Characterization of the azide-dependent bacteriorhodopsin-like photocycle of salinarum halorhodopsin

A Unique Light-Driven Proton Transportation Signal in Halorhodopsin from Natronomonas pharaonis

Halorhodopsin (HR) is a seven-transmembrane retinylidene protein from haloarchaea that is commonly known to function as a light-driven inward chloride pump. However, previous studies have indicated that despite the general characteristics that most HRs share, HRs from distinct species differ in many aspects. We present indium-tin-oxide-based photocurrent measurements that reveal a light-induced signal generated by proton release that is observed solely in NpHR via purified protein-based assays, demonstrating that indeed HRs are not all identical. We conducted mutagenesis studies on several conserved residues that are considered critical for chloride stability among HRs. Intriguingly, the photocurrent signals were eliminated after specific point mutations. We propose an NpHR light-driven, cytoplasmic-side proton circulation model to explain the unique light-induced photocurrent recorded in NpHR. Notably, the photocurrent and various photocycle intermediates were recorded simultaneously. This approach provides a high-resolution method for further investigations of the proton-assisted chloride translocation mechanism.

Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide

Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.

Photosynthetic reaction centers/ITO hybrid nanostructure

Photosynthetic reaction center proteins purified from Rhodobacter sphaeroides purple bacterium were deposited on the surface of indium tin oxide (ITO), a transparent conductive oxide, and the photochemical/-physical properties of the composite were investigated. The kinetics of the light induced absorption change indicated that the RC was active in the composite and there was an interaction between the protein cofactors and the ITO. The electrochromic response of the bacteriopheophytine absorption at 771 nm showed an increased electric field perturbation around this chromophore on the surface of ITO compared to the one measured in solution. This absorption change is associated with the charge-compensating relaxation events inside the protein. Similar life time, but smaller magnitude of this absorption change was measured on the surface of borosilicate glass. The light induced change in the conductivity of the composite as a function of the concentration showed the typical sigmoid saturation characteristics unlike if the photochemically inactive chlorophyll was layered on the ITO. In this later case the light induced change in the conductivity was oppositely proportional to the chlorophyll concentration due to the thermal dissipation of the excitation energy. The sensitivity of the measurement is very high; few picomole RC can change the light induced resistance of the composite.

Tuning the primary reaction of channelrhodopsin-2 by imidazole, pH, and site-specific mutations

Femtosecond time-resolved absorption measurements were performed to investigate the influence of the pH, imidazole concentration, and point mutations on the isomerization process of Channelrhodopsin-2. Apart from the typical spectral characteristics of retinal isomerization, an additional absorption feature rises for the wild-type (wt) on a timescale from tens of ps to 1 ns within the spectral range of the photoproduct and is attributed to an equilibration between different K-intermediates. Remarkably, this absorption feature vanishes upon addition of imidazole or lowering the pH. In the latter case, the isomerization is dramatically slowed down, due to protonation of negatively charged amino acids within the retinal binding pocket, e.g., E123 and D253. Moreover, we investigated the influence of several point mutations within the retinal binding pocket E123T, E123D, C128T, and D156C. For E123T, the isomerization is retarded compared to wt and E123D, indicating that a negatively charged residue at this position functions as an effective catalyst in the isomerization process. In the case of the C128T mutant, all primary processes are slightly accelerated compared to the wt, whereas the isomerization dynamics for the D156C mutant is similar to wt after addition of imidazole.

Stabilization effect of single-walled carbon nanotubes on the functioning of photosynthetic reaction centers

The interaction between single-walled carbon nanotubes and photosynthetic reaction centers purified from purple bacterium Rhodobacter sphaeroides R-26 has been investigated. Atomic force microscopy studies provide evidence that reaction center protein can be attached effectively to the nanotubes. The typical diameter of the nanotube is 1-4 nm and 15 +/- 2 nm without and with the reaction centers, respectively. Light-induced absorption change measurements indicate the stabilization of the P+(Q(A)Q(B))- charge pair, which is formed after single saturating light excitation after the attachment to nanotubes. The separation of light-induced charges is followed by slow reorganization of the protein structure. The stabilization effect of light-initiated charges by the carbon nanotubes opens a possible direction of several applications, the most promising being in energy conversion and storage devices.

Selectivity of Retinal Photoisomerization in Proteorhodopsin Is Controlled by Aspartic Acid 227

Similarly to bacteriorhodopsin, proteorhodopsin that normally contains all-trans and 13-cis retinal is transformed at low pH to a species containing 9-cis retinal under continuous illumination at lambda > 530 nm. This species, absorbing around 430 nm, returns thermally in tens of minutes to initial pigment and can be reconverted also with blue-light illumination. The yield of the 9-cis species is negligibly small at neutral pH but increases manyfold (>100) at acid pH with a pK(a) of 2.6. This indicates that protonation of acidic group(s) alters the photoreaction pathway that leads normally to all-trans --> 13-cis isomerization. In the D97N mutant, in which one of the two acidic groups in the vicinity of the retinal Schiff base is not ionizable, the yield of 9-cis species at low pH shows a pH dependence similar to that in the wild-type but with a somewhat increased pK(a) of 3.3. In contrast to this relatively minor effect, replacement of the other acidic group, Asp227, with Asn results in a remarkable, more than 50-fold, increase in the yield of the light-induced formation of 9-cis species in the pH range 4-6. It appears that protonation of Asp227 at low pH is what causes the dramatic increase in the yield of the 9-cis species in wild-type proteorhodopsin. We conclude that the photoisomerization pathways in proteorhodopsin to 13-cis or 9-cis photoproducts are controlled by the charge state of Asp227.

Modeling of ionic relaxation around a biomembrane disk

A simplified Brownian dynamics model and the corresponding software implementation have been developed for the simulation of electrolyte dynamics on the mesoscopic scale. In addition to direct control simulations, the model system has been verified by a quantitative comparison with the Debye-Hückel theory. As a first application, the model was used to simulate ionic relaxation processes following abrupt intramembrane charge rearrangements in the case of a disk shaped membrane. In addition to its general implications, the obtained properties of the relaxation kinetics confirm the assumptions of the theory of the so-called suspension method, a technique capable of tracing molecular charge motions of membrane proteins in three dimensions.

Halorhodopsin: light-driven ion pumping made simple?

Halorhodopsin, a light-driven halide pump, is the second archaeal rhodopsin involved in ion pumping to be studied at high resolution by X-ray crystallography. Like its cousin bacteriorhodopsin, halorhodopsin couples vectorial ion transport to the isomerisation state of a covalently linked retinal. Given the similarity and interconvertability of these two ion pumps, a unified mechanism for ion translocation by archaeal rhodopsins is now emerging.