Low-temperature photoreactions of halorhodopsin. 1. Detection of conformational substates of the chromoprotein

Chromophore Structural Change during the Photocycle of a Light-Driven Cl- Pump from Mastigocladopsis repens: A Cryogenic Raman Study

Microbial rhodopsins are the most widely distributed photoreceptors that bind a retinal Schiff base chromophore. Among them, a light-driven Cl- pump discovered from Mastigocladopsis repens (MrHR) is distinctive in that it has the structural features of both H+ and Cl- pumps. While the photocycle has been characterized by light-induced changes of the absorption spectrum, the structural changes of the retinal chromophore remain largely unknown. In this study, we examined the chromophore structural changes of MrHR by using cryogenic Raman spectroscopy. We observed five photointermediates─K, L, N1, N2, and MrHR'─that show distinct vibrational spectra, indicating atypical chromophore structures, e.g., small distortion in the K intermediate and Schiff base configurational change in the MrHR' intermediate. Based on the Raman spectra of two N intermediates (N1 and N2), we propose that N1 is the Cl--bound state and N2 is the Cl--unbound state, which are responsible for the Cl- release and uptake, respectively, to achieve Cl- pumping.

Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts

From the low-temperature absorption and Raman measurements of halorhodopsin from Natronomonas pharaonis (pHR), we observed that the two photoproducts were generated after exciting pHR at 80 K by green light. One photoproduct was the red-shifted K intermediate (pHR_K) as the primary photointermediate for Cl^- pumping, and the other was the blue-shifted one (pHR_hypso), which was not involved in the Cl^- pumping and thermally relaxed to the original unphotolyzed state by increasing temperature. The formation of these two kinds of photoproducts was previously reported for halorhodopsin from Halobacterium sarinarum [ Zimanyi et al. Biochemistry 1989 , 28 , 1656 ]. We found that the same took place in pHR, and we revealed the chromophore structures of the two photointermediates from their Raman spectra for the first time. pHR_hypso had the distorted all-trans chromophore, while pHR_K contained the distorted 13-cis form. The present results revealed that the structural analyses of pHR_K carried out so far at ∼80 K potentially included a significant contribution from pHR_hypso. pHR_hypso was efficiently formed via the photoexcitation of pHR_K, indicating that pHR_hypso was likely a side product after photoexcitation of pHR_K. The formation of pHR_hypso suggested that the active site became tight in pHR_K due to the slight movement of Cl^-, and the back photoisomerization then produced the distorted all-trans chromophore in pHR_hypso.

Photochemical reaction cycle and proton transfers in Neurospora rhodopsin

It was recently found that NOP-1, a membrane protein of Neurospora crassa, shows homology to haloarchaeal rhodopsins and binds retinal after heterologous expression in Pichia pastoris. We report on spectroscopic properties of the Neurospora rhodopsin (NR). The photocycle was studied with flash photolysis and time-resolved Fourier-transform infrared spectroscopy in the pH range 5-8. Proton release and uptake during the photocycle were monitored with the pH-sensitive dye, pyranine. Kinetic and spectral analysis revealed six distinct states in the NR photocycle, and we describe their spectral properties and pH-dependent kinetics in the visible and infrared ranges. The phenotypes of the mutant NR proteins, D131E and E142Q, in which the homologues of the key carboxylic acids of the light-driven proton pump bacteriorhodopsin, Asp-85 and Asp-96, were replaced, show that Glu-142 is not involved in reprotonation of the Schiff base but Asp-131 may be. This implies that, if the NR photocycle is associated with proton transport, it has a low efficiency, similar to that of haloarchaeal sensory rhodopsin II. Fourier-transform Raman spectroscopy revealed unexpected differences between NR and bacteriorhodopsin in the configuration of the retinal chromophore, which may contribute to the less effective reprotonation switch of NR.

Static and time-resolved step-scan Fourier transform infrared investigations of the photoreaction of halorhodopsin from Natronobacterium pharaonis: consequences for models of the anion translocation mechanism

The molecular changes during the photoreaction of halorhodopsin from Natronobacterium pharaonis have been monitored by low-temperature static and by time-resolved step-scan Fourier transform infrared difference spectroscopy. In the low-temperature L spectrum anions only influence a band around 1650 cm(-1), tentatively assigned to the C=N stretch of the protonated Schiff base of L. The analysis of the time-resolved spectra allows to identify the four states: K, L(1), L(2), and O. Between L(1) and L(2), only the apoprotein undergoes alterations. The O state is characterized by an all-trans chromophore and by rather large amide I spectral changes. Because in our analysis the intermediate containing O is in equilibrium with a state indistinguishable from L(2), we are unable to identify an N-like state. At very high chloride concentrations (>5 M), we observe a branching of the photocycle from L(2) directly back to the dark state, and we provide evidence for direct back-isomerization from L(2). This branching leads to the reported reduction of transport activity at such high chloride concentrations. We interpret the L(1) to L(2) transition as an accessibility change of the anion from the extracellular to the cytosolic side, and the large amide I bands in O as an indication for opening of the cytosolic channel from the Schiff base toward the cytosolic surface and/or as indication for changes of the binding constant of the release site.

Roles of cytoplasmic arginine and threonine in chloride transport by the bacteriorhodopsin mutant D85T

In the light-driven anion pump halorhodopsin (HR), the residues arginine 200 and threonine 203 are involved in anion release at the cytoplasmic side of the membrane. Because of large sequence homology and great structural similarities between HR and bacteriorhodopsin (BR), it has been suggested that anion translocation by HR and by the chloride-pumping BR mutant BR-D85T occurs by the same mechanism. Consequently, the functions of the R200/T203 pair in HR should be the same as those of the corresponding pair in BR-D85T (R175/T178). We have put this hypothesis to a test by creating two mutants of BR-D85T in which R175 and T178 were replaced by glutamine and valine, respectively. Chloride transport activities were essentially the same for all three mutants, whereas chloride binding and the kinetics of parts of the photocycle were markedly affected by the replacement of T178. In contrast, the consequences of mutating R175 proved to be less significant. These findings are consistent with evidence obtained on HR and therefore support the idea that the respective mechanistic roles of the cytoplasmic arginine/threonine pairs in HR and BR-D85T are equal.

Structural factors controlling ligand binding to myoglobin: a kinetic hole-burning study

Using temperature-derivative spectroscopy in the temperature range below 100 K, we have studied the dependence of the Soret band on the recombination barrier in sperm whale carbonmonoxy myoglobin (MbCO) after photodissociation at 12 K. The spectra were separated into contributions from the photodissociated species, Mb*CO, and CO-bound myoglobin. The line shapes of the Soret bands of both photolyzed and liganded myoglobin were analyzed with a model that takes into account the homogeneous bandwidth, coupling of the electronic transition to vibrational modes, and static conformational heterogeneity. The analysis yields correlations between the activation enthalpy for rebinding and the model parameters that characterize the homogeneous subensembles within the conformationally heterogeneous ensemble. Such couplings between spectral and functional parameters arise when they both originate from a common structural coordinate. This effect is frequently denoted as "kinetic hole burning." The study of these correlations gives direct insights into the structure-function relationship in proteins. On the basis of earlier work that assigned spectral parameters to geometric properties of the heme, the connections with the heme geometry are discussed. We show that two separate structural coordinates influence the Soret line shape, but only one of the two is coupled to the enthalpy barrier for rebinding. We give evidence that this coordinate, contrary to widespread belief, is not the iron displacement from the mean heme plane.

Photocycle of halorhodopsin from Halobacterium salinarium

The light-driven chloride pump, halorhodopsin, is a mixture containing all-trans and 13-cis retinal chromophores under both light and dark-adapted conditions and can exist in chloride-free and chloride-binding forms. To describe the photochemical cycle of the all-trans, chloride-binding state that is associated with the transport, and thereby initiate study of the chloride translocation mechanism, one must first dissect the contributions of these species to the measured spectral changes. We resolved the multiple photochemical reactions by determining flash-induced difference spectra and photocycle kinetics in halorhodopsin-containing membranes prepared from Halobacterium salinarium, with light- and dark-adapted samples at various chloride concentrations. The high expression of cloned halorhodopsin made it possible to do these measurements with unfractionated cell envelope membranes in which the chromophore is photostable not only in the presence of NaCl but also in the Na2SO4 solution used for reference. Careful examination of the flash-induced changes at selected wavelengths allowed separating the spectral changes into components and assigning them to the individual photocycles. According to the results, a substantial revision of the photocycle model for H. salinarium halorhodopsin, and its dependence on chloride, is required. The cycle of the all-trans chloride-binding form is described by the scheme, HR-hv-->K<==>L1<==>L2<==>N-->HR, where HR, K, L, and N designate halorhodopsin and its photointermediates. Unlike the earlier models, this is very similar to the photoreaction of bacteriorhodopsin when deprotonation of the Schiff base is prevented (e.g., at low pH or in the D85N mutant). Also unlike in the earlier models, no step in this photocycle was noticeably affected when the chloride concentration was varied between 20 mM and 2 M in an attempt to identify a chloride-binding reaction.

Steric constraints in the retinal binding pocket of sensory rhodopsin I

Steric constraints in the retinal binding pocket of sensory rhodopsin I (SR-I) are analyzed by studying effects of sample temperature and retinal analogs. The flash-induced yield of the earliest detected intermediate S610, which corresponds to the K intermediate in the bacteriorhodopsin (BR) photocycle, decreases below 220 K and reaches zero at 100 K, while K formation is independent of temperature. The reduced S610 formation at low temperatures indicates a more restricted retinal binding pocket in SR-I during primary photochemical events. Introduction of bulky substituents on the retinal polyene chain in four retinal analogs greatly retards or blocks the final step of chromophore binding to the apoprotein of SR-I. Except for the 14-methyl substitution, these modifications exhibit little or no effect on chromophore binding to BR apoprotein. These results corroborate that the retinal polyene chain binding domain in SR-I is more sterically constrained than that of the retinal pocket in BR. Deletion of the beta-ionone ring renders the analog SR-I pigments nonfunctional, as does deletion of the 13-methyl group, but the corresponding BR analogs are both photochemically and physiologically active. In contrast to the corresponding BR analog, photolysis of the analog SR-I reconstituted with 13-desmethylretinal does not produce an S610-like intermediate at room temperature. The above results and the previous findings that protein constraints inhibit the accommodation of a stable 13-cis-retinal configuration in SR-I suggest a model in which the 13-methyl group functions as a fulcrum to permit movement of one or both ends of retinal to overcome an energy barrier against isomerization.

The low-temperature heat capacity of solid proteins

Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low-frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T less than 30 K. The experimental b's of proteins are 1.6-1.8, and the theoretical, 1.1-1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100-200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.