The role of water in the extracellular half channel of bacteriorhodopsin

Protonation of Asp116 and distortion of the all-trans retinal chromophore in Krokinobacter eikastus rhodopsin 2 causes a redshift in absorption maximum upon dehydration

Water is usually indispensable for protein function. For ion-pumping rhodopsins, water molecules inside the proteins play an important role in ion transportation. In addition to amino acid residues, water molecules regulate the colors of retinal proteins. It was reported that a sodium-pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2), showed a color change from red to purple upon dehydration under crystalline conditions. Here, we applied comprehensive visible and IR absorption spectroscopy and resonance Raman spectroscopy to KR2 in liposomes under hydration-controlled conditions. A large increase in the hydrogen-out-of-plane (HOOP) vibration at 947 (H-C11=C12-H Au mode) and moderate increases at 893 (C7-H and C10-H) and 808 (C14-H) cm-1 were observed under dehydrated conditions, which were assigned by using systematically deuterated retinal. Moreover, the Asn variant at Asp116, which functions as a counter ion for the protonated retinal Schiff base (PRSB), caused a large redshift in the absorption maximum and constitutive increase in the HOOP modes under hydrated and dehydrated conditions. The protonation of a counter ion at Asp116 clearly causes a redshift in the absorption maximum as the all-trans retinal chromophore twists upon dehydration. Namely, the results strongly suggested that water molecules are important for maintaining the hydrogen-bonding network at the PRSB and deprotonation state of Asp116 in KR2.

Photoisomerization of azobenzene units drives the photochemical reaction cycles of proteorhodopsin and bacteriorhodopsin analogues

In this study we substituted the retinal units in proteorhodopsin (PR) and bacteriorhodopsin (BR) with azo chromophores to investigate the mechanism of photoinduced proton pumping in rhodopsins and potentially develop new artificial molecular pumps. We used an indium tin oxide electrode to investigate the photoinduced proton transfer of the azo analogues of PR and BR. We also employed flash photolysis to determine the characteristic photocycles, comprising multiple transient intermediates, of the azo chromophore-bound PR and BR. Moreover, our studies of the photoinduced proton pumping functions of azo-proteoopsin and azo-bacterioopsin complexes revealed that they did not pump protons upon illumination, even though they underwent photoinduced proton transfer and the characteristic photocycle. Mutational analysis suggested that the proton pumping malfunction of the azo analogues of PR and BR resulted from the absence of proton transfer reactions through cytoplasmic channels, even though these reactions were evoked in extracellular channels. Based on our experimental findings, we propose herein a putative model of the proton transfer reaction mechanism for the azo analogues of PR and BR.

Investigation of spectral and kinetic properties of polymer films based on some analogs of bacteriorhodopsin

We investigated the characteristics of modified forms of bacteriorhodopsin in which the native retinal chromophore is replaced by a chemical analog ("bacteriorhodopsin analogs"), embedded in a polymer film. We found they displayed differential absorption spectra and kinetic curves for the most long-lived intermediates of the BR photocycle. We also studied the influence of chemical reagents on the functioning of bacteriorhodopsin analogs in polymeric films. We found that the immobilization of BR analogs in polymer leads, as in the case of native BR, to a slowing down of their photocycles. Kinetic analysis showed that M-like state intermediates of all the BR analogs have a longer dark relaxation time than native BR. The retention and retardation of the photocycle in these films suggest that films based on BR analogs can be used as photochromic materials. Moreover, 4-keto BR seems to be more promising for this application as compared not only with native BR, but also with other analogs of BR studied in this work.

Some factors affecting the process of photoinduced hydroxylaminolysis in different bacteriorhodopsin-based media

This review presents the results of studies concerning some factors that affect the process of photoinduced hydroxylaminolysis (PHA) in bacteriorhodopsin (BR) and different BR-based media. We consider the peculiar properties of the PHA reaction in water suspensions of BR and BR-based media depending on variation in PHA ingredients, and in particular the use of O-substituted hydroxylamines instead of hydroxylamine hydrochloride. In addition, we discuss how such factors as preliminary ultra-sonication affect the reaction of PHA in the course of BR bleaching and following the reconstitution of bacterioopsin. All the results are considered from the viewpoint of improving the performance of BR-based media as photosensitive materials for the processing and storage of optical information.

A role for internal water molecules in proton affinity changes in the Schiff base and Asp85 for one-way proton transfer in bacteriorhodopsin

Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M.

Direct observation of protein motion during the photochemical reaction cycle of bacteriorhodopsin

Platinum-coated, conductive atomic force microscope cantilevers were used to deposit electrophoretically purple membranes from Halobacterium salinarum on the bottom part of the cantilevers. By illuminating the bacteriorhodopsin-containing purple membranes, the protein goes through its photochemical reaction cycle, during which a conformational change happens in the protein, changing its shape and size. The size change of the protein acts upon the cantilever by causing its deflection, which can be monitored by the detection system of the atomic force microscope. The shape of the signal, the action spectrum of the deflection amplitude, and the blue light inhibition of the deflection all prove that the origin of the signal is the conformational change arising in the bacteriorhodopsin during the photocycle. From the size of the signal, the magnitude of the protein motion could be estimated. Using polarized light, the orientation of the motion was determined, relative to the transition moment of the retinal.

Photoelectric properties of a detector based on dried bacteriorhodopsin film

The photoelectric response of a detector using dried bacteriorhodopsin (bR) film as the light sensing material is mathematically modeled and experimentally verified in this paper. The photocycle and proton transfer kinetics of dried bR film differ dramatically from the more commonly studied aqueous bR material because of the dehydration process. The photoelectric response of the dried film is generated by charge displacement and recombination instead of transferring a proton from the cytoplasmic side to the extracellular side of the cell membrane. In this work, the wild-type bR samples are electrophoretically deposited onto an indium tin oxide (ITO) electrode to construct a simple multiple layered photo-detector with high sensitivity to small changes in incident illumination. The light absorption characteristics of the thin bR film are mathematically represented using the kinetics of the bR photocycle and the charge displacement theorem. An electrically equivalent RC circuit is used to describe the intrinsic photoelectric properties of the film and external measurement circuitry to analyze the detector's response characteristics. Simulated studies and experimental results show that the resistance of the dried bR film is in the order of 10(11) Omega. When the input impedance of the measurement circuitry is one order of magnitude smaller than the dried film, the detector exhibits a strong differential response to the original time-varying light signal. An analytical solution of the equivalent circuit also reveals that the resistance and capacitance values exhibited by the dried bR film, in the absence of incident light, are almost twice as large as the values obtained while the material is under direct illumination. Experimental observations and a predictive model both support the notion that dried bR film can be used in simple highly sensitive photo-detector designs.

Monolithically integrated bacteriorhodopsin/semiconductor opto-electronic integrated circuit for a bio-photoreceiver

The light-sensitive protein, bacteriorhodopsin (BR), is monolithically integrated with an InP-based amplifier circuit to realize a novel opto-electronic integrated circuit (OEIC) which performs as a high-speed photoreceiver. The circuit is realized by epitaxial growth of the field-effect transistors, currently used semiconductor device and circuit fabrication techniques, and selective area BR electro-deposition. The integrated photoreceiver has a responsivity of 175 V/W and linear photoresponse, with a dynamic range of 16 dB, with 594 nm photoexcitation. The dynamics of the photochemical cycle of BR has also been modeled and a proposed equivalent circuit simulates the measured BR photoresponse with good agreement.

The influence of water on the photochemical reaction cycle of proteorhodopsin at low and high pH

Dried samples were prepared from suspension of proteorhodopsin. With HCl and NaOH the pH of the samples was adjusted below and above the pKa of the proton acceptor Asp-97, which was established earlier to be 7.1. Both types of samples were photoactive, and exhibited a truncated photocycle, compared to that measured in suspension. The photocycle of the low pH sample had a K like red shifted intermediate, decaying through an energized PR' intermediate to the ground state protein. The high pH sample had a more complex photocycle in which beside of the red shifted intermediate an M like intermediate could be identified, having a deprotonated Schiff-base. This blue shifted intermediate decays through an intermediate we designated PR', which is spectrally identical to the unphotolysed ground state. The humidity and temperature dependence of the photocycle in both cases was studied to understand the role of water in the function of the proteorhodopsin. The effects measured on proteorhodopsin were very similar to that measured earlier on bacteriorhodopsin.

Direct measurement of the photoelectric response time of bacteriorhodopsin via electro-optic sampling

The photovoltaic signal associated with the primary photochemical event in an oriented bacteriorhodopsin film is measured by directly probing the electric field in the bacteriorhodopsin film using an ultrafast electro-optic sampling technique. The inherent response time is limited only by the laser pulse width of 500 fs, and permits a measurement of the photovoltage with a bandwidth of better than 350 GHz. All previous published studies have been carried out with bandwidths of 50 GHz or lower. We observe a charge buildup with an exponential formation time of 1.68 +/- 0.05 ps and an initial decay time of 31.7 ps. Deconvolution with a 500-fs Gaussian excitation pulse reduces the exponential formation time to 1.61 +/- 0.04 ps. The photovoltaic signal continues to rise for 4.5 ps after excitation, and the voltage profile corresponds well with the population dynamics of the K state. The origin of the fast photovoltage is assigned to the partial isomerization of the chromophore and the coupled motion of the Arg-82 residue during the primary event.

Rhodopsin: insights from recent structural studies

The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.

Specific effects of chloride on the photocycle of E194Q and E204Q mutants of bacteriorhodopsin as measured by FTIR spectroscopy

Low-temperature Fourier transform infrared spectroscopy has been used to study mutants of Glu194 and Glu204, two amino acids that are involved in proton release to the extracellular side of bacteriorhodopsin. Difference spectra of films of E194Q, E204Q, E194Q/E204Q, E9Q/E194Q/E204Q, and E9Q/E74Q/E194Q/E204Q at 243, 277, and 293 K and several pH values were obtained by continuous illumination. A specific effect of Cl(-) ions was found for the mutants, promoting a N-like intermediate at alkaline pH and an O' intermediate at neutral or acid pH. The apparent pK(a) of Asp85 in the M intermediate was found to be decreased for E194Q in the presence of Cl(-) (pK(a) of 7.6), but it was unchanged for E204Q, as compared to wild-type. In the absence of Cl(-) (i.e., in the presence of SO(4)(2)(-)), mutation of Glu194 or of Glu204 produces M- (or M(N), M(G))-like intermediates under all of the conditions examined. The absence of N, O, and O' intermediates suggests a long-range effect of the mutation. Furthermore, it is suggested that Cl(-) acts by reaching the interior of the protein, rather than producing surface effects. The effect of low water content was also examined, in the presence of Cl(-). Similar spectra corresponding to the M(1) intermediate were found for dry samples of both mutants, indicating that the effects of the mutations or of Cl(-) ions are confined to the second part of the photocycle. The water O-H stretching data further confirms altered photocycles and the effect of Cl(-) on the accumulation of the N intermediate.

Transient absorption and photovoltage study of' self-assembled bacteriorhodopsin/polycation multilayer films

A series of organized (PDAC/PM)(n) (poly(diallyldimethylammonium chloride)/purple membrane) multilayer films were prepared by alternate adsorptions of positively charged PDAC polyelectrolyte and negatively charged purple membrane (PM). The kinetics of the photocycle of bacteriorhodopsin (bR) in PM was studied by flash photolysis and transient photovoltage methods. Although the orientation of the adsorbed bR depends on the pH of the PM suspension, the kinetics of the photo-induced reaction cycle in dehydrated films is independent of the deposition pH. In dry (PDAC/PM)(n) films the decay of the M intermediate to the initial bR state is multiexponential and delayed to several minutes for both orientations. A simultaneous two-exponential decay in millisecond time domain was observed at red wavelengths. The source of the red-shifted absorption is suggested to be the C(610) intermediate of the cis photocycle of bR.

Time-resolved X-ray diffraction reveals movement of F helix of D96N bacteriorhodopsin during M-MN transition at neutral pH

D96N bacteriorhodopsin has two photointermediates with the deprotonated Schiff base: the M and MN intermediates. We measure the time-resolved x-ray diffraction of the D96N purple membrane after flash photoexcitation (pH 7.0, 25 degrees C). The data clearly show the M-MN transition during the D96N photocycle. Low-resolution projection maps of these states show that the F helix of the MN intermediate shifts from its original position and this shift is much larger than that of the M intermediate. This indicates that the F helix moves in the M-MN transition of the D96N bacteriorhodopsin photocycle. Moreover, the existence of the MN intermediate in the D96N photocycle under neutral pH indicates that the MN intermediate is not peculiar to the alkaline condition. It is notable that the structural transition of M-MN is independent of the protonation state of the Schiff base. Therefore, the F helix movement precedes reprotonation of the Schiff base in the bacteriorhodopsin photocycle. Our previous study showed that the M-MN transition is hydration-dependent and that the MN intermediate is more hydrated than the M intermediate. Considering this together with the present results, we conclude that the movement of the F helix causes hydration of the cytoplasmic side, which promotes the reprotonation of the Schiff base.

Photocycle of dried acid purple form of bacteriorhodopsin

The photocycle of dried bacteriorhodopsin, pretreated in a 0.3 M HCl solution, was studied. Some properties of this dried sample resemble that of the acid purple suspension: the retinal conformation is mostly all-trans, 15-anti form, the spectrum of the sample is blue-shifted by 5 nm to 560 nm, and it has a truncated photocycle. After photoexcitation, a K-like red-shifted intermediate appears, which decays to the ground state through several intermediates with spectra between the K and the ground state. There are no other bacteriorhodopsin-like intermediates (L, M, N, O) present in the photocycle. The K to K' transition proceeds with an enthalpy decrease, whereas during all the following steps, the entropic energy of the system decreases. The electric response signal of the oriented sample has only negative components, which relaxes to zero. These suggest that the steps after intermediate K represent a relaxation process, during which the absorbed energy is dissipated and the protein returns to its original ground state. The initial charge separation on the retinal is followed by limited charge rearrangements in the protein, and later, all these relax. The decay times of the intermediates are strongly influenced by the humidity of the sample. Double-flash experiments proved that all the intermediates are directly driven back to the ground state. The study of the dried acid purple samples could help in understanding the fast primary processes of the protein function. It may also have importance in technical applications.

Electrical-to-mechanical coupling in purple membranes: membrane as electrostrictive medium

In this paper, we present acousto-electrical measurements performed on dry films of purple membranes (PM) of Halobacterium salinarium. The purpose of these measurements is to determine the relation between mechanical and electrical phenomena in bacteriorhodopsin and to define the role of the protein in the proton transfer process. Electrical-to-mechanical coupling in PMs manifests itself as direct and inverse piezoelectric effects. Measurements performed on the samples with different degrees of PM orientation and at various values of the externally applied cross-membrane electric field indicate that piezoelectric phenomena in PMs arise from the electric asymmetry of the membranes, i.e., they originate from electrostriction. Experiments with samples made of oriented PMs allow estimation of the value of the intrinsic cross-membrane electric field, which is approximately 10(8) V/m. A hypothetical model of PM is presented where the electrical-to-mechanical coupling is suggested to be the main driving force for the proton translocation against the Coulomb forces acting in the membrane.

Chemical and physical evidence for multiple functional steps comprising the M state of the bacteriorhodopsin photocycle

In the photocycle of bacteriorhodopsin (bR), light-induced transfer of a proton from the Schiff base to an acceptor group located in the extracellular half of the protein, followed by reprotonation from the cytoplasmic side, are key steps in vectorial proton pumping. Between the deprotonation and reprotonation events, bR is in the M state. Diverse experiments undertaken to characterize the M state support a model in which the M state is not a static entity, but rather a progression of two or more functional substates. Structural changes occurring in the M state and in the entire photocycle of wild-type bR can be understood in the context of a model which reconciles the chloride ion-pumping phenotype of mutants D85S and D85T with the fact that bR creates a transmembrane proton-motive force.

Function and picosecond dynamics of bacteriorhodopsin in purple membrane at different lipidation and hydration

By neutron scattering experiments and time-resolved absorption spectroscopy we have investigated picosecond equilibrium fluctuations and the kinetics of the photocycle of bacteriorhodopsin (BR) in the purple membrane (PM). Natural PM samples composed of 75% BR (w/w) and 25% lipid (w/w) as well as delipidated PM having only 5% lipid (w/w) were measured at different levels of hydration. We observed a reduced 'flexibility', due to a diminished weight of stochastic large-amplitude motions occurring in the delipidated PM as compared to the natural PM. This effect is more pronounced for wet samples, indicating the importance of lipid hydration for protein dynamics. The reduced flexibility is accompanied by significantly larger time constants describing the decay of the M-intermediate. Therefore, a correlation between the dynamical behavior of the protein-lipid complex and BR function emerges.

The structure and mechanism of the family of retinal proteins from halophilic archaea

Retinal proteins from halophilic archaea provide a unique opportunity to analyze vectorial ion translocation. Studies on its structure, conformational changes, proton conduction and electrogenic steps have helped to elucidate the catalytic cycle of bacteriorhodopsin in increasing detail. Experimental modulation of the vectoriality and ion specificity by altering the substrate availability, point mutations and light conditions for the different retinal proteins allows the proposal of a general model of ion transport for this protein family.