Bacteriorhodopsin: a biological material for information processing

Characterization of Langmuir-Blodgett films of rhodopsin: thermal stability studies

Two-dimensional close packing of purified bovine rhodopsin, made by the Langmuir-Blodgett technique, was characterized by small angle x-ray scattering and nanogravimetric measurements. The area occupied by a molecule of rhodopsin in the film was approximately 1100 Angstrum2 and the periodicity of the layers resulted in 59 Angstrum. The circular dichroism measurements showed that bleached rhodopsin in Langmuir-Blodgett film had high thermal stability, in fact, reaching a temperature of 150 degrees C without a loss of the secondary structure. Moreover, when the film was made up in the dark, rhodopsin maintained its stability up to at least 200 degrees C and its characteristic absorbance peak at 500 nm up to about 90 degrees C.

The cycle of photochromic reactions of a bacteriorhodopsin analog with 4-keto-retinal

Photochemical reactions in a bacteriorhodopsin analog with 4-keto-retinal (4-keto-BR) were studied by using low-temperature and pulsed laser absorption spectroscopy. A photocycle of the photochemical reactions of 4-keto-BR is proposed, which, unlike the photocycle of native BR, includes several spectrally and kinetically distinguishable M-type and O-type intermediates.

Holographic properties of Triton X-100-treated bacteriorhodopsin embedded in gelatin films

Bacteriorhodopsin (b) thin films have been fabricated with varying amounts of the detergent Triton X-100 to measure the effect of this additive on the holographic performance of these thin films. Holographic spectroscopy is used to measure the effect of these detergents on the overall diffraction efficiency as well as on the phase and amplitude components of the overall signal. The diffracted rise and decay kinetics of these materials will also be presented as a function of varying detergent concentration. This research also studied the effect of this additive on the absorptive properties of bR-based thin films. Comparisons of the two complimentary sets of data are drawn.

4-Keto-bacteriorhodopsin films as a promising photochromic and electrochromic biological material

Photochromic and electrochromic spectral properties of 4-keto-bacteriorhodopsin (4-keto-BR) embedded in a polymer matrix were studied. The light-induced spectral changes were found to be similar to those for 4-keto-BR in suspension, but the duration of the photocycle is substantially longer (up to ten of h). Application of a constant electric field induces a bathochromic shift of the main absorption band, the amplitude of the field-induced spectral changes, showing a quadratic dependence on the field strength. Polymer films containing bacteriorhodopsin analogs show promise as new spectrally-selective photochromic and electrochromic materials.

Motion-sensitive position sensor using bacteriorhodopsin

A concept of motion-sensitive position sensing that uses a film of bacteriorhodopsin (bR) treated with a high-pH buffer is proposed. The polarity of photo-emf, which depends on the excited intermediates of the bR molecule, can be used to determine movement direction. The M intermediate state with a long lifetime can be used to record the initial position. The bR-based position sensor can sense two positions of a moving object at two different times.

Time-resolved detection of structural changes during the photocycle of spin-labeled bacteriorhodopsin

Bacteriorhodopsin was selectively spin labeled at residues 72, 101, or 105 after replacement of the native amino acids by cysteine. Only the electron paramagnetic resonance spectrum of the label at 101 was time-dependent during the photocycle. The spectral change rose with the decay of the M intermediate and fell with recovery of the ground state. The transient signal is interpreted as the result of movement in the C-D or E-F interhelical loop, or in both, coincident with protonation changes at the key aspartate 96 residue. These results link the optically characterized intermediates with localized conformational changes in bacteriorhodopsin during the photocycle.

Dynamic self-pumped phase-conjugating mirror based on the bacteriorhodopsin variant D96N

A self-pumped, phase-conjugating mirror (diameter 17 mm) is described that contains the bacteriorhodopsin variant D96N as the photoactive material. Resonant reflectivities up to 30% were obtained with an intensity of 25 mW/cm(2) at 647 nm. Rise times of less than 1 ms were observed with an intensity of 500 mW/cm(2) at 532 nm. Wave-front restoration with spatial light modulators as the dynamic input device was demonstrated, and the dependence of the reflectivity on the intensity and polarization was analyzed. The reflectivity shows no significant decrease with increasing angle between the pump and signal beams as a result of the high resolution of the bacteriorhodopsin films.

Determination of the refractive index of a bacteriorhodopsin film

The wavelength-dependent refractive index of a bacteriorhodopsin thin film is measured by the use of a modified critical-angle technique. The effect of the host bovine skin gelatin on the refractive index is analyzed. The measured data on the thin film can be useful for system applications. The methods and procedures are generally applicable to any optically absorbing thin films.

Adaptive bacteriorhodopsin-based holographic correlator for speed measurement of randomly moving three-dimensional objects

An adaptive correlator system is presented that uses a bacteriorhodopsin film as the active holographic material. Because M-type holography with bacteriorhodopsin films is used, the TV frame rate is met at fairly low intensities. No limitations arising from the heterodyne operation of the dual-axis joint-Fourier-transform correlator were observed. The system's capability to monitor autonomously the speed of an object moving randomly in the whole viewing field of a video camera is demonstrated.

Hyper-Rayleigh light scattering from an aqueous suspension of purple membrane

Here we report the first observation of hyper-Rayleigh light scattering from bacteriorhodopsin in the form of an aqueous suspension of unoriented purple membranes. A typical purple membrane suspension used in our experiments contains approximately 10(8) randomly oriented purple membranes. Each purple membrane contains approximately 10(5) bacteriorhodopsin molecules in a two-dimensional crystallinearray. Hyper-Rayleigh light scattering is observed when the purple membrane suspension is illuminated with light that has a wavelength of 1064 nm. We propose that the 532-nm scattered light from each of the bacteriorhodopsin molecules in a single purple membrane is coherent, and that the scattered light from different purple membranes is incoherent. This proposal is supported by the following experimental observations: (a) the 532-nm light intensity is proportional to the square of the incident power, (b) the intensity of the 532-nm signal is linearly proportional to the concentration of purple membrane in solution, (c) the scattered 532-nm light is incoherent, (d) the scattered 532-nm light intensity decreases if the size of the purple membranes is reduced while the bacteriorhodopsin concentration is kept constant, and (e) the 532-nm light is due to the retinal chromophore of the bacteriorhodopsin molecule. The ratio of horizontal polarized hyper-Rayleigh scattered light to vertically polarized hyper-Rayleigh scattered light gives the angle (23 ± 4°) of the retinal axis with respect to the plane of the purple membrane. The hyperpolarizability of the bacteriorhodopsin molecule is found to be 5 ± 0.4 × 10(-27) esu.

Phylogenetic relationships among bacteriorhodopsins

Retinal-containing proteins of archaea comprise a single family of homologous proteins that fall into three clusters correlating with function: the proton-transporting bacteriorhodopsins, the chloride-transporting halorhodopsins and the colour-discriminating sensory rhodopsins. Statistical and phylogenetic analyses, a multiple alignment and average hydropathy and similarity plots of these protein sequences are presented. Available evidence suggests that sequence conservation generally correlates with functional significance. Little or no evidence substantiates the proposal that these proteins arose by a tandem intragenic duplication event. The bacterial rhodopsin family appears to have evolved from a common ancestor without recognizable intragenic rearrangements.

Rotational orientation of transmembrane alpha-helices in bacteriorhodopsin. A neutron diffraction study

The rotational orientation of the seven transmembrane alpha-helices (A-G) in bacteriorhodopsin has been investigated by neutron diffraction. The current model of bacteriorhodopsin is based on an electron density map obtained by high-resolution electron microscopy (EM). Assigning helix rotational positions in the EM model depended on fitting large side-chains, mainly aromatic residues, into bulges in the electron density map. For helix D, which contains no aromatic residues, the EM map is more difficult to interpret. For helices A and B, whose position and orientation had been determined previously by neutron diffraction, the positions defined by EM agree within experimental error with these earlier conclusions. The orientation of all seven helices has been examined by using neutron diffraction on bacteriorhodopsin samples with specifically deuterated valine, leucine and tryptophan residues. Experimental peak intensities were compared to those predicted for an extensive set of structural models. The models were generated by (1) rotating all helices around their axis; (2) moving deuterated residues in the extramembrane loops about their probable positions and changing the weight of their contribution to the neutron diffraction pattern; (3) allowing deuterated side-chains to change their conformation. The analysis confirmed exactly the positions previously determined for helices A and B. For an optimal fit to the data to be obtained, the other five helices, including helix D, must lie either at or within 20 degrees of their position in the current EM model. The complementarity of medium-resolution EM, neutron diffraction and model building for the structural study of integral membrane proteins is discussed.

Retinal-protein complexes as optoelectronic components

Naturally occurring retinal-protein complexes (RPCs) have recently received much attention with regard to their potential use as light-sensitive elements for optical recording. The best-known RPC is bacteriorhodopsin (BR), a photosensitive protein from the membrane of extreme halophilic bacteria, which has been studied in great detail. The remarkably robust nature of BR, coupled with its ability to reversibly change color upon illumination and its high cyclicity of ground-to-photoinduced state transitions, makes BR a promising material for optical information processing.

Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution

Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed.

Nonlinear optical properties of a bacteriorhodopsin film in a Fabry-Perot cavity

Bacteriorhodopsin is a photosensitive molecule found in the purple membrane of Halobacterium halobium. To investigate the possibility of using photoinduced changes in its refractive index in the 650-800-nm region for photonic switching, we prepared solid dry bacteriorhodopsin films with low scattering and examined their optical properties in a Fabry-Perot cavity. Interference fringes, generated on irradiation of the cavity with a near-IR laser beam at 792 nm, were shifted by simultaneous exposure to a 5-mW/mm(2) beam at 543.5 nm. This result indicates that such a Fabry-Perot cavity may be used as a photonically controlled spatial light modulator.

Photochemical conversion of the O-intermediate to 9-cis-retinal-containing products in bacteriorhodopsin films

The photochemical activity of the O-state was investigated in bacteriorhodopsin (BR) films containing wildtype BR at pH 6.5 in the presence of glycerol. The formation of a photoproduct of O with an absorption maximum at 490 nm and 9-cis-retinal configuration was found. This 490-nm product was named P and shows a slow thermal reaction into a compound with a maximal absorption at 380 nm which was named Q and contains free 9-cis-retinal in the proteins binding site. The photoproducts of O, i.e., P and Q, are very similar, or even identical, to those previously observed in blue membranes. Common to the O-state and blue membrane forms of bacteriorhodopsin is a protonated aspartic acid 85, and we suggest that it is the reduced negative charge around the Schiff base which is responsible for the 9-cis photoisomerization. The release of a proton from aspartic acid 85 is linked to the conversion of the O-state back to the initial state of BR. Therefore the conditions of low proton mobility in BR films containing glycerol favor the accumulation of the O-state. For optical and holographic applications such BR films are very attractive. It is possible to create photoproducts with red light which are thermally stable at room temperature and that can be photochemically erased. Dependent on the light composition both properties can be realized in the same sample material. This feature may bridge the gap between information processing and short-term and long-term storage of information with BR.

Picosecond time-resolved absorption and fluorescence dynamics in the artificial bacteriorhodopsin pigment BR6.11

The picosecond molecular dynamics in an artificial bacteriorhodopsin (BR) pigment containing a structurally modified all-trans retinal chromphore with a six-membered ring bridging the C11=C12-C13 positions (BR6.11) are measured by picosecond transient absorption and picosecond time-resolved fluorescence spectroscopy. Time-dependent intensity and spectral changes in absorption in the 570-650-nm region are monitored for delays as long as 5 ns after the 7-ps, 573-nm excitation of BR6.11. Two intermediates, J6.11 and K6.11/1, both with enhanced absorption to the red (> 600 nm) of the BR6.11 spectrum are observed within approximately 50 ps. The J6.11 intermediate decays with a time constant of 12 +/- 3 ps to form K6.11/1. The K6.11/1 intermediate decays with an approximately 100-ps time constant to form a third intermediate, K6.11/2, which is observed through diminished 650-nm absorption (relative to that of K6.11/1). No other transient absorption changes are found during the remainder of the initial 5-ns period of the BR6.11 photoreaction. Fluorescence in the 650-900-nm region is observed from BR6.11, K6.11/1, and K6.11/2, but no emission assignable to J6.11 is found. The BR6.11 fluroescence spectrum has a approximately 725-nm maximum which is blue-shifted by approximately 15 nm relative to that of native BR-570 and is 4.2 +/- 1.5 times larger in intensity (same sample optical density). No differences in the profile of the fluorescence spectra of BR6.11 and the intermediates K6.11/1 and K6.11/2 are observed. Following ground-state depletion of the BR6.11 population, the time-resolved fluroescence intensity monitored at 725 nm increases with two time constants, 12 +/- 3 and approximately 100 ps, both of which correlate well with changes in the picosecond transient absorption data. The resonance Raman spectrum of ground-state BR6.11, measured with low-energy, 560-nm excitation, is significantly different from the spectrum of native BR-570, thus confirming that the picosecond transient absorption and picosecond time resolved fluorescence data are assignable to BR6.11 and its photoreaction alone and not to BR-570 reformed during there constitution process (<5% of the BR6.11 sample could be attributed to native BR-570).The J6.11 and K6.11 absorption and fluorescence data presented here are generally analogous to those measured for native J-625 and K-590, respectively, and therefore, the primary events in the BR6.11 photoreaction can be correlated with those in the native BR photocycle. The BR6.11 photoreaction, however, exhibits important differences including slower formation rates for J and K intermediates as well as the presence of a second K intermediate. These results demonstrate that the restricted motion in the C11=C12-C13 region of retinal found in BR6.11 does not greatly change the overall photoreaction mechanism,but does alter the rates at which processes occur.

Protein-based artificial retinas

Artificial retinas based on the light transducing photoelectric protein bacteriorhodopsin exhibit differential responsivity, edge enhancement and motion detection. Under appropriate conditions, these artificial receptors mimic the differential responsivity characteristic of mammalian photoreceptor cells. The use of orientated bacteriorhodopsin to generate the photoelectrical signal provides rapid responsivity, high quantum efficiency and offers the potential of directly coupling the protein response to charge-sensitive semiconductor arrays. The ability to manipulate the properties of the protein via chemical and genetic methods enhances design flexibility.

Optical limiting by chemically enhanced bacteriorhodopsin films

The optical limiting properties of a thin film (~150 microm) of chemically enhanced bacteriorhodopsin under cw laser illumination is investigated. The effective nonlinearity n(2) of the film is measured with the z-scan method. Anomalous absorption at different wavelengths as a function of illumination intensity is observed.

Homologous bacterio-opsin-encoding gene expression via site-specific vector integration

Homologous recombination in the archaebacterium Halobacterium halobium has been investigated and exploited for the wild-type (wt) level of expression of the bacterio-opsin-encoding gene (bop). The Haloferax volcanii-Escherichia coli shuttle vector, pWL102, was used to construct a shuttle-mutagenesis vector, pEF191, bearing bop and short flanking sequences. Transformation of a bacteriorhodopsin (BR)-negative H. halobium strain with pEF191 resulted in plasmid integration at the homologous bop locus. A model for this site-specific vector integration is presented which has been confirmed by determining the arrangement of the repeated homologous sequences on the chromosome. Two different configurations are obtained after integrative transformation due to the presence of an insertion element in the genomic copy of bop. In one configuration, the functional bop cluster containing the regulatory bat and brp genes was in wt arrangement. In the second configuration, the bop cluster is interrupted by 10 kb of plasmid vector sequences, and the upstream region required for bop expression was limited to 400 bp. The BR production for both configurations was determined and found to be at wt level. These results suggest that the function of the putative bop promoter does not depend on the defined upstream positions of bat and brp. The system presented here can be easily exploited for structure-function studies on BR and introduces homologous gene targeting as a powerful tool in the study of halobacterial genetics.

Real-time holographic correlation of two video signals by using bacteriorhodopsin films

A dual-axis joint-Fourier-transform correlator is described with two liquid-crystal television screens as input devices and a bacteriorhodopsin film as the active holographic material in the Fourier plane. The experimental data presented demonstrate that this system is capable of processing two independent video signals in real time with a signal-to-noise ratio of 45 dB.

Protein engineering for molecular electronics

Recombinant DNA technology allows the manipulation of the physical properties of proteins that perform electron transport and photochemical processes. Recent work is reviewed that has a potential impact on the development of molecular electronic devices, within a general framework outlining strategies for device fabrication. This review is also published in Current Opinion in Structural Biology 1992, 2:587-592.

A unifying concept for ion translocation by retinal proteins

First, halorhodopsin is capable of pumping protons after illumination with green and blue light in the same direction as chloride. Second, mutated bacteriorhodopsin where the proton acceptor Asp85 and the proton donor Asp96 are replaced by Asn showed proton pump activity after illumination with blue light in the same direction as wildtype after green light illumination. These results can be explained by and are discussed in light of our new hypothesis: structural changes in either molecule lead to a change in ion affinity and accessibility for determining the vectoriality of the transport through the two proteins.

Biotechnology of the Archaea

The Archaea, designated since 1979 as a separate Super-Kingdom (the highest taxonomic order), are a highly novel group of microorganisms which look much like bacteria but have many molecular and genetic characteristics that are more typical of eukaryotes. These unusual organisms can be conveniently divided according to their 'extreme' environmental niche, into three broad phenotypes: the thermophiles, methanogens and extreme halophiles. Each group has unique biochemical features which can be exploited for use in the biotechnological industries. The extreme molecular stability of thermophile enzymes, the novel C1 pathways of the methanogens and the synthesis of organic polymers by some halophiles are all currently or potentially valuable examples of the biotechnology of the Archaea.