Optical and electrical characterization of bacteriorhodopsin films

Hydrogen-bonding changes of internal water molecules upon the actions of microbial rhodopsins studied by FTIR spectroscopy

Microbial rhodopsins are classified into type-I rhodopsins, which utilize light energy to perform wide varieties of function, such as proton pumping, ion pumping, light sensing, cation channels, and so on. The crystal structures of several type-I rhodopsins were solved and the molecular mechanisms have been investigated based on the atomic structures. However, the crystal structures of proteins of interest are not always available and the basic architectures are sometimes quite similar, which obscures how the proteins achieve different functions. Stimulus-induced difference FTIR spectroscopy is a powerful tool to detect minute structural changes providing a clue for elucidating the molecular mechanisms. In this review, the studies on type-I rhodopsins from fungi and marine bacteria, whose crystal structures have not been solved yet, were summarized. Neurospora rhodopsin and Leptosphaeria rhodopsin found from Fungi have sequence similarity. The former has no proton pumping function, while the latter has. Proteorhodopsin is another example, whose proton pumping machinery is altered at alkaline and acidic conditions. We described how the structural changes of protein were different and how water molecules were involved in them. We reviewed the results on dynamics of the internal water molecules in pharaonis halorhodopsin as well. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

Mechanism of nonlinear photoinduced anisotropy in bacteriorhodopsin and its derivatives

Polymer films made with photosensitive chromophore protein bacteriorhodopsin (BR) from the extreme halophile Halobacterium salinarium as well as films made with BR derivatives exhibit a nonlinear photoinduced anisotropy. Two different methods can be used to induce anisotropy in polymer BR films. The first method is based on the anisotropic properties of the initial form of the photocycle, BR570 (B-type anisotropy). Another method is based on the anisotropic properties of the longest-lived photocycle intermediate M412 (M-type anisotropy). CW gas lasers were employed to induce a reversible anisotropy in polymer BR films. Nonlinear photoinduced anisotropy is discussed in the context of a model for the anisotropic photoselection of BR molecules under linearly polarized light. A comparison of the experimental dependencies of nonlinear photoinduced anisotropy on laser intensity with similar calculated dependencies enables one to determine the molecular dichroism of BR and its derivatives not only for the initial form of the photocycle, B but also for the longest-lived intermediate M. Here we present the data showing the correlation between the laser induced nonlinear anisotropic properties and chromophore/protein interactions in BR. The effect of polymer binder on the nonlinear photoanisotropic properties of polymer BR films is also described.

Monitoring intermediate states of bacteriorhodopsin monolayers using near-field optical microscopy

We demonstrate single-molecule-level features using near-field optical microscopy on bacteriorhodopsin (bR), a membrane protein that functions as a light-driven proton pump. The photophysical properties of bR are utilized in this imaging technique, using a combination of photoexcitation sources, to accurately identify the active regions and quantify the optical parameters. The studies of bR monolayers are carried out on inert quartz substrates as well as active conducting polymer (polyaniline) substrates. The substrate also plays an important role in the photocycle quantum efficiencies. We speculate on mechanisms governing the higher near-field absorption strength of bR molecules.

Conformational coupling between the cytoplasmic carboxylic acid and the retinal in a fungal light-driven proton pump

Many fungal rhodopsins, eukaryotic structural homologues of the archaeal light-driven proton pump bacteriorhodopsin, have been discovered in the course of genome sequencing projects. Recently, two fungal rhodopsins were characterized in vitro and exhibited very different photochemical behavior. Neurospora rhodopsin possesses a slow photocycle and shows no ion transport, reminiscent of sensory rhodopsins, while Leptosphaeria rhodopsin has a fast bacteriorhodopsin-like photocycle and pumps protons light-dependently. Such a dramatic difference is surprising considering the very high degree of sequence homology of the two proteins. In this paper, we investigate whether the chemical structure of a cytoplasmic carboxylic acid, the homologue of Asp-96 of bacteriorhodopsin serving as a proton donor for the retinal Schiff base, can define the photochemical properties of fungal rhodopsins. We studied mutants of Leptosphaeria rhodopsin in which this aspartic acid was replaced with Glu or Asn using spectroscopy in the infrared and visible ranges. We show that Glu at this position is inefficient as a proton donor similar to a nonprotonatable Asn. Moreover, this replacement induces long-range structural perturbations of the retinal environment, as evidenced by changes in the vibrational bands of retinal (especially, hydrogen-out-of-plane modes) and neighboring aspartic acids and water molecules. The conformational coupling of the mutation site to the retinal may be mediated by helical rearrangements as suggested by the changes in amide and proline vibrational bands. We conclude that the difference in the photochemical behavior of fungal rhodopsins from Leptosphaeria and Neurospora may be ascribed, to some extent, to the replacement of the cytoplasmic proton donor Asp with Glu.

Bacteriorhodopsin—Novel biomolecule for nano devices

The aim of this article is to provide insight on the use of a biological molecule--bacteriorhodopsin (bR) having all the basic properties necessary for the assembly of nanoscale electronic devices. Recent developments made during last decade supported by key references are reviewed in this contribution. Major emphasis on bR-based observations conducted in our laboratory has been elaborated. Important issues concerning structure, widely accepted photocycle of bR has been summarized. The possibility of nano-devices emanating from this biomolecule is briefly presented.

Bacteriorhodopsin-like proteins of eubacteria and fungi: the extent of conservation of the haloarchaeal proton-pumping mechanism

A stereotypical image of a retinal-binding proton pump derived from extensive studies of halobacterial ion-transporting and sensory rhodopsins is a fast-cycling protein which possesses two strategically placed carboxylic acids serving as proton donor and acceptor for the retinal Schiff base. We review recent biophysical and bioinformatic data on the novel eubacterial and eucaryotic rhodopsins to analyze the extent of conservation of the haloarchaeal mechanism of transmembrane proton transport. We show that only the most essential elements of the haloarchaeal proton-pumping machinery are conserved universally, and that a mere presence of these elements in primary structures does not guarantee the proton-pumping ability.

Opto-electrical processes in a conducting polymer–bacteriorhodopsin system

In this report, we highlight the opto-electrical processes at a conducting polymer-bacteriorhodopsin (bR) interface in presence of a voltage bias. Oriented bR on a conducting polymer substrate forms a unique hybrid system where the oxidation state of the polymer controls the optically activated proton gradient in the bR side. The internal conversion of the intermediate deprotonated M-state and the proton transfer/transport of bR at the interface can be controlled by the electrostatic environment and leads to interesting device features in this process.

Phototransformation and proton pumping activity of the 14-fluoro bacteriorhodopsin derivatives

The photoinduced behavior and proton pumping characteristics of some bacteriorhodopsin (BR) analogs with fluorinated chromophores (all-trans 14-fluorinated [14-F] retinal and 13-cis 14-F retinal) derived from wild type (WT) and D96N mutant BR were investigated. These analogs were characterized using spectrophotometry and a highly sensitive electrochemical technique. Similar to the white membrane JW2N, the apomembranes WT ET 1000 and D96N form photoactive pigments with the 14-F chromophores. The resulting analogs have a major absorption band at 588 nm. Red-shifted pigment (lambdamax</=680 nm) has been previously observed as a minor component of the major 587-nm pigment in 14-F BR made with white membrane JW2N. A similar red-shifted pigment is formed under yellow light (lambda>500 nm) only in the 14-F analogs derived from WT ET 1000. The measurements of the photoinduced transformation in 14-F WT analogs show that the photocycle of the major pigment occurs simultaneously with the process in the red region and is partially masked by the formation of the red-shifted species. The 14-F D96N samples have a significantly slower and more complicated photoinduced behavior. Electrochemical measurements show that the photoinduced transformation of the red species is not accompanied by proton transport.