbonmonoxyhemoglobin were studied in a nanosecond double-excitation-pulse time-resolved absorption experiment. The second laser pulse, delayed by intervals as long as 400 ns after the first, provided a measure of the geminate kinetics by rephotolyzing ligands that have recombined during the delay time. The peak-to-trough magnitude of the Soret band photolysis difference spectrum measured as a function of the delay between excitation pulses showed that the room temperature kinetics of geminate recombination in adult human hemoglobin are best described by two exponential processes, with lifetimes of 36 and 162 ns. The relative amounts of bimolecular recombination to T- and R-state hemoglobins and the temperature dependence of the submicrosecond kinetics between 283 and 323 K are also consistent with biexponential kinetics for geminate recombination. These results are discussed in terms of two models: geminate recombination kinetics modulated by concurrent protein relaxation and heterogeneous kinetics arising from alpha and beta chain differences.

Characterization of equilibrium intermediates in denaturant-induced unfolding of ferrous and ferric cytochromes c using magnetic circular dichroism, circular dichroism, and optical absorption spectroscopies

Protein unfolding during guanidine HCl denaturant titration of the reduced and oxidized forms of cytochrome c is monitored with magnetic circular dichroism (MCD), natural CD, and absorption of the heme bands and far-UV CD of the amide bands. Direct MCD spectral evidence is presented for bis-histidinyl heme ligation in the unfolded states of both the reduced and oxidized protein. For both redox states, the unfolding midpoints measured with MCD, which is an indicator of tertiary structure, are significantly lower than those measured with far-UV CD, an indicator of secondary structure. The disparate titration curves are interpreted in terms of a compound mechanism for denaturant-induced folding and unfolding involving a molten globulelike intermediate state (MG) with near-native secondary structure and nonnative tertiary structure and heme ligation. A comparison of the dependence of the free energy of formation of the MG intermediate on the redox state with the known contributions from heme ligation and solvation suggests that the heme is significantly more accessible to solvent in the MG intermediate than it is in the native state.

pH dependence of photolysis intermediates in the photoactivation of rhodopsin mutant E113Q

Glutamic acid at position 113 in bovine rhodopsin ionizes to form the counterion to the protonated Schiff base (PSB), which links the 11-cis-retinylidene chromophore to opsin. Photoactivation of rhodopsin requires both Schiff base deprotonation and neutralization of Glu-113. To better understand the role of electrostatic interactions in receptor photoactivation, absorbance difference spectra were collected at time delays from 30 ns to 690 ms after photolysis of rhodopsin mutant E113Q solubilized in dodecyl maltoside at different pH values at 20 degrees C. The PSB form (pH 5. 5, lambda(max) = 496 nm) and the unprotonated Schiff base form (pH 8. 2, lambda(max) = 384 nm) of E113Q rhodopsin were excited using 477 nm or 355 nm light, respectively. Early photointermediates of both forms of E113Q were qualitatively similar to those of wild-type rhodopsin. In particular, early photoproducts with spectral shifts to longer wavelengths analogous to wild-type bathorhodopsin were seen. In the case of the basic form of E113Q, the absorption maximum of this intermediate was at 408 nm. These results suggest that steric interaction between the retinylidene chromophore and opsin, rather than charge separation, plays the dominant role in energy storage in bathorhodopsin. After lumirhodopsin, instead of deprotonating to form metarhodopsin I(380) on the submillisecond time scale as is the case for wild type, the acidic form of E113Q produced metarhodopsin I(480), which decayed very slowly (exponential lifetime = 12 ms). These results show that Glu-113 must be present for efficient deprotonation of the Schiff base and rapid visual transduction in vertebrate visual pigments.

Lutein and zeaxanthin are associated with photoreceptors in the human retina

PURPOSE

Previous studies showed that lutein and zeaxanthin, the major human retinal carotenoids, are concentrated in the macula. In this study, the carotenoids in human macular and peripheral retina and the retinal pigment epithelium (RPE) were analyzed. They were also determined in the rod outer segments (ROS) before and after removal of extrinsic membrane proteins.

METHODS

Carotenoids were extracted from the macular and peripheral sections of human retina and RPE with hexane in dim light and analyzed by high performance liquid chromatography (HPLC). ROS samples equivalent to the amount in a single retina were also analyzed.

RESULTS

Retinal carotenoid amounts were similar to previous reports, but only low levels were detected in the RPE. Regional ratios of lutein:zeaxanthin were similar in the retina and RPE. Approximately 25% of the total retinal carotenoids were found in the ROS, indicating that a substantial portion of peripheral retinal carotenoids are present in the ROS. However, after removal of the extrinsic membrane proteins and subsequent analysis, carotenoids were not detected.

CONCLUSIONS

Most of the carotenoids in the human peripheral retina are present in the ROS. These ROS carotenoids are associated with soluble or salt-dependently bound proteins.

Multiple pathways on a protein-folding energy landscape: kinetic evidence

The funnel landscape model predicts that protein folding proceeds through multiple kinetic pathways. Experimental evidence is presented for more than one such pathway in the folding dynamics of a globular protein, cytochrome c. After photodissociation of CO from the partially denatured ferrous protein, fast time-resolved CD spectroscopy shows a submillisecond folding process that is complete in approximately 10(-6) s, concomitant with heme binding of a methionine residue. Kinetic modeling of time-resolved magnetic circular dichroism data further provides strong evidence that a 50-microseconds heme-histidine binding process proceeds in parallel with the faster pathway, implying that Met and His binding occur in different conformational ensembles of the protein, i.e., along respective ultrafast (microseconds) and fast (milliseconds) folding pathways. This kinetic heterogeneity appears to be intrinsic to the diffusional nature of early folding dynamics on the energy landscape, as opposed to the late-time heterogeneity associated with nonnative heme ligation and proline isomers in cytochrome c.

Spectroscopic evidence for nanosecond protein relaxation after photodissociation of myoglobin-CO

Nanosecond time-resolved absorption and magnetic optical rotatory dispersion (MORD) measurements of photolyzed myoglobin-CO visible bands (500-650 nm) are presented. These measurements reveal a 400 ns process, spectrally distinct from ligand recombination, that accounts for 7% of the observed spectral evolution in the visible absorption bands and 4% in the MORD. The time-resolved MORD, more sensitive to heme coordination geometry than absorption, suggests that this process is most likely associated with protein relaxation on the distal side of the heme pocket, perhaps accompanying rehydration of the deoxymyoglobin photoproduct or accommodation of protein side chains to ligand escape.

The effects of octanol on the late photointermediates of rhodopsin

Membrane suspensions of unperturbed rhodopsin and rhodopsin perturbed with 2.5 mM octanol were photolyzed with 477 nm laser pulses at 20 degrees C and 35 degrees C. Changes in absorbance were monitored at times ranging from 1 microsecond to 80 ms after excitation. The data were analyzed using singular value decomposition, global exponential fitting and kinetic modeling. A recently proposed model involving the photointermediate Meta-I380 (T. E. Thorgeirsson, J. W. Lewis, S. E. Wallace-Williams, and D. S. Kliger, Biochemistry 32, 13861-13872, 1993) fits data for samples with and without octanol. Comparison of the microscopic rates shows this alcohol accelerates the formation of Meta-II via Meta-I380. Activation and equilibrium thermodynamic parameters obtained from Arrhenius plots suggest that octanol reduces the entropy increase in forming both Meta-I380 and Meta-II. It also lowers the enthalpy of Meta-I380 relative to Lumi and of Meta-II relative to Meta-I480. To help determine whether octanol affects the protein directly or indirectly through the lipid bilayer, similar experiments were conducted using rhodopsin solubilized in 0.13% dodecyl maltoside with and without octanol. Spectral shifts in the presence of octanol suggest that a direct protein interaction exists in addition to previously reported effects dependent on membrane free volume.

Proton transfer reactions linked to rhodopsin activation

Purified bovine rhodopsin solubilized in dodecyl maltoside was photolyzed at 20 degreesC with 477 nm light, and difference spectra were collected at time delays ranging from 10 micros to 10 ms after photolysis. Bromocresol purple was added to the samples to detect pH changes in the aqueous environment due to changes in the protonation state of rhodopsin. The data were analyzed using singular value decomposition and global exponential fitting, which revealed three exponential processes indicating the presence of at least four intermediates. Spectral changes of the indicator dye were separated from those of rhodopsin, and proton release and uptake rates were analyzed within the framework of rhodopsin photoreaction kinetics. Proton release occurred during Lumi decay to Meta-I380 followed by uptake upon Meta-I380 decay and by a more significant proton uptake with the time course of Meta-I480 decay. On the basis of the estimated number of protons released and taken up in each step of the rhodopsin photoreaction, we concluded that two forms of Meta-II are present. The two forms of Meta-II, Meta-IIa' and Meta-IIb, differ in protonation state from one another as do both from the earlier, 380 nm absorbing form, Meta-I380.

Effects of pH on rhodopsin photointermediates from lumirhodopsin to metarhodopsin II

Time-resolved absorption difference spectra of membrane suspensions of bovine rhodopsin at pH 5, 6, 7, 8, 9, and 10 were collected in the time range from 1 micro s to 200 ms after laser photolysis with 7-ns pulses of 477-nm light. The data were analyzed using singular value decomposition (SVD) and global exponential fitting. At pH 7 the data agree well with previously obtained data (Thorgeirsson et al. (1993) Biochemistry 32, 13861-13872) with fits improved at all pH's by inclusion of a small component due to an absorbance change caused by rotational diffusion which is detectable even at magic angle polarization. A "square scheme" suggested to best explain the previous data, which involves two branches following decay of the lumi intermediate with pathways (1) lumi --> MI480 right harpoon over left harpoon MII and (2) lumi right harpoon over left harpoon MI380 --> MII, could be confirmed throughout the entire pH range. However, to account for the increased rate of the MII --> MI480 reaction in path 1 for rising pH values, we propose that the MII in the square scheme consists of deprotonated MII and protonated MIIH+ forms in rapid equilibrium with each other, resulting in an extended square scheme and increasing the number of 380-nm products from two to three. In addition to the kinetic processes described by the extended square scheme, above pH 8 fast ( approximately 10 micro s) and slow ( approximately 50 ms) components were found. The fast component was assigned to the decay of a blue-shifted lumi intermediate, and the slow component, resolvable only at pH 10, was assigned to formation of a 450 nm absorbing photoproduct.

Time-resolved circular dichroism studies of protein folding intermediates of cytochrome c

The circular dichroism spectra of cytochrome c (cytc) in 4.6 M guanidine hydrochloride (pH 6.5) indicate that the secondary structure in reduced cytc is near-native, whereas in the CO-bound species (COCytc) it is substantially unfolded. Photolysis of COCytc should thus induce large changes in the secondary structure, which can be probed with time-resolved circular dichroism (TRCD) spectroscopy in the far-UV region. Time-resolved absorption (TROA) and TRCD methods were used to study the photolysis reaction of COCytc in efforts to identify structural intermediates in cytc folding on time scales from nanoseconds to seconds. TROA data from the Soret region, similar to previous studies, showed four intermediates with lifetimes of 2, 50, 225, and 880 micros. The 2-micros process is proposed to involve Fe(II)-Met80 coordination. Approximately 7% of the native CD signal was observed in the TRCD signal at 220 nm within 500 ns, with no significant additional secondary structure formation observed. Further folding after 2 micros may be inhibited by ligation of His26/His33 with Fe(II), which is suggested to be associated with the 50-micros phase. The two slowest components, tau = 225 and 880 micros, are attributed to CO rebinding on the basis of mixed-gas experiments. CO rebinding is expected to compete with protein folding and favor the unfolded state. However, when the two CO rebinding lifetimes are extended into milliseconds by reducing the CO concentration, there is still no significant increase in CD signal at 220 nm.

Fast natural and magnetic circular dichroism spectroscopy

The addition of circular or, more generally, elliptical polarization state detection to fast optical absorption spectroscopy can increase the amount of electronic and nuclear conformational information obtained about transient molecular species. To accomplish this, fast circular dichroism methods have emerged over the past decade that overcome the millisecond limit on time resolution associated with conventional modulation techniques and enable structural studies of excited states and kinetic intermediates. This article reviews techniques for time-resolved natural and magnetic circular dichroism spectroscopy covering the picosecond to millisecond time regimes and their applications, with particular emphasis on quasi-null ellipsometric techniques for nanosecond multichannel measurements of circular dichroism. Closely related quasi-null polarimetric techniques for nanosecond optical rotatory dispersion and linear dichroism measurements are also discussed.

Absorbance changes by aromatic amino acid side chains in early rhodopsin photointermediates

Absorbance changes were monitored from 250 to 650 nm during the first microsecond after photolysis of detergent suspensions of bovine rhodopsin at 20 degrees C. Global analysis of the resulting data produced difference spectra for bathorhodopsin, BSI and lumirhodopsin which give the change in absorbance of the aromatic amino acid side chains in these photointermediates relative to rhodopsin. These spectra show that the significant bleaching of absorbance near 280 nm, which has been seen previously for the lumirhodopsin, metarhodopsin I and metarhodopsin II intermediates, extends to times as early as bathorhodopsin. Because no corresponding absorbance increase is observed in the 250-275 nm region, the earliest bleaching of the 280 nm absorbance in rhodopsin is attributed to disruption of a hyperchromic interaction affecting Trp265. Partial decay of this 280 nm bleaching as bathorhodopsin converts to BSI takes place maximally near 290 nm, where Trp265 has been shown to absorb, and could be due to the ring of the retinylidene chromophore resuming a position at the BSI stage that reestablishes the hyperchromic interaction with Trp265. A subsequent change in the 250-300 nm region, which has no counterpart in the visible chromophore bands, indicates the possible presence of a protein-localized process as lumirhodopsin is formed.

Early photolysis intermediates of gecko and bovine artificial visual pigments

Nanosecond laser photolysis measurements were conducted on digitonin extracts of artificial pigments prepared from the cone-type visual pigment, P521, of the Tokay gecko (Gekko gekko) retina. Artificial pigments were prepared by regeneration of bleached gecko photoreceptor membranes with 9-cis-retinal, 9-cis-14-methylretinal, or 9-cis-alpha-retinal. Absorbance difference spectra were recorded at a sequence of time delays from 30 ns to 60 microseconds following excitation with a pulse of 477-nm actinic light. Global analysis showed the kinetic data for all three artificial gecko pigments to be best fit by two-exponential processes. These two-exponential decays correspond to similar decays observed after photolysis of P521 itself, with the first process being the decay of the equilibrated P521 Batho<-->P521 BSI mixture to P521 Lumi and the second process being the decay of P521 Lumi to P521 Meta I. In spite of its large blue shift relative to P521, iso-P521 displays a normal chloride depletion induced blue shift. Iso-P521's early intermediates up to Lumi were also blue-shifted, with the P521 Batho<-->P521 BSI equilibrated mixture being 15 nm blue-shifted and P521 Lumi being 8 nm blue-shifted relative to the intermediates formed after P521 photolysis. The blue shift associated with the iso-pigment is reduced or disappears entirely by P521 Meta I. Similar blue shifts were observed for the early intermediates observed after photolysis of bovine isorhodopsin, with the Lumi intermediate blue-shifted 5 nm compared to the Lumi intermediate formed after photolysis of bovine rhodopsin. These shifts indicate that a difference exists between the binding sites of 9- and 11-cis pigments which persists for microseconds at 20 degrees C.

Properties of early photolysis intermediates of rhodopsin are affected by glycine 121 and phenylalanine 261

Glycine 121 in transmembrane (TM) helix 3 and phenylalanine 261 in TM helix 6 of bovine rhodopsin have been shown to be critical residues for creating an appropriate chromophore binding pocket for 11-cis-retinal [Han, M., Lin, S. W., Smith, S. O., and Sakmar, T. P. (1996) J. Biol. Chem. 271, 32330-32336; Han, M., Lin, S. W., Minkova, M., Smith, S. O., and Sakmar, T. P. (1996) J. Biol. Chem. 271, 32337-32342]. To further explore structure-function relationships in the vicinity of receptor helices 3 and 6, time-resolved absorption difference spectra of rhodopsin mutants G121A, G121V, and G121L/F261A were obtained at 20 degrees C. Data were collected from 30 ns to 690 ms after laser photolysis with 7 ns pulses (lambdamax = 477 nm) and analyzed using a global exponential fitting procedure after singular value decomposition (SVD). For each mutant, the decay of its bathorhodopsin photoproduct (batho) into an equilibrium with its blue-shifted intermediate (bsi) was too fast to resolve (<20 ns). The reaction scheme found for the mutants G121A and G121L/F261A was batho/bsi --> lumirhodopsin (lumi) --> metarhodopsin I (MI) --> metarhodopsin II (MII). For G121V, an additional early 380 nm absorber, with a back-reaction to lumi, had to be included in the above scheme. For the three Gly121 mutants, the main pathway to reach the active MII state is via lumi and MI. This is in contrast to rhodopsin where the main pathway in detergent samples is via lumi and an early 380 nm absorber, MI380. From the accelerated batho decay present in all three mutants, we conclude that Gly121 is likely to participate in the earliest chromophore-protein interactions. In addition, bsi decay is further accelerated in mutant G121L/F261A, suggesting that Phe261 is an essential determinant of the protein processes involved in bsi decay.

Chromophore structural changes in rhodopsin from nanoseconds to microseconds following pigment photolysis

Rhodopsin is a prototypical G protein-coupled receptor that is activated by photoisomerization of its 11-cis-retinal chromophore. Mutant forms of rhodopsin were prepared in which the carboxylic acid counterion was moved relative to the positively charged chromophore Schiff base. Nanosecond time-resolved laser photolysis measurements of wild-type recombinant rhodopsin and two mutant pigments then were used to determine reaction schemes and spectra of their early photolysis intermediates. These results, together with linear dichroism data, yielded detailed structural information concerning chromophore movements during the first microsecond after photolysis. These chromophore structural changes provide a basis for understanding the relative movement of rhodopsin's transmembrane helices 3 and 6 required for activation of rhodopsin. Thus, early structural changes following isomerization of retinal are linked to the activation of this G protein-coupled receptor. Such rapid structural changes lie at the heart of the pharmacologically important signal transduction mechanisms in a large variety of receptors, which use extrinsic activators, but are impossible to study in receptors using diffusible agonist ligands.

Deriving reaction mechanisms from kinetic spectroscopy. Application to late rhodopsin intermediates

A general algebraic approach to the kinetic analysis of time-dependent absorption data is presented that allows the calculation of possible kinetic schemes. The kinetic matrices of all possible reaction mechanisms are calculated from experimental eigenvalues and eigenvectors derived from the decay constants and amplitude spectra (b-spectra) of the global exponential fit to the time-dependence of the absorption data. The eigenvalues are directly related to the decay constants, and the eigenvectors are obtained by decomposing the b-spectra into spectral components representing the intermediates. The analysis method is applied to the late intermediates (lumi, meta I, meta I-380, and meta II) of the rhodopsin photoreaction. The b-spectra are decomposed into lumi, meta I, meta-380, and rhodopsin spectra. The meta-380 component is partitioned into isospectral meta I-380 and meta II components based on physical criteria. The calculated kinetic matrices yield a number of reaction mechanisms (linear scheme with back reactions, branched schemes with equilibrium steps, and a variety of square models) consistent with the photolysis data at 25 degrees C. The problems associated with isospectral intermediates (meta I-380 and meta II) are treated successfully with this method.

Evidence for heme-heme excitonic coupling in the Soret circular dichroism of hemoglobin

In order to study interdimer heme-heme electronic interactions in human hemoglobin, the Soret circular dichroism spectrum of the carboxy adduct is measured as a function of protein concentration, the spectrum at the highest concentration representing primarily that of alpha2beta2 tetramers (93%) and the lowest concentration representing primarily alphabeta dimers (68%). The tetramer-dimer difference spectrum, obtained using singular value decomposition and linear least squares fitting from a matrix of CD spectra measured at ten concentrations, is roughly conservative, with a larger negative lobe at shorter wavelengths and a peak-to-trough magnitude that is 18% of the tetramer's maximum Soret CD magnitude. It is tentatively assigned to heme-heme excitonic interactions on the basis of theoretical predictions by R. W. Woody [(1985) in Optical Properties and Structure of Tetrapyrroles (Blauer, G., and Sund, H., Eds.), pp. 239-256, Walter de Gruyter, New York].

Dynamics of the N-terminal alpha-helix unfolding in the photoreversion reaction of phytochrome A

Time-resolved circular dichroism spectroscopy in the far-UV spectral region was used to examine the intermediates of the phytochrome photoreversion reaction (Pfr --> Pr). Three intermediates, lumi-F (tau = 320 ns), meta-Fa (tau = 265 micros) and meta-Fb (tau = 5.5 ms), have been identified in a simple sequential kinetic photoreversion mechanism by absorption spectroscopy [Linschitz, H., Kasche, V., Butler, W. L., & Siegelman, H. W. (1966) J. Biol. Chem. 241, 3395-3403; Pratt, L. H., & Butler, W. L. (1968) Photochem. Photobiol. 8, 477-485; Burke, M., Pratt, D. C., & Moscowitz, A. (1972) Biochemistry 11, 4025-4031; Spruit, C. J. P., Kendrick, R. E., & Cooke, R. J. (1975) Planta (Berlin) 127, 121-132; Eilfeld, P., & Rüdiger, W. (1985) Z. Naturforsch. 40c, 109-114; Chen, E., Lapko, V. N., Lewis, J. W., Song, P.-S., & Kliger, D. S. (1996) Biochemistry 35, 843-850]. In order to correlate the unfolding of the N-terminal alpha-helical segment with one or more of the intermediate species, time-resolved methods were coupled with the structurally sensitive probe of CD in the far-UV spectral region. Analysis of the TRCD data associates the decrease in alpha-helical content that occurs upon formation of Pr with decay of the meta-Fa intermediate. This unfolding process occurs with a time constant of 310 +/- 125 micros, which is consistent with the 265-micros lifetime for meta-Fa.

Time-resolved spectroscopy of the early photolysis intermediates of rhodopsin Schiff base counterion mutants

Time-resolved absorption difference spectra of COS-cell expressed rhodopsin and rhodopsin mutants (E113D, E113A/A117E, and G90D), solubilized in detergent, were collected from 20 ns to 510 ms after laser photolysis with 7 ns pulses (lambda(max) = 477 nm). The data were analyzed using a global exponential fitting procedure following singular value decomposition (SVD). Over the entire time range excellent agreement was achieved between results for COS-cell and rod outer segment rhodopsin both in kinetics and in the lambda(max) values of the intermediates. The Schiff base counterion mutant E113D showed strong similarities to rhodopsin up to lumi, following the established scheme: batho <==> bsi --> lumi. Including late delay times (past 1 micros), the mutant E113D lumi decayed to metarhodopsin II (MII), showing that the detergent strongly favors MII over metarhodopsin I (MI). However, a back-reaction from MII to lumi was observed that was not seen for rhodopsin. The kinetic schemes for the mutants E113A/A117E and G90D were significantly different from that of rhodopsin. In both mutants batho decay into an equilibrium with bsi was too fast to resolve (<20 ns). The batho/bsi mixtures decayed with the following reaction scheme: batho/bsi <==> lumi <==> MI-like <==> MII-like. However, the back-reaction from MI-like to lumi was not seen in G90D. MI-like spectral intermediates absorbing around 460 nm appeared in both mutants. They have been shown to be the transducin-activating species (R*). These data, interpreted in the context of previous NMR, FTIR, and Raman data, are consistent with a picture in which the kinetics of batho decay is dependent on a protein-induced perturbation near C12-C13 of the retinal chromophore. The lambda(max) values of the bsi and lumi intermediates in the mutant pigments are interpreted in terms of movement of the Schiff base relative to its counterion.

Metarhodopsin III formation and decay kinetics: comparison of bovine and human rhodopsin

Absorbance spectra were recorded at various times after photolysis of hypotonically washed membrane suspensions of human and bovine rhodopsin (pH 7 or 8, T = 20 or 37 degrees C). Global data analysis showed that at 20 degrees C, metarhodopsin III formation was the only process occurring from 1 to 30 min following photolysis. At pH 8, a significant amount of human metarhodopsin I was present before metarhodopsin III formed. At 37 degrees C, two decay processes were seen, formation of metarhodopsin III (lifetime 113 +/- 3 sec bovine, 93 +/- 2 sec human) and formation of a species with the properties of n-retinylidine opsin (lifetime 900 +/- 150 sec bovine, 2000 +/- 350 sec human). A larger fraction of human rhodopsin (approximately 50%) is converted to metarhodopsin III than is the case for bovine rhodopsin (approximately 35%).

Nanosecond time-resolved spectroscopy of biomolecular processes

Over the past two decades, nanosecond absorption and vibrational spectroscopies have developed into powerful tools for monitoring the secondary, tertiary, and quaternary structural relaxations of biological macromolecules under near-physiological conditions of solvent and temperature. Observed through such methods, the dynamic response of a biomolecule to photoinitiated excursions from equilibrium can reveal valuable information about the structure-function relationship, information beyond that obtained from the static structures provided by X-ray crystallography, nuclear magnetic resonance spectroscopy, and other steady-state methods. Most recently, the development of ultra-sensitive polarization techniques for absorption spectroscopy has greatly enhanced the amount of time-resolved structural information that can be obtained from the broadened electronic spectra of biomolecules. This review examines nanosecond absorption, vibrational, and polarized absorption methods, and their applications to protein function and folding, emphasizing the complementary nature of information obtained from electronic and vibrational spectra measured on the nanosecond time scale.

Nanosecond time-resolved absorption studies of human oxyhemoglobin photolysis intermediates

The time-resolved spectra of photoproducts from ligand photodissociation of oxyhemoglobin are measured in the Soret spectral region for times from 10 ns to 320 microseconds after laser photolysis. Four processes are detected at a heme concentration of 80 microM: a 38-ns geminate recombination, a 137-ns tertiary relaxation, and two bimolecular processes for rebinding of molecular oxygen. The pseudo-first-order rate constants for rebinding to the alpha and beta subunits of hemoglobin are 3.2 x 10(4) s-1 (31 microseconds lifetime) and 9.4 x 10(4) s-1 (11 microseconds lifetime), respectively. The significance of kinetic measurements made at different heme concentrations is discussed in terms of the equilibrium compositions of hemoglobin tetramer and dimer mixtures. The rebinding rate constants for alpha and beta chains are observed to be about two times slower in the dimer than in the tetramer, a finding that appears to support the observation of quaternary enhancement in equilibrium ligand binding by hemoglobin tetramers.

Allosteric intermediates in hemoglobin. 2. Kinetic modeling of HbCO photolysis

Nanosecond absorption spectra are measured in the Soret and near-UV spectral regions of human hemoglobin (Hb) after laser photolysis of the carbonyl adduct in order to study the dynamics of globin tertiary and quaternary conformational changes. Spectra and concentrations of physical intermediates, distinguished by extent of heme ligation and intraprotein relaxation, are obtained from a global analysis using a microscopic kinetic model that explicitly accounts for six observed relaxation and recombination processes. Three observed rate constants for CO rebinding and two intraprotein relaxation constants obtained are similar to constants determined by Hofrichter et al. [(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2235], the latter two comprising the 20-30-microseconds R --> T quaternary transition and a previously unassigned 1-microseconds intraprotein relaxation. On the basis of the modeled intermediate spectra, as well as UV circular dichroism results observed on this time scale [Björling, S.C., Goldbeck, R.A., Paquette, S.J., Milder, S.J., & Kliger, D.S. (1996) Biochemistry 35, 8619-8627], the 1-microsecond relaxation is assigned to heme conformational changes concomitant with a relaxation of protein conformation at the alpha 1 beta 2 interface corresponding to an initial step in a compound R --> T reaction path.

Allosteric intermediates in hemoglobin. 1. Nanosecond time-resolved circular dichroism spectroscopy

Time-resolved circular dichroism (TRCD) studies performed on photolyzed hemoglobin-CO complex (HbCO) probe room temperature protein relaxations in Hb, including the R --> T allosteric transition. TRCD spectroscopy of photolysis intermediates in the near-UV (250-400 nm) spectral region provides a diagnostic for T-like structure at the alpha 1 beta 2 interface via the effect of quaternary structure on the UV CD of aromatic residues. The TRCD of porphyrin-based transitions in the UV and Soret regions, reflecting transition-dipole couplings between hemes and aromatic residues over a radius wide enough to permit heme-interface and inter-dimer interactions, is modulated by the tertiary and quaternary structure of photolysis intermediates. In the allosteric core model of Hb cooperativity, Fe-CO bond breakage initiates a heme structural change, thought to be heme doming, that is transmitted to the alpha 1 beta 2 interface via the F helix. The TRCD results, analyzed in light of kinetic information from time-resolved absorption studies, suggest specific features for the mechanism by which the ensuing tertiary and quaternary conformational changes propagate through the protein. In particular, the UV-TRCD indicates that the alpha 1 beta 2 interface responds within several hundred nanoseconds to initial events at the heme by shifting from an R toward a T-like interface. The appearance of T-like character at the alpha 1 beta 2 interface tens of microseconds before the appearance of equilibrated T state deoxyHb indicates that the R --> T transition in photolyzed HbCO is a stepwise process, as previously suggested by time-resolved resonance Raman studies.

A study of the mechanisms of slow religation to sickle cell hemoglobin polymers following laser photolysis

Time-resolved linear dichroism (TRLD) measurements are conducted on gels of sickle cell hemoglobin following laser photolysis of the carbonyl adduct to monitor religation kinetics to hemoglobin S polymers. The return of the polymer phase to its equilibrium ligation state has been found to be about 1000 times slower than that of the solution phase hemoglobin tetramers. Several mechanisms describing this slow religation to the polymer were proposed: (1) religation occurs through a biomolecular process involving all polymer hemes, (2) religation occurs through a bimolecular process in which only hemoglobin molecules at the polymer ends can participate, and (3) religation occurs through the exchange of ligated hemoglobin molecules in the monomer phase with unligated ones in the polymer phase. To test these mechanisms, measurements are performed on gels having different domain sizes. The results show no relation between domain size and religation kinetics. The independence of religation kinetics and domain size is most consistent with the first of the three mechanisms described above (bimolecular recombination involving all polymer hemes). This result is discussed in terms of a model in which diffusion of the ligand is inhibited in the polymer phase. An understanding of the ligand binding kinetics of sickle hemoglobin polymers could have pathophysiological significance in its relevance to polymer formation and melting during red blood cell circulation.

Chromophore reorientations in the early photolysis intermediates of bacteriorhodopsin

The photoselection-induced time-resolved linear dichroism of a bacteriorhodopsin suspension of purple membrane from 350 to 750 nm is measured by a new pseudo-null measurement technique. In combination with time-resolved absorption measurements, these linear dichroism measurements are used to determine the reorientation of the retinal chromophore of bacteriorhodopsin from 50 ns to 50 microseconds after photolysis. This time range covers the times when the K photointermediate decays to form L, as well as the early times during the formation of the M intermediate in the photocycle. An analysis of the photoselection-induced linear dichroism measured directly, along with the absorbance changes polarized parallel to the linearly polarized excitation, shows that the anisotropy is invariant over this time period, implying that the photolyzed chromophore rotates less than 8 degrees C with respect to unphotolyzed chromophores during this part of the photocycle.

Mechanism of native oat phytochrome photoreversion: a time-resolved absorption investigation

The regulation of plant photomorphogenesis is mediated by the thermal reactions that follow light absorption by the phytochrome photoreceptor. Phytochromes are tetrapyrrolic chromoproteins that exist in two photochromically interconvertible forms, a red light absorbing species, Pr, and a far-red light absorbing form, Pfr. Upon irradiation with 670 nm light, the inactive, red light sensing Pr form is converted to the active Pfr form. Although the forward phototransformation has been studied extensively by several groups using various techniques, the Pfr-->Pr photoreversion reaction that occurs upon irradiation with 730 nm light is not as thoroughly characterized. In this study, time-resolved absorption (TROD) spectroscopy is used to examine the intermediate species involved in the phytochrome photoreversion mechanism at 10 degrees C. Analysis of the TROD data identifies three species with lifetimes of 320 ns, 265 microseconds, and 5.5 ms. TROD results are described in terms of the simplest parallel and sequential kinetic models. Comparison of intermediate spectra from these mechanisms with those of previously reported species from flash photoreversion and low-temperature studies indicates that Pfr photoreversion follows a sequential pathway that does not share any intermediates with the Pr phototransformation pathway.

Carbon monoxide religation kinetics to hemoglobin S polymers following ligand photolysis

The re-equilibration rate of carbon monoxide binding to hemoglobin S polymers is determined by time-resolved measurements of linear dichroism spectra. Linear dichroism is used to detect religation to hemoglobin in the polymer in the presence of rebinding to free hemoglobin S tetramers. Measurement of the linear dichroism resulting from photolysis of the small percentage of ligand bound to the polymer is accomplished through the use of an ultrasensitive, ellipsometric linear dichroism technique developed for this purpose. The major finding is that the return of the polymer phase to its equilibrium ligation state is much slower than that of the solution phase hemoglobin tetramers. Assuming all hemes in the polymer are equally likely to participate in rebinding, the re-equilibration rate for carbon monoxide religation to hemoglobin S polymers is found to be 0.14 +/- 0.07 (s-1 mM-1), about 1000 times slower than the rebinding rate of carbon monoxide to T-state monomer hemoglobin. Several interpretations of this result are discussed. An understanding of the ligand binding kinetics to hemoglobin S polymers could have pathophysiological significance in its relevance to polymer formation and melting during red blood cell circulation.

Low-temperature trapping of early photointermediates of alpha-isorhodopsin

Alpha-Isorhodopsin, an artificial visual pigment with a 9-cis-4,5-dehydro-5,6-dihydro(alpha)retinal chromophore, was photolyzed at low temperatures and absorption difference spectra were collected as the sample was warmed. A bathorhodopsin (Batho)-like intermediate absorbing at ca 495 nm was detected below 55 K,a blue-shifted intermediate (BSI)-like intermediate absorbing at ca 453 nm was observed when the temperature was raised to 60 K and a lumirhodopsin (Lumi)-like intermediate absorbing at ca 470 nm was found when the sample was warmed to 115 K. Photointermediates from this pigment were compared to those of native rhodopsin and 5,6-dihydroisorhodopsin. As in native rhodopsin, Batho is the first intermediate detected in alpha-isorhodopsin, though unlike native rhodopsin at low temperatures BSI is observed prior to Lumi formation. Alpha-Isohodopsin behaves similarly to 5,6-dihydroisorhodopsin, with the same early intermediates observed in both artificial visual pigments lacking the C5-C6 double bond. The transition temperature for BSI formation is higher in alpha-isorhodopsin, suggesting an interaction involving the chromophore ring in BSI formation. The transition temperature for Lumi formation is similar for these two pigments as well as for native rhodopsin, suggesting comparable changes in the protein environment in that transition.

Chloride effect on the early photolysis intermediates of a gecko cone-type visual pigment

Nanosecond laser photolysis measurements were conducted on the cone-type visual pigment P521 in digitonin extracts of Tokay gecko (Gekko gekko) retina containing physiological chloride ion levels and also on samples which had been chloride depleted or which contained high levels (4 M) of chloride. Absorbance difference spectra were recorded at a sequence of time delays from 30 ns to 60 microseconds following excitation with a pulse of either 532- or 477-nm actinic light. Global analysis showed the kinetic decay data for gecko pigment P521 to be best fit by two exponential processes under all chloride conditions. The initial photoproduct detected had a broad spectrum characteristic of an equilibrated mixture of a Batho P521 intermediate with its blue-shifted intermediate (BSI P521) decay product. The first exponential process was assigned to the decay of this mixture to the Lumi P521 intermediate. The second exponential process was identified as the decay of Lumi P521 to Meta I P521. The initial photoproduct's spectrum exhibited a strong dependence on chloride concentration, indicating that chloride affects the composition of the equilibrated mixture of Batho P521 and BSI P521. These results suggest that the affinity for chloride is reduced approximately 5-fold in the Batho P521 intermediate and approximately 50-fold in the BSI P521 intermediate. Chloride concentration also affects the apparent decay rate of the equilibrated mixture. When the apparent decay rate is corrected for the composition of the equilibrated mixture, a relatively invariant microscopic rate constant is obtained for BSI decay (k = 1/55 ns-1).(ABSTRACT TRUNCATED AT 250 WORDS)

Nanosecond optical rotatory dispersion spectroscopy: application to photolyzed hemoglobin-CO kinetics

A standard technique for static optical rotatory dispersion (ORD) measurements is adapted to the measurement of ORD changes on a nanosecond (ns) time scale, giving approximately a million-fold improvement in time-resolution over conventional instrumentation. The technique described here is similar in principle to a technique recently developed for ns time-resolved circular dichroism (TRCD) spectroscopy, although the time-resolved optical rotatory dispersion (TRORD) technique requires fewer optical components. As with static ORD, TRORD measurements may be interpreted by empirical comparisons or may be transformed, via the Kramers-Kronig relations, to more easily interpreted TRCD spectra. TRORD can offer experimental advantages over TRCD in studying kinetic processes effecting changes in the chiral structures of biological molecules. In particular, the wider dispersion of ORD bands compared with the corresponding CD bands means that ORD information may often be obtained outside of absorption bands, a signal-to-noise advantage for multichannel measurements. Demonstration of the technique by its application to ns TRORD and the transform-calculated TRCD of carboxy-hemoglobin (Hb-CO) after laser photolysis is presented.

Nanosecond absorption study of kinetics associated with carbon monoxide rebinding to hemoglobin S and hemoglobin C following ligand photolysis

The absorption spectra of photolysis intermediates of the CO complex of hemoglobin S and hemoglobin C, in the tetramer form, have been measured between 10 ns and 200 ms after excitation. These data were analyzed using singular value decomposition (SVD) and global analysis to determine kinetic lifetimes associated with various processes involved in CO recombination. The results of this analysis show that, in the tetramer (non-aggregated) form, hemoglobin S and hemoglobin C exhibit the same kinetics associated with CO recombination as hemoglobin A.

Effects of temperature on rhodopsin photointermediates from lumirhodopsin to metarhodopsin II

Absorbance changes following the photolysis of mildly sonicated membrane suspensions of bovine rhodopsin are monitored using multichannel detection at 15, 20, 25, 30, and 35 degrees C. Difference spectra collected with microsecond time resolution are analyzed by singular value decomposition and multiexponential fitting. Several kinetic schemes are tested using methods that compare the observed rates and associated spectral amplitudes to the eigenvalues and eigenvectors of kinetic matrices. The time evolution of the spectra is more complex than can be accounted for by the traditional lumi-->metarhodopsin I<-->metarhodopsin II scheme. Above 25 degrees C, the formation of metarhodopsin II is achieved without a large transient accumulation of metarhodopsin I. Within the framework of first-order kinetics, the observations are explained by simple kinetic schemes that lead to the formation of a deprotonated Schiff's base species temporally distinct from metarhodopsin II directly upon the decay of lumirhodopsin.