Proton translocation mechanism and energetics in the light-driven pump bacteriorhodopsin

Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins

Microbial rhodopsins are membrane proteins that use the energy absorbed by the covalently bound retinal chromophore to initiate reaction cycles resulting in ion transport or signal transduction. Thousands of distinct microbial rhodopsins are known and, for many rhodopsins, three-dimensional structures have been solved with structural biology, including as entire sets of structures solved with serial femtosecond crystallography. This sets the stage for comprehensive studies of large datasets of static protein structures to dissect structural elements that provide functional specificity to the various microbial rhodopsins. A challenge, however, is how to analyze efficiently intra-molecular interactions based on large datasets of static protein structures. Our perspective discusses the usefulness of graph-based approaches to dissect structural movies of microbial rhodopsins solved with time-resolved crystallography.

Reaction cycle of operating pump protein studied with single-molecule spectroscopy

Biological machinery relies on nonequilibrium dynamics to maintain stable directional fluxes through complex reaction cycles. For such reaction cycles, the presence of microscopically irreversible conformational transitions of the protein, and the accompanying entropy production, is of central interest. In this work, we use multidimensional single-molecule fluorescence lifetime correlation spectroscopy to measure the forward and reverse conformational transitions of bacteriorhodopsin during trans-membrane H + pumping. We quantify the flux, affinity, enthalpy and entropy production through portions of the reaction cycle as a function of temperature. We find that affinity of irreversible conformational transitions decreases with increasing temperature, resulting in diminishing flux and entropy production. We show that the temperature dependence of the transition affinity is well fit by the Gibbs-Helmholtz relation, allowing the DH trans to be experimentally extracted.

Fast and robust two-dimensional inverse Laplace transformation of single-molecule fluorescence lifetime data

Fluorescence spectroscopy at the single-molecule scale has been indispensable for studying conformational dynamics and rare states of biological macromolecules. Single-molecule two-dimensional (2D) fluorescence lifetime correlation spectroscopy is an emerging technique that holds promise for the study of protein and nucleic acid dynamics, as the technique is 1) capable of resolving conformational dynamics using a single chromophore, 2) resolves forward and reverse transitions independently, and 3) has a dynamic window ranging from microseconds to seconds. However, the calculation of a 2D fluorescence relaxation spectrum requires an inverse Laplace transform (ILT), which is an ill-conditioned inversion that must be estimated numerically through a regularized minimization. Current methods for performing ILTs of fluorescence relaxation can be computationally inefficient, sensitive to noise corruption, and difficult to implement. Here, we adopt an approach developed for NMR spectroscopy (T1-T2 relaxometry) to perform one-dimensional (1D) and 2D-ILTs on single-molecule fluorescence spectroscopy data using singular-valued decomposition and Tikhonov regularization. This approach provides fast, robust, and easy to implement Laplace inversions of single-molecule fluorescence data. We compare this approach to the widely used maximal entropy method.

Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins

Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H⁺, Na⁺, Cl^-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.

Proton Transfer in Bacterial Reaction Centers and Bacteriorhodopsin in the Presence of Dipyridamole

Dipyridamole, 2,6-bis(diethanolamino)-4,8-dipiperidinopyrimido[5,4-d]pyrimidine (DIP), a well known vasodilator and inhibitor of membrane peroxidation has recently been shown a potential co-activator (modulator) in the MDR phenomenon in cancer therapy. It inhibits P-glycoprotein (Pgp) which is a efflux pump of anticancer drugs in tumor cells. For the first time it is shown that dipyridamole, markedly slows down the kinetics of the electrogenic phase of the photoelectric response in Rb. sphaeroides chromatophores which is due to the proton transfer from the external medium to the secondary quinone acceptor in the reaction center. In purple membranes from H. salinarium containing bacteriorhodopsin (bR) dipyridamole (in its charged state) significantly slows down the kinetics of the proton transfer to the Schiff base from the primary donor Asp-96 (in wild type bacteria) or from the surrounding (in D96N mutant). Dipyridamole is supposed to affect the proton-transfer via changes in structural dynamics of membrane proteins including modification of their system of hydrogen-bonds.

Unsymmetrical Tetradentate Schiff Bases Derived from 2-[(2-2 Amino-Phenylimino)-Methyl]-Phenol and 2-[1-(2-Amino-Phenylimino)-Ethyl]-Phenol

The novel unsymmetrical, diimino-tetradentate Schiff bases derived from 2-[(2-amino-phenylimino)- methyl]-phenol and 2-[1-(2-amino-phenylimino)-ethyl]-phenol were synthesised and characterised by template and non-template methods.

The ins and outs of vesicular monoamine transporters

Yaffe et al. review structure-guided studies that have provided insight into the mechanism of proton-monoamine antiport by VMATs.

The H⁺-coupled vesicular monoamine transporter (VMAT) is a transporter essential for life. VMAT mediates packaging of the monoamines serotonin, dopamine, norepinephrine, and histamine from the neuronal cytoplasm into presynaptic vesicles, which is a key step in the regulated release of neurotransmitters. However, a detailed understanding of the mechanism of VMAT function has been limited by the lack of availability of high-resolution structural data. In recent years, a series of studies guided by homology models has revealed significant insights into VMAT function, identifying residues that contribute to the binding site and to specific steps in the transport cycle. Moreover, to characterize the conformational transitions that occur upon binding of the substrate and coupling ion, we have taken advantage of the unique and powerful pharmacology of VMAT as well as of mutants that affect the conformational equilibrium of the protein and shift it toward defined conformations. This has allowed us to identify an important role for the proton gradient in driving a shift from lumen-facing to cytoplasm-facing conformations.

Mistic-fused expression of algal rhodopsins in Escherichia coli and its photochemical properties

BACKGROUND

Since algal rhodopsins, the eukaryotic seven-transmembrane proteins, are generally difficult to express in Escherichia coli, eukaryotic cells have been used for heterologous expression. Mistic, a membrane-associated protein that was originally discovered in Bacillus subtilis, has been shown to improve the expression levels of many foreign integral membrane proteins in E. coli when used as a fusion partner linked to the N-terminus of cargo proteins.

METHODS

Here, we expressed two algal rhodopsins with N- and C-terminal Mistic domains in E. coli-Acetabularia rhodopsin I (ARI) and Chlamydomonas sensory rhodopsin B (CSRB, channel rhodopsin 2). UV/VIS spectroscopy, pH titration of proton acceptor residue, laser-induced photolysis and electrophysiological measurement were used for investigating important residues in proton transport and spectroscopic characters of the proteins.

RESULTS

Protein yield of two algal rhodopsins was enhanced, obtaining 0.12mg of Mistic-ARI and 0.04mg of Mistic-CSRB per liter of culture. Spheroplast expression Mistic-ARI had outward proton-pumping activity, indicating protein functionality. Asp89 of ARI changed its protonation state by light absorption, and Asp100 was important for O(600) formation. Electrophysiology revealed that both residues took part in proton transport. The spectroscopic analyses of Mistic-CSRB revealed its characteristics.

CONCLUSIONS

Fusion to the membrane-integrating protein Mistic can enhance overexpression of eukaryotic type I rhodopsins in E. coli.

GENERAL SIGNIFICANCE

These findings indicate that Mistic fusion and E. coli expression method could be an effective, low cost technique for studying eukaryotic membrane proteins. This may have useful implications, for example, in studying structural characteristics and optogenetics for rhodopsins.

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins

All-optical electrophysiology-spatially resolved simultaneous optical perturbation and measurement of membrane voltage-would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond response times and produce no photocurrent. We engineered a channelrhodopsin actuator, CheRiff, which shows high light sensitivity and rapid kinetics and is spectrally orthogonal to the QuasArs. A coexpression vector, Optopatch, enabled cross-talk-free genetically targeted all-optical electrophysiology. In cultured rat neurons, we combined Optopatch with patterned optical excitation to probe back-propagating action potentials (APs) in dendritic spines, synaptic transmission, subcellular microsecond-timescale details of AP propagation, and simultaneous firing of many neurons in a network. Optopatch measurements revealed homeostatic tuning of intrinsic excitability in human stem cell-derived neurons. In rat brain slices, Optopatch induced and reported APs and subthreshold events with high signal-to-noise ratios. The Optopatch platform enables high-throughput, spatially resolved electrophysiology without the use of conventional electrodes.

Philosophy of voltage-gated proton channels

In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.

Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle

Proton-transfer reactions in the bacteriorhodopsin light-driven proton pump are coupled with structural rearrangements of protein amino acids and internal water molecules. It is generally thought that the first proton-transfer step from retinal Schiff base to the nearby Asp85 is coupled with movement of the Arg82 side chain away from Asp85 and toward the extracellular proton release group. This movement of Arg82 likely triggers the release of the proton from the proton release group to the extracellular bulk. The exact timing of the movement of Arg82 and how this movement is coupled with proton transfer are still not understood in molecular detail. Here, we address these questions by computing the free energy for the movement of the Arg82 side chain. The calculations indicate that protonation of Asp85 leads to a fast reorientation of the Arg82 side chain toward the extracellular proton release group.

Melittin-regenerated purple membrane

We have investigated the character of melittin-regenerated purple membrane. Adding melittin to blue membrane causes the color transition and partial regeneration of the photocycle and the proton pump. The reconstitution of bacteriorhodopsin by melittin is proved to be charge-dependent. In studying the location of melittin binding on the blue membrane, we suggest that melittin anchors on the membrane through both hydrophobic and electrostatic interactions. The electrostatic interaction is dominant. The binding sites for the electrostatic interaction should be on the surface of the membrane.

Protein conformational changes in the bacteriorhodopsin photocycle: comparison of findings from electron and X-ray crystallographic analyses

Light-driven conformational changes in the membrane protein bacteriorhodopsin have been studied extensively using X-ray and electron crystallography, resulting in the deposition of >30 sets of coordinates describing structural changes at various stages of proton transport. Using projection difference Fourier maps, we show that coordinates reported by different groups for the same photocycle intermediates vary considerably in the extent and nature of conformational changes. The different structures reported for the same intermediate cannot be reconciled in terms of differing extents of change on a single conformational trajectory. New measurements of image phases obtained by cryo-electron microscopy of the D96G/F171C/F219L triple mutant provide independent validation for the description of the large protein conformational change derived at 3.2 A resolution by electron crystallography of 2D crystals, but do not support atomic models for light-driven conformational changes derived using X-ray crystallography of 3D crystals. Our findings suggest that independent determination of phase information from 2D crystals can be an important tool for testing the accuracy of atomic models for membrane protein conformational changes.

Long-distance proton transfer with a break in the bacteriorhodopsin active site

Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.

In situ studies of metal coordinations and molecular orientations in monolayers of amino-acid-derived Schiff bases at the air-water interface

The surface behaviors of monolayers of amino-acid-derived Schiff bases, namely, 4-(4-(hexadecyloxy)benzylideneamino)benzoic acid (HBA), at the air-water interface on pure water and ion-containing subphases (Cu2+, Ca2+, and Ba2+) have been clarified by a combination of surface pressure-area isotherms and surface plasmon resonance (SPR) technique, and the metal coordinations and molecular orientations in the monolayers have been investigated using in situ infrared reflection absorption spectroscopy (IRRAS). The presence of metal ions gives rise to condensation of the monolayers (Cu2+, pH 6.1; Ca2+, pH 11; Ba2+, pH 10), even leading to the formation of three-dimensional structures of the compressed monolayer in the case of Ba2+ (pH 12). The metal coordinations with the carboxyl groups at the interface depend on the type of metal ions and pH of the aqueous subphase. The orientations of the aromatic Schiff base segments with surface pressure are elaborately described. The spectral behaviors of the Schiff base segments with incidence angle in the case of Ba2+ (pH 12) have so far presented an excellent example for the selection rule of IRRAS at the air-water interface for p-polarization with vibrational transition moments perpendicular to the water surface. The chain orientations in the monolayers are quantitatively determined on the assumption that the thicknesses of the HBA monolayers at the air-water interface are composed of the sublayers of alkyl chains and Schiff base segments.

Screening and characterization of proteorhodopsin color-tuning mutations in Escherichia coli with endogenous retinal synthesis

Proteorhodopsin is photoactive 7-transmembrane protein, which uses all-trans retinal as a chromophore. Proteorhodopsin subfamilies are spectrally tuned in accordance with the depth of habitat of the host organisms, numerous species of marine picoplankton. We try to find residues critical for the spectral tuning through the use of random PCR mutagenesis and endogenous retinal biosynthesis. We obtained 16 isolates with changed color by screening in Escherichia coli with internal retinal biosynthesis system containing genes for beta-carotene biosynthesis and retinal synthase. Some isolates contained multiple substitutions, which could be separated to give 20 single mutations influencing the spectral properties. The color-changing residues are distributed through the protein except for the helix A, and about a half of the mutations is localized on the helices C and D, implying their importance for color tuning. In the pumping form of the pigment, absorption maxima in 8 mutants are red-shifted and in 12 mutants are blue-shifted compared to the wild-type. The results of flash-photolysis showed that most of the low pumping activity mutants possess slower rates of M decay and O decay. These results suggest that the color-tuning residues are not restricted to the retinal binding pocket, in accord with a recent evolutionary analysis.

Temperature investigations of E/Z isomers in ketimines based of p-dibenzoylobenzene with aniline and 2,6-dimethylaniline by infrared spectroscopy

The reaction of aniline with p-dibenzoylobenzene (K1) can lead to Z/Z, Z/E and E/E isomers however the only Z/Z and E/E were formed. At room temperature these isomers may be separated, thus the corresponding FTIR spectra could be recorded. The observed bands were assigned and temperature investigations were lead to monitor the structural changes during heating Z and E forms of K1 from 20 to 240 degrees C. FTIR spectroscopy showed that the bigger changes of the Z form was observed with an increase of temperature. Similar experience was lead with the ketimine synthesized from 2,6-dimethylaniline and p-dibenzoylobenzene (K2) investigated as a mixture of isomers.

Bacteriorhodopsin mutants D85N, D85T and D85,96N as proton pumps

Proton translocation in the BR mutants D85N, D85T and D85,96N was studied by attachment of purple membranes to planar lipid bilayers. Pump currents in these mutants were measured via capacitive coupling and by use of the appropriate ionophores. All mutants have a reduced pK of their Schiff bases around 8-8.5 in common. At physiological pH, a mixture of chromophores absorbing at 410 nm (deprotonated form) and around 600 nm (protonated form) coexists. Excitation with continuous blue light induces in all three mutants an outwardly directed stationary pump current. These currents are enhanced upon addition of azide in D85N and D85,96N by a factor of 50, but no azide enhancement is observed in D85T. Yellow light alone induces transient inwardly directed currents in the mutants but additional blue light leads to a stationary current with the same direction. All the observed currents are carried by protons, so that the consecutive absorption of a yellow and a blue photon leads to inverted stationary photocurrents by the mutants, as observed with halorhodopsin (HR). A mechanistic model describing the inversion of proton pumping is discussed by the cis-trans, trans-cis isomerization of the retinal and the different proton accessibility of the Schiff base from the extracellular or the cytoplasmic side of the membrane.

Macrodipoles. Unusual electric properties of biological macromolecules

The wide range of different effects induced by electric fields in biological macromolecules is clearly due to the unusual quality and quantity of their electric parameters. A general concept for a quantitative description of the polarizability of macromolecules remains to be established. In the case of DNA, experimental data indicate the existence of an effective polarization length N(p); at chain lengths N < N(p) the polarizability increases with N(2), whereas saturation is approached at N > or = N(p). The polarization length decreases with increasing ionic strength in close analogy to the Debye length, but is approximately 10 times larger than the Debye length. The dynamics of DNA polarization at high field strengths has been observed in the ns time range and is consistent with biased field induced ion dissociation. In the range of chain lengths from approximately 400 to approximately 850 base pairs DNA molecules exhibit permanent dipole moments, which are in a preferentially perpendicular direction to the end-to-end-vector, leading to a positive electric dichroism. These results are consistent with a "frozen" ensemble of bent DNA configurations and provide evidence for the existence of slow, non-elastic bending transitions. The electric parameters of proteins are usually dominated by a permanent anisotropy of the charge distribution, corresponding to permanent dipole moments of the order of several hundred Debye up to about 1500 Debye. Relatively small dipole moments of protein monomers add up to millions of Debye, when these proteins are in a vectorial organization in membrane patches, as found for bacteriorhodopsin and Na (+)K (+)-ATPase . In these cases the dipole vector may support vectorial ion transport. It is remarkable that the dipole moments of proteins usually show a relatively small dependence on the salt concentration; a rational for these observations is provided by a dipole potential at the plane of shear for rotational diffusion, which is defined in close analogy to the zeta-potential for translational diffusion. Symmetry breaking leading to huge electric dipole moments may be expected for mixed lipid vesicles: according to model calculations the phase separation of lipid components with and without net charges may lead to very high dipole moments; the expectation has been verified experimentally for vesicles containing DMPA and DMPC. The state of these systems should be extremely sensitive to electric fields. In summary, there is an unusual wide variation of electric parameters associated with biological macromolecules and with biomolecular assemblies, which is the basis for the complexity of different phenomena induced by electric fields in biological systems.

Evidence for parallel photocycles and implications for the proton pump in bacteriorhodopsin

In order to account for the large variety of kinetic phenomena in the light-induced reactions of bacteriorhodopsin's retinal chromophore (BR), a scheme of parallel photocycles has been proposed [W. Eisfeld, C. Pusch, R. Diller, R. Lohrmann and M. Stockburger, Biochemistry, 32 (1993) 7196-7215]. In the present study an experimental test for the validity of this model is described which is based on the fact that in the alkaline region the longest-living intermediates M(f), M(S) or N in each of the proposed cycles have significantly different lifetimes. A condition for the existence of parallel cycles would be that the population of M(f), M(S) or N is accompanied by a respective depletion of BR in each individual cycle. Dual-beam laser experiments were performed which showed that this condition is fulfilled. It is concluded that those proton transfer steps which are important for the function as a proton pump are the same for all cycles.

Minimum Energy Pathways for Proton Transfer between Adjacent Sites Exposed to Water

The capacity to transfer protons between surface groups is an innate property of many proteins. The transfer of a proton between donor and acceptor, located as far as 6-7 A apart, necessitates the participation of water molecules in the process. In a previous study we investigated the mechanism of proton transfer (PT) between bulk exposed sites, a few ångströms apart, using as a model the proton exchange between the proton-binding sites of the fluorescein molecule in dilute aqueous solution.1 The present study expands the understanding of PT reactions between adjacent sites exposed to water through the calculation the minimum energy pathways (MEPs) by the conjugate peak refinement algorithm2 and a quantum-mechanical potential. The PT reaction trajectories were calculated for the fluorescein system with an increasing number of water molecules. The MEP calculations reveal that the transition state is highly strained and involves a supramolecular structure in which fluorescein and the interconnecting water molecules are covalently bonded together and the protons are shared between neighboring oxygens. These findings are in accord with the high activation energy, as measured for the reaction, and indicate that PT reactions on the surface proceed by a semi- or fully concerted rather than stepwise mechanism. A similar mechanism is assumed to be operative on the surface of proteins and renders water-mediated PT reactions as highly efficient as they are.

External electric control of the proton pumping in bacteriorhodopsin

Comparative analysis of the photoelectric response of dried films of purple membranes (PM) depending on their degree of orientation is presented. Time dependence of the photo-induced protein electric response signal (PERS) of oriented and non-oriented films to a single laser pulse in the presence of the external electric field (EEF) was experimentally determined. The signal does not appear in the non-oriented films when the EEF is absent, whereas the PERS of the oriented PM films demonstrates the variable polarity on the microsecond time scale. In the presence of the EEF the PERS of the non-oriented film rises exponentially preserving the same polarization. The polarization of the PERS changes by changing the polarity of the EEF with no influence on the time constant of the PERS kinetics. The EEF effect on the PERS of the oriented films is more complicated. By subtracting the PERS when EEF not equal 0 from the PERS when EEF = 0 the resulting signal is comparable to that of the non-oriented films. Generalizing the experimental data we conclude that the EEF influence is of the same origin for the films of any orientation. To explain the experimental results the two-state model is suggested. It assumes that the EEF directionally changes the pK(a) values of the Schiff base (SB) and of the proton acceptor aspartic acid D85 in bacteriorhodopsin. Because of that the SB-->D85 proton transfer might be blocked and consequently the L-->M intermediate transition should vanish. Thus, on the characteristic time scale tau( L --> M ) approximately 30 micros; both intermediates, the M intermediate, appearing under normal conditions, and the L intermediate as persisting under the blocked conditions when D85 is protonated, should coexist in the film. The total PERS is a result of the potentials corresponding to the electrogenic products of intermediates L and M that are of the opposite polarity. It is concluded that the ratio of bacteriorhodopsin concentrations corresponding to the L and M intermediates is driven by the EEF and, consequently, it should define the PERS of the non-oriented films. According to this model the orientation degree of the film could be evaluated by describing the PERS.

pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin

The pH-dependence of photocycle of archaerhodopsin 4 (AR4) was examined, and the underlying proton pumping mechanism investigated. AR4 is a retinal-containing membrane protein isolated from a strain of halobacteria from a Tibetan salt lake. It acts as a light-driven proton pump like bacteriorhodopsin (BR). However, AR4 exhibits an "abnormal" feature--the time sequence of proton release and uptake is reversed at neutral pH. We show here that the temporal sequence of AR4 reversed to "normal"--proton release preceding proton uptake--when the pH is increased above 8.6. We estimated the pK(a) of the proton release complex (PRC) in the M-intermediate to be approximately 8.4, much higher than 5.7 of wide-type BR. The pH-dependence of the rate constant of M-formation shows that the pK(a) of PRC in the initial state of AR4 is approximately 10.4, whereas it is 9.7 in BR. Thus in AR4, the chromophore photoisomerization and subsequent proton transport from the Schiff base to Asp-85 is coupled to a decrease in the pK(a) of PRC from 10.4 to 8.4, which is 2 pK units less than in BR (4 units). This weakened coupling accounts for the lack of early proton release at neutral pH and the reversed time sequence of proton release and uptake in AR4. Nevertheless the PRC in AR4 effectively facilitates deprotonation of primary proton acceptor and recovery of initial state at neutral pH. We found also that all pK(a)s of the key amino acid residues in AR4 were elevated compared to those of BR.

A nanomechanical device based on light-driven proton pumps

In this paper, a hybrid device based on a microcantilever interfaced with bacteriorhodopsin (bR) is constructed. The microcantilever, on which the highly oriented bR film is self-assembled, undergoes controllable and reversible bending when the light-driven proton pump protein, bR, on the microcantilever surface is activated by visible light. Several control experiments are carried out to preclude the influence of heat and photothermal effects. It is shown that the nanomechanical motion is induced by the resulting gradient of protons, which are transported from the KCl solution on the cytoplasmic side of the bR film towards the extracellular side of the bR film. Along with a simple physical interpretation, the microfabricated cantilever interfaced with the organized molecular film of bR can simulate the natural machinery in converting solar energy to mechanical energy.

Controllable snail-paced light in biological bacteriorhodopsin thin film

We observe that the group velocity of light is reduced to an extremely low value of 0.091 mm/s in a biological thin film of bacteriorhodopsin at room temperature. By exploiting unique features of a flexible photoisomerization process for coherent population oscillation, the velocity is all-optically controlled over an enormous span, from snail-paced to normal light speed, with no need of modifying the characteristics of the incident pulse. Because of the large quantum yield for the photoreaction in this biochemical system, the ultraslow light is observed even at low light levels of microwatts, indicating high energy efficiency.

The protonation-deprotonation kinetics of the protonated Schiff base in bicelle bacteriorhodopsin crystals

In the recently published x-ray crystal structure of the "bicelle" bacteriorhodopsin (bbR) crystal, the protein has quite a different structure from the native and the in cubo bacteriorhodopsin (cbR) crystal. Instead of packing in parallel trimers as do the native membrane and the cbR crystals, in the bbR crystal the protein packs as antiparallel monomers. To date, no functional studies have been performed, to our knowledge, to investigate if the photocycle is observed in this novel protein packing structure. In this study, both Raman and time-resolved transient absorption spectroscopy are used to both confirm the presence of the photocycle and investigate the deprotonation-reprotonation kinetics of the Schiff base proton in the bbR crystal. The observed rates of deprotonation and reprotonation processes of its Schiff base have been compared to those observed for native bR under the same conditions. Unlike the previously observed similarity of the rates of these processes for cbR crystals and those for native bacteriorhodopsin (bR), in bbR crystals the rate of deprotonation has increased by 300%, and the rate of reprotonation has decreased by nearly 700%. These results are discussed in light of the changes observed when native bR is delipidated or monomerized by detergents. Both the change of the hydrophobicity of the environment around the protonated Schiff base and Asp85 and Asp96 (which could change the pKa values of proton donor-acceptor pairs) and the water structure in the bbR crystal are offered as possible explanations for the different observations.

Supramolecular Assemblies and Molecular Recognition of Amphiphilic Schiff Bases with Barbituric Acid in Organized Molecular Films

A bolaform Schiff base, N,N'-bis(salicylidene)-1,10-decanediamine (BSC10), has been synthesized and its interfacial hydrogen bond formation or molecular recognition with barbituric acid was investigated in comparison with that of a single chain Schiff base, 2-hydroxybenzaldehyde-octadecylamine (HBOA). It has been found that while HBOA formed a monolayer at the air/water interface, the bolaform Schiff base formed a multilayer film with ordered layer structure on water surface. When the Schiff bases were spread on the subphase containing barbituric acid, both of the Schiff bases could form hydrogen bonds with barbituric acid in situ in the spreading films. As a result, an increase of the molecular areas in the isotherms was observed. The in situ H-bonded films could be transferred onto solid substrates, and the transferred multilayer films were characterized by various methods such as UV-vis and FT-IR spectrosopies. Spectral changes were observed for the films deposited from the barbituric acid subphase, which supported the hydrogen bond formation between the Schiff bases and barbituric acid. By measuring the MS-TOF of the deposited films dissolved in CHCl3 solution, it was concluded that a 2:1 complex of HBOA with barbituric acid and a 1:2 complex of BSC10 with barbituric acid were formed. On the other hand, when the multilayer films of both Schiff bases were immersed in an aqueous solution of barbituric acid, a similar molecular recognition through the hydrogen bond occurred. A clear conformational change of the alkyl spacer in the bolaform Schiff base was observed during the complex formation with the barbituric acid.