Direct measurement of electric current generation by cytochrome oxidase, H+-ATPase and bacteriorhodopsin

Electrometric and Electron Paramagnetic Resonance Measurements of a Difference in the Transmembrane Electrochemical Potential: Photosynthetic Subcellular Structures and Isolated Pigment-Protein Complexes

A transmembrane difference in the electrochemical potentials of protons (ΔμH+) serves as a free energy intermediate in energy-transducing organelles of the living cell. The contributions of two components of the ΔμH+ (electrical, Δψ, and concentrational, ΔpH) to the overall ΔμH+ value depend on the nature and lipid composition of the energy-coupling membrane. In this review, we briefly consider several of the most common instrumental (electrometric and EPR) methods for numerical estimations of Δψ and ΔpH. In particular, the kinetics of the flash-induced electrometrical measurements of Δψ in bacterial chromatophores, isolated bacterial reaction centers, and Photosystems I and II of the oxygenic photosynthesis, as well as the use of pH-sensitive molecular indicators and kinetic data regarding pH-dependent electron transport in chloroplasts, have been reviewed. Further perspectives on the application of these methods to solve some fundamental and practical problems of membrane bioenergetics are discussed.

Features of the Mechanism of Proton Transport in ESR, Retinal Protein from Exiguobacterium sibiricum

Retinal-containing light-sensitive proteins - rhodopsins - are found in many microorganisms. Interest in them is largely explained by their role in light energy storage and photoregulation in microorganisms, as well as the prospects for their use in optogenetics to control neuronal activity, including treatment of various diseases. One of the representatives of microbial rhodopsins is ESR, the retinal protein of Exiguobacterium sibiricum. What distinguishes ESR from homologous proteins is the presence of a lysine residue (Lys96) as a proton donor for the Schiff base. This feature, along with the hydrogen bond of the proton acceptor Asp85 with the His57 residue, determines functional characteristics of ESR as a proton pump. This review examines the results of ESR studies conducted using various methods, including direct electrometry. Comparison of the obtained data with the results of structural studies and with other retinal proteins allows us to draw conclusions about the mechanisms of transport of hydrogen ions in ESR and similar retinal proteins.

Retinal-Based Anion Pump from the Cyanobacterium Tolypothrix campylonemoides

In this work, TcaR rhodopsin from the cyanobacterium Tolypothrix campylonemoides was characterized. Analysis of the amino acid sequence of TcaR revealed that this protein possesses a TSD motif that differs by only one amino acid from the TSA motif of the known halorhodopsin chloride pump. The TcaR protein was expressed in E. coli, purified, and incorporated into proteoliposomes and nanodiscs. Functional activity was measured by electric current generation through the planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one side of the membrane surface, as well as by fluorescence using the voltage-dependent dye oxonol VI. We have shown that TcaR rhodopsin functions as a powerful anion pump. Our results show that the novel microbial anion transporter, TcaR, deserves deeper investigation and may be of interest both for fundamental studies of membrane proteins and as a tool for optogenetics.

Generation of Membrane Potential by Cytochrome bd

An overview of current notions on the mechanism of generation of a transmembrane electric potential difference (Δψ) during the catalytic cycle of a bd-type triheme terminal quinol oxidase is presented in this work. It is suggested that the main contribution to Δψ formation is made by the movement of H+ across the membrane along the intra-protein hydrophilic proton-conducting pathway from the cytoplasm to the active site for oxygen reduction of this bacterial enzyme.

Investigation of the Mechanism of Membrane Potential Generation by Heme-Copper Respiratory Oxidases in a Real Time Mode

Heme-copper respiratory oxidases are highly efficient molecular machines. These membrane enzymes catalyze the final step of cellular respiration in eukaryotes and many prokaryotes: the transfer of electrons from cytochromes or quinols to molecular oxygen and oxygen reduction to water. The free energy released in this redox reaction is converted by heme-copper respiratory oxidases into the transmembrane gradient of the electrochemical potential of hydrogen ions H+). Heme-copper respiratory oxidases have a unique mechanism for generating H+, namely, a redox-coupled proton pump. A combination of direct electrometric method for measuring the kinetics of membrane potential generation with the methods of prestationary kinetics and site-directed mutagenesis in the studies of heme-copper oxidases allows to obtain a unique information on the translocation of protons inside the proteins in real time. The review summarizes the data of studies employing time-resolved electrometry to decipher the mechanisms of functioning of these important bioenergetic enzymes.

Lel A. Drachev and the Direct Electrometric Method

In the bioenergetics studies, the direct electrometric method played an important role. This method is based on measuring the electrical potential difference (Δψ) between two compartments of the experimental cell generated by some membrane proteins. These proteins are incorporated into closed lipid-protein membrane vesicles associated with an artificial lipid membrane that separates the compartments. The very existence of such proteins able to generate Δψ was one of the consequences of Peter Mitchell's chemiosmotic concept. The discovery and investigation of their functioning contributed to the recognition of this concept and, eventually the well-deserved awarding of the Nobel Prize to P. Mitchell. Lel A. Drachev (1926-2022) was one of the main authors of the direct electrometrical method. With his participation, key studies were carried out on the electrogenesis of photosynthetic and respiratory membrane proteins, including bacteriorhodopsin, visual rhodopsin, photosynthetic bacterial reaction centers, cytochrome oxidase and others.

Mechanisms of inward transmembrane proton translocation

Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elucidation of such mechanisms is a challenge. It requires true-atomic-resolution structures of all key proton-conducting states. Here we present a comprehensive function-structure study of a light-driven bacterial inward proton pump, xenorhodopsin, from Bacillus coahuilensis in all major proton-conducting states. The structures reveal that proton translocation is based on proton wires regulated by internal gates. The wires serve as both selectivity filters and translocation pathways for protons. The cumulative results suggest a general concept of proton translocation. We demonstrate the use of serial time-resolved crystallography at a synchrotron source with sub-millisecond resolution for rhodopsin studies, opening the door for principally new applications. The results might also be of interest for optogenetics since xenorhodopsins are the only alternative tools to fire neurons.

Mirror proteorhodopsins

Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different pH environment. Here we describe conceptually new bacterial rhodopsins which are operating as outward proton pumps at acidic pH. A comprehensive function-structure study of a representative of a new clade of proton pumping rhodopsins which we name "mirror proteorhodopsins", from Sphingomonas paucimobilis (SpaR) shows cavity/gate architecture of the proton translocation pathway rather resembling channelrhodopsins than the known rhodopsin proton pumps. Another unique property of mirror proteorhodopsins is that proton pumping is inhibited by a millimolar concentration of zinc. We also show that mirror proteorhodopsins are extensively represented in opportunistic multidrug resistant human pathogens, plant growth-promoting and zinc solubilizing bacteria. They may be of optogenetic interest.

Application of direct electrometry in studies of microbial rhodopsins reconstituted in proteoliposomes

Microbial rhodopsins are the family of retinal-containing proteins that perform primarily the light-driven transmembrane ion transport and sensory functions. They are widely distributed in nature and can be used for optogenetic control of the cellular activities by light. Functioning of microbial rhodopsins results in generation of the transmembrane electric potential in response to a flash that can be measured by direct time-resolved electrometry. This method was developed by L. Drachev and his colleagues at the Belozersky Institute and successfully applied in the functional studies of microbial rhodopsins. First measurements were performed using bacteriorhodopsin from Halobacterium salinarum-the prototype member of the microbial retinal protein family. Later, direct electrometric studies were conducted with proteorhodopsin from Exiguobacterium sibiricum (ESR), the sodium pump from Dokdonia, and other proteins. They allowed detailed characterization of the charge transfer steps during the photocycle of microbial rhodopsins and provided new insights for profound understanding of their mechanism of action.

Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells

This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F₁F_O) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V₁V_O). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.

Natural computation and its limits: Efim Liberman at the dawn of a new science

Efim A. Liberman (1925-2011) can be considered as a founder of the new field of science that explores natural computation and its limits. He named it Chaimatics and suggested its generalization to the ultimate all-encompassing theory that unites biology, physics and mathematics. He made a number of experimental discoveries, including color coding in the retina, the participation mechanisms of Ca²⁺ ions in synaptic transmission, and the measurement of potential in the coupling membranes of mitochondria and chloroplasts. He also made a decisive contribution to the proof of the chemiosmotic hypothesis of oxidative phosphorylation. In a series of works started in 1972, Liberman developed the concept of the molecular computer of the cell, which includes the programs written on DNA and RNA nucleotide sequences and executed by enzymes playing the role of processing units whereas nucleotide sequences are interpreted as commands and addresses. In this framework, Liberman predicted RNA splicing before its discovery and suggested the role of processing of small informational molecules (later defined as small RNAs) in controlling biological processes. Efim Liberman defined the fundamental property of life as a molecular and quantum computational system and introduced the idea of quantum computing inside a cell for making decisions on complex control tasks described by equations of mathematical physics. He approached the brain as a net of molecular computers and created a model of neuron operation based on the transmission of hypersound signals via cytoskeleton where the molecular computational system encodes the digital output. In 1979 Liberman published a hypothesis of human self-consciousness associated with not a chemical, but with a physical quantum coherent system and named it "extremal quantum regulator". We review here the contributions of Liberman in understanding the mechanisms of intracellular processing of information and his efforts to create an integrative theory of natural computation that aims to unite biology, physics and mathematics.

Efim Liberman toward the comprehension of the phenomenon of life

Efim Liberman was a proud scholar of biophysics-a genuine scientific discipline that strives for high accuracy in contrast to descriptive biology. He played a major role at the Pushchino Institute of Biophysics and participated in Gelfand's famous seminar. He developed a groundbreaking model of neural impulses and discovered the decisive role of cell membranes and membrane channels in neural cell excitation. Efim Liberman studied artificial and biological membranes, and conducted seminal experiments to proof Mitchell's hypothesis of oxidative phosphorylation. He discovered penetrating ions in pioneering studies of mitochondrial electrical energetics. He put forward a trailblazing idea of an intracell analog-digital molecular computer capable of using genetically coded algorithms for processing information. His ideas and research gave impetus to academic studies in various areas, such as a role of small RNАs as universal regulators of life. Efim Liberman was an outstanding, versatile and bright personality whose lifelong journey was to pursue the comprehension of the Universe and to understand the phenomenon of life.

Mechanism of Energy Storage and Transformation in the Mitochondria at the Water-Membrane Interface

In this review, we discuss the mechanisms of generation of membrane-bound protons using different energy sources in model and natural systems. Analysis of these mechanisms revealed that all three types of reactions include the same principal stage, which is dissociation of electrically neutral Brønsted acids at the interface during transition from the hydrophobic phase to water with a low dielectric constant. Special attention is paid to the fact that in one of the analyzed model systems, membrane-bound protons provide energy for the reaction of ATP synthesis. Similar mechanism for the generation of membrane-bound protons has been found in natural membranes involved in oxidative phosphorylation, in particular, on the membranes of mitoplasts and mitochondria. The energy of oxidative reactions required for ATP synthesis, is stored at the intermediate stage not only in the form of transmembrane electrochemical potential of protons, but also and perhaps mostly, as protons attached to the inner mitochondrial membrane. The process of energy storage in mitochondria is linked to the transfer of protons that simultaneously perform two functions. Protons on the membrane surface carry free energy and, at the same time, act as substrates facilitating the movement of F₁F₀-ATP-synthase biological machine.

Fifty Years of Research on Protonophores: Mitochondrial Uncoupling As a Basis for Therapeutic Action

Protonophores are compounds capable of electrogenic transport of protons across membranes. Protonophores have been intensively studied over the past 50 years owing to their ability to uncouple oxidation and phosphorylation in mitochondria and chloroplasts. The action mechanism of classical uncouplers, such as DNP and CCCP, in mitochondria is believed to be related to their protonophoric activity; i.e., their ability to transfer protons across the lipid part of the mitochondrial membrane. Given the recently revealed deviations in the correlation between the protonophoric activity of some uncouplers and their ability to stimulate mitochondrial respiration, this review addresses the involvement of some proteins of the inner mitochondrial membrane, such as the ATP/ADP antiporter, dicarboxylate carrier, and ATPase, in the uncoupling process. However, these deviations do not contradict the Mitchell theory but point to a more complex nature of the interaction of DNP, CCCP, and other uncouplers with mitochondrial membranes. Therefore, a detailed investigation of the action mechanism of uncouplers is required for a more successful pharmacological use, including their antibacterial, antiviral, anticancer, as well as cardio-, neuro-, and nephroprotective effects.

Electrophysiological Characterization of Microbial Rhodopsin Transport Properties: Electrometric and ΔpH Measurements Using Planar Lipid Bilayer, Collodion Film, and Fluorescent Probe Approaches

Electrophysiological approaches to the study of the activity of retinal-containing protein bacteriorhodopsin (bR) or other proteins of this family are based usually on measurements of electrical current through a planar bilayer lipid membrane (BLM) with proteoliposomes attached to the BLM surface at one side of the membrane. Here, we describe the measurements of the pumping activity of bR and channelrhodopsin 2 (ChR2) with special attention to the study of voltage dependence of the light-induced currents. Strong voltage dependence of ChR2 suggests light-triggered ion channel activity of ChR2. We also describe electrophysiological measurements with the help of collodion film instead of BLM for the measurements of fast stages of a rhodopsin photocycle as well as the estimation of the activity of proteoliposomes without a macro membrane using fluorescent probes such as oxonol VI or 9-aminoacridine.

Rhodopsin Channel Activity Can Be Evaluated by Measuring the Photocurrent Voltage Dependence in Planar Bilayer Lipid Membranes

The studies of the functional properties of retinal-containing proteins often include experiments in model membrane systems, e.g., measurements of electric current through planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one of the membrane surfaces. However, the possibilities of this method have not been fully explored yet. We demonstrated that the voltage dependence of stationary photocurrents for two light-sensitive proteins, bacteriorhodopsin (bR) and channelrhodopsin 2 (ChR2), in the presence of protonophore had very different characteristics. In the case of the bR (proton pump), the photocurrent through the BLM did not change direction when the polarity of the applied voltage was switched. In the case of the photosensitive channel protein ChR2, the photocurrent increased with the increase in voltage and the current polarity changed with the change in the voltage polarity. The protonophore 4,5,6,7-tetrachloro-2-trifluoromethyl benzimidazole (TTFB) was more efficient in the maximizing stationary photocurrents. In the presence of carbonyl cyanide-m-chlorophenylhydrazone (CCCP), the amplitude of the measured photocurrents for bR significantly decreased, while in the case of ChR2, the photocurrents virtually disappeared. The difference between the effects of TTFB and CCCP was apparently due to the fact that, in contrast to TTFB, CCCP transfers protons across the liposome membranes with a higher rate than through the decane-containing BLM used as a surface for the proteoliposome adsorption.

Current problems and future avenues in proteoliposome research

Membrane proteins (MPs) are the gatekeepers between different biological compartments separated by lipid bilayers. Being receptors, channels, transporters, or primary pumps, they fulfill a wide variety of cellular functions and their importance is reflected in the increasing number of drugs that target MPs. Functional studies of MPs within a native cellular context, however, is difficult due to the innate complexity of the densely packed membranes. Over the past decades, detergent-based extraction and purification of MPs and their reconstitution into lipid mimetic systems has been a very powerful tool to simplify the experimental system. In this review, we focus on proteoliposomes that have become an indispensable experimental system for enzymes with a vectorial function, including many of the here described energy transducing MPs. We first address long standing questions on the difficulty of successful reconstitution and controlled orientation of MPs into liposomes. A special emphasis is given on coreconstitution of several MPs into the same bilayer. Second, we discuss recent progress in the development of fluorescent dyes that offer sensitive detection with high temporal resolution. Finally, we briefly cover the use of giant unilamellar vesicles for the investigation of complex enzymatic cascades, a very promising experimental tool considering our increasing knowledge of the interplay of different cellular components.

Specific inhibition of proton pumping by the T315V mutation in the K channel of cytochrome ba3 from Thermus thermophilus

Cytochrome ba₃ from Thermus thermophilus belongs to the B family of heme-copper oxidases and pumps protons across the membrane with an as yet unknown mechanism. The K channel of the A family heme-copper oxidases provides delivery of a substrate proton from the internal water phase to the binuclear heme-copper center (BNC) during the reductive phase of the catalytic cycle, while the D channel is responsible for transferring both substrate and pumped protons. By contrast, in the B family oxidases there is no D-channel and the structural equivalent of the K channel seems to be responsible for the transfer of both categories of protons. Here we have studied the effect of the T315V substitution in the K channel on the kinetics of membrane potential generation coupled to the oxidative half-reaction of the catalytic cycle of cytochrome ba₃. The results suggest that the mutated enzyme does not pump protons during the reaction of the fully reduced form with molecular oxygen in a single turnover. Specific inhibition of proton pumping in the T315V mutant appears to be a consequence of inability to provide rapid (τ ~ 100 μs) reprotonation of the internal transient proton donor(s) of the K channel. In contrast to the A family, the K channel of the B-type oxidases is necessary for the electrogenic transfer of both pumped and substrate protons during the oxidative half-reaction of the catalytic cycle.

The Mechanisms of Electrogenic Reactions in Bacterial Photosynthetic Reaction Centers: Studies in Collaboration with Alexander Konstantinov

In this review, we discuss our studies conducted in 1985-1988 in collaboration with A. A. Konstantinov, one of the top scientists in the field of membrane bioenergetics. Studying fast kinetics of membrane potential generation in photosynthetic reaction centers (RCs) of purple bacteria in response to a laser flash has made it possible to examine in detail the mechanisms of electrogenic reactions at the donor and acceptor sides of RCs. Electrogenesis associated with the intraprotein electron transfer from the exogenous secondary donors, redox dyes, and soluble cytochrome (cyt) c to the photooxidized dimer of bacteriochlorophyll P₈₇₀ was studied using proteoliposomes containing RCs from the non-sulfur purple bacterium Rhodospirillum rubrum. It was found that reduction of the secondary quinone electron acceptor Q_B accompanied by its protonation in the chromatophores from R. rubrum in response to every second light flash was electrogenic. Spectral characteristics and redox potentials of the four hemes in the tightly bound cyt c in the RC of Blastochloris viridis and electrogenic reactions associated with the electron transfer within the RC complex were identified. For the first time, relative amplitudes of the membrane potential generated in the course of individual electrogenic reactions were compared with the distances between the redox cofactors determined based on the three-dimensional structure of the Bl. viridis RC.

Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space

In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.

Photovoltage generation by photosystem II core complexes immobilized onto a Millipore filter on an indium tin oxide electrode

The light-induced functioning of photosynthetic pigment-protein complex of photosystem II (PSII) is linked to the vectorial translocation of charges across the membrane, which results in the formation of voltage. Direct measurement of the light-induced voltage (∆V) generated by spinach oxygen-evolving PSII core complexes adsorbed onto a Millipore membrane filter (MF) on an indium tin oxide (ITO) electrode under continuous illumination has been performed. PSII was shown to participate in electron transfer from water to the ITO electrode, resulting in ∆V generation. No photovoltage was detected in PSII deprived of the water-oxidizing complex. The maximal and stable photoelectric signal was observed in the presence of disaccharide trehalose and 2,6-dichloro-1,4-benzoquinone, acting as a redox mediator between the primary quinone acceptor Q_A of PSII and electrode surface. Long time preservation of the steady-state photoactivity at room temperature in a simple in design ITO|PSII-MF|ITO system may be related to the retention of water molecules attached to the PSII surface in the presence of trehalose.

High-resolution structural insights into the heliorhodopsin family

Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.

Electron Transfer on the Donor Side of Manganese-Depleted Photosystem 2

After removal of manganese ions responsible for light-driven water oxidation, redox-active tyrosine Y_Z (tyrosine 161 of the D1 subunit) still remains the dominant electron donor to the photooxidized chlorophyll P₆₈₀ (P₆₈₀⁺) in the reaction center of photosystem 2 (PS2). Here, we investigated P₆₈₀⁺ reduction by Y_Z under single-turnover flashes in Mn-depleted PS2 core complexes in the presence of weak acids and NH₄Cl. Analysis of changes in the light-induced absorption at 830 nm (reflecting P₆₈₀ redox transitions) at pH 6.0 showed that P₆₈₀⁺ reduction is well approximated by two kinetic components with the characteristic times (τ) of ~7 and ~31 μs and relative contributions of ~54 and ~37%, respectively. In contrast to the very small effect of sodium formate (200 mM), addition of sodium acetate and NH₄Cl increased the rate of electron transfer between Y_Z and P₆₈₀⁺ approx. by a factor of 5. The suggestion that direct electron transfer from Y_Z to P₆₈₀⁺ has a biphasic kinetics and reflects the presence of two different populations of PS2 centers was confirmed by the data obtained using direct electrometrical technique. It was demonstrated that the submillisecond two-phase kinetics of the additional electrogenic phase in the kinetics of photoelectric response due to the electron transfer between Y_Z and P₆₈₀⁺ is significantly accelerated in the presence of acetate or ammonia. These results contribute to the understanding of the mechanism of interaction between the oxidized tyrosine Y_Z and exogenous substances (including synthetic manganese-containing compounds) capable of photooxidation of water molecule in the manganese-depleted PS2 complexes.

Time-resolved generation of membrane potential by ba3 cytochrome c oxidase from Thermus thermophilus coupled to single electron injection into the O and OH states

Two electrogenic phases with characteristic times of ~14μs and ~290μs are resolved in the kinetics of membrane potential generation coupled to single-electron reduction of the oxidized "relaxed" O state of ba₃ oxidase from T. thermophilus (O→E transition). The rapid phase reflects electron redistribution between Cu_A and heme b. The slow phase includes electron redistribution from both Cu_A and heme b to heme a₃, and electrogenic proton transfer coupled to reduction of heme a₃. The distance of proton translocation corresponds to uptake of a proton from the inner water phase into the binuclear center where heme a₃ is reduced, but there is no proton pumping and no reduction of Cu_B. Single-electron reduction of the oxidized "unrelaxed" state (O_H→E_H transition) is accompanied by electrogenic reduction of the heme b/heme a₃ pair by Cu_A in a "fast" phase (~22μs) and transfer of protons in "middle" and "slow" electrogenic phases (~0.185ms and ~0.78ms) coupled to electron redistribution from the heme b/heme a₃ pair to the Cu_B site. The "middle" and "slow" electrogenic phases seem to be associated with transfer of protons to the proton-loading site (PLS) of the proton pump, but when all injected electrons reach Cu_B the electronic charge appears to be compensated by back-leakage of the protons from the PLS into the binuclear site. Thus proton pumping occurs only to the extent of ~0.1 H⁺/e^-, probably due to the formed membrane potential in the experiment.

Analyzing the electrogenicity of cytochrome c oxidase

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically "invisible" steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

Real-time kinetics of electrogenic Na(+) transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95

Discovery of the light-driven sodium-motive pump Na⁺-rhodopsin (NaR) has initiated studies of the molecular mechanism of this novel membrane-linked energy transducer. In this paper, we investigated the photocycle of NaR from the marine flavobacterium Dokdonia sp. PRO95 and identified electrogenic and Na⁺-dependent steps of this cycle. We found that the NaR photocycle is composed of at least four steps: NaR₅₁₉ + hv → K₅₈₅ → (L₄₅₀↔M₄₉₅) → O₅₈₅ → NaR₅₁₉. The third step is the only step that depends on the Na⁺ concentration inside right-side-out NaR-containing proteoliposomes, indicating that this step is coupled with Na⁺ binding to NaR. For steps 2, 3, and 4, the values of the rate constants are 4×10⁴ s^–1, 4.7 × 10³ M^–1 s^–1, and 150 s^–1, respectively. These steps contributed 15, 15, and 70% of the total membrane electric potential (Δψ ~ 200 mV) generated by a single turnover of NaR incorporated into liposomes and attached to phospholipid-impregnated collodion film. On the basis of these observations, a mechanism of light-driven Na⁺ pumping by NaR is suggested.

Modeling gating charge and voltage changes in response to charge separation in membrane proteins

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on mechanisms of charge transport and displacement processes. A recent example is provided by studies of cytochrome c oxidase. However, the interpretation of the observed voltage changes in terms of the number of charge equivalents and transfer distances is far from being trivial or unique. Using continuum approaches to describe the voltage generation may involve significant uncertainties and reliable microscopic simulations are not yet available. Here, we attempt to solve this problem by using a coarse-grained model of membrane proteins, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The model evaluates the gating charges and the electrode potentials (c.f. measured voltage) upon charge transfer within the protein. The accuracy of the model is evaluated by a comparison of measured voltage changes associated with electron and proton transfer in bacterial photosynthetic reaction centers to those calculated using our coarse-grained model. The calculations reproduce the experimental observations and thus indicate that the method is of general use. Interestingly, it is found that charge-separation processes with different spatial directions (but the same distance perpendicular to the membrane) can give similar observed voltage changes, which indicates that caution should be exercised when using simplified interpretation of the relationship between charge displacement and voltage changes.

Gloeobacter rhodopsin, limitation of proton pumping at high electrochemical load

We studied the photocurrents of a cyanobacterial rhodopsin Gloeobacter violaceus (GR) in Xenopus laevis oocytes and HEK-293 cells. This protein is a light-driven proton pump with striking similarities to marine proteorhodopsins, including the D121-H87 cluster of the retinal Schiff base counterion and a glutamate at position 132 that acts as a proton donor for chromophore reprotonation during the photocycle. Interestingly, at low extracellular pH(o) and negative voltage, the proton flux inverted and directed inward. Using electrophysiological measurements of wild-type and mutant GR, we demonstrate that the electrochemical gradient limits outward-directed proton pumping and converts it into a purely passive proton influx. This conclusion contradicts the contemporary paradigm that at low pH, proteorhodopsins actively transport H(+) into cells. We identified E132 and S77 as key residues that allow inward directed diffusion. Substitution of E132 with aspartate or S77 with either alanine or cysteine abolished the inward-directed current almost completely. The proton influx is likely caused by the pK(a) of E132 in GR, which is lower than that of other microbial ion pumping rhodopsins. The advantage of such a low pK(a) is an acceleration of the photocycle and high pump turnover at high light intensities.

Of ion pumps, sensors and channels - perspectives on microbial rhodopsins between science and history

We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl⁻ into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

Electrophysiological characterization of membrane transport proteins

Active transport in biological membranes has been traditionally studied using a variety of biochemical and biophysical techniques, including electrophysiology. This review focuses on aspects of electrophysiological methods that make them particularly suited for the investigation of transporter function. Two major approaches to electrical recording of transporter activity are discussed: (a) artificial planar lipid membranes, such as the black lipid membrane and solid supported membrane, which are useful for studies on bacterial transporters and transporters of intracellular compartments, and (b) patch clamp and voltage clamp techniques, which investigate transporters in native cellular membranes. The analytical power of these methods is highlighted by several examples of mechanistic studies of specific membrane proteins, including cytochrome c oxidase, NhaA Na(+)/H(+) exchanger, ClC-7 H(+)/Cl(-) exchanger, glutamate transporters, and neutral amino acid transporters. These examples reveal the wealth of mechanistic information that can be obtained when electrophysiological methods are used in combination with rapid perturbation approaches.

Initiation of the proton pump of cytochrome c oxidase

Cytochrome c oxidase is the terminal enzyme of the respiratory chain that is responsible for biological energy conversion in mitochondria and aerobic bacteria. The membrane-bound enzyme converts free energy from oxygen reduction to an electrochemical proton gradient by functioning as a redox-coupled proton pump. Although the 3D structure and functional studies have revealed proton conducting pathways in the enzyme interior, the location of proton donor and acceptor groups are not fully identified. We show here by time-resolved optical and FTIR spectroscopy combined with time-resolved electrometry that some mutant enzymes incapable of proton pumping nevertheless initiate catalysis by proton transfer to a proton-loading site. A conserved tyrosine in the so-called D-channel is identified as a potential proton donor that determines the efficiency of this reaction.

Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel

The N139L substitution in the D-channel of cytochrome oxidase from Rhodobacter sphaeroides results in an approximately 15-fold decrease in the turnover number and a loss of proton pumping. Time-resolved absorption and electrometric assays of the F --> O transition in the N139L mutant oxidase result in three major findings. (1) Oxidation of the reduced enzyme by O(2) shows approximately 200-fold inhibition of the F --> O step (k approximately 2 s(-1) at pH 8) which is not compatible with enzyme turnover ( approximately 30 s(-1)). Presumably, an abnormal intermediate F(deprotonated) is formed under these conditions, one proton-deficient relative to a normal F state. In contrast, the F --> O transition in N139L oxidase induced by single-electron photoreduction of intermediate F, generated by reaction of the oxidized enzyme with H(2)O(2), decelerates to an extent compatible with enzyme turnover. (2) In the N139L mutant, the protonic phase of Deltapsi generation coupled to the flash-induced F --> O transition greatly decreases in rate and magnitude and can be assigned to the movement of a proton from E286 to the binuclear site, required for reduction of heme a(3) from the Fe(4+) horizontal lineO(2-) state to the Fe(3+)-OH(-) state. Electrogenic reprotonation of E286 from the inner aqueous phase is missing from the F --> O step in the mutant. (3) In the N139L mutant, the KCN-insensitive rapid electrogenic phase may be composed of two components with lifetimes of approximately 10 and approximately 40 mus and a magnitude ratio of approximately 3:2. The 10 mus phase matches vectorial electron transfer from Cu(A) to heme a, whereas the 40 mus component is assigned to intraprotein proton displacement across approximately 20% of the membrane dielectric thickness. This proton displacement might be triggered by rotation of the charged K362 side chain coupled to heme a reduction. The two components of the rapid electrogenic phase have been resolved subsequently with other D-channel mutants as well as with cyanide-inhibited wild-type oxidase. The finding helps to reconcile the unusually high relative contribution of the microsecond electrogenic phase in the bacterial enzyme ( approximately 30%) with the net electrogenicity of the F --> O transition coupled to transmembrane transfer of two charges per electron.

Elevated proton leak of the intermediate OH in cytochrome c oxidase

The kinetics of the formation and relaxation of transmembrane electric potential (Deltapsi) during the complete single turnover of CcO was studied in the bovine heart mitochondrial and the aa(3)-type Paracoccus denitrificans enzymes incorporated into proteoliposome membrane. The real-time Deltapsi kinetics was followed by the direct electrometry technique. The prompt oxidation of CcO and formation of the activated, oxidized (O(H)) state of the enzyme leaves the enzyme trapped in the open state that provides an internal leak for protons and thus facilitates dissipation of Deltapsi (tau(app) < or = 0.5-0.8 s). By contrast, when the enzyme in the O(H) state is rapidly re-reduced by sequential electron delivery, Deltapsi dissipates much slower (tau(app) > 3 s). In P. denitrificans CcO proteoliposomes the accelerated Deltapsi dissipation is slowed down by a mutational block of the proton conductance through the D-, but not K-channel. We concluded that in contrast to the other intermediates the O(H) state of CcO is vulnerable to the elevated internal proton leak that proceeds via the D-channel.

The proton donor for O-O bond scission by cytochrome c oxidase

Cytochrome c oxidase is the main catalyst of oxygen consumption in mitochondria and many aerobic bacteria. The key step in oxygen reduction is scission of the O-O bond and formation of an intermediate P(R) of the binuclear active site composed of heme a(3) and Cu(B). The donor of the proton required for this reaction has been suggested to be a unique tyrosine residue (Tyr-280) covalently cross-linked to one of the histidine ligands of Cu(B). To test this idea we used the Glu-278-Gln mutant enzyme from Paracoccus denitrificans, in which the reaction with oxygen stops at the P(R) intermediate. Three different time-resolved techniques were used. Optical spectroscopy showed fast (approximately 60 micros) appearance of the P(R) species along with full oxidation of heme a, and FTIR spectroscopy revealed a band at 1,308 cm(-1), which is characteristic for the deprotonated form of the cross-linked Tyr-280. The development of electric potential during formation of the P(R) species suggests transfer of a proton over a distance of approximately 4 A perpendicular to the membrane plane, which is close to the distance between the oxygen atom of the hydroxyl group of Tyr-280 and the bound oxygen. These results strongly support the hypothesis that the cross-linked tyrosine is the proton donor for O-O bond cleavage by cytochrome c oxidase and strengthens the view that this tyrosine also provides the fourth electron in O(2) reduction in conditions where heme a is oxidized.

The purple membrane of Halobacterium halobium: a new system for light energy conversion

Patches of a distinctly different structure from the rest of the cell membrane occur in Halobacterium halobium. The isolated patches are called the purple membrane. It derives its colour from a retinal-protein complex, bacteriorhodopsin, which is the only protein species in this membrane serving a phototransducing function. Light energy is converted by a photochemical cycle going on continuously under illumination and accompanied by a cyclic release and uptake of protons. In the intact cell, this cycle operates as a vectorial process and therefore builds up an electrochemical gradient across the cell membrane conserving part of the absorbed light energy. The cell apparently uses this electrochemical gradient for the synthesis of ATP. Photophosphorylation is shown to be insensitive to cyanide but sensitive to dicyclohexylcarbodiimide (DCCD) and uncouplers. The concentration of ATP and the pH are tightly coupled but can be uncoupled by DCCD. Bacteriorhodopsin, as a light-driven proton pump, can then be studied in the cell as an isolated process. Quantitation of light energy conversion is possible by the indirect method of inhibition of respiration by light and the comparison of the number of absorbed quanta which prevent consumption of one molecule of oxygen.

Charge transfer in P-type ATPases investigated on planar membranes

Planar lipid bilayers, e.g., black lipid membranes (BLM) and solid supported membranes (SSM), have been employed to investigate charge movements during the reaction cycle of P-type ATPases. The BLM/SSM method allows a direct measurement of the electrical currents generated by the cation transporter following chemical activation by a substrate concentration jump. The electrical current transients provides information about the reaction mechanism of the enzyme. In particular, the BLM/SSM technique allows identification of electrogenic steps which in turn may be used to localize ion translocation during the reaction cycle of the pump. In addition, using the high time resolution of the technique, especially when rapid activation via caged ATP is employed, rate constants of electrogenic and electroneutral steps can be determined. In the present review, we will discuss the main results obtained by the BLM and SSM methods and how they have contributed to unravel the transport mechanism of P-type ATPases.

Molecular mechanism of proton translocation by cytochrome c oxidase

Cytochrome c oxidase (CcO) is a terminal protein of the respiratory chain in eukaryotes and some bacteria. It catalyzes most of the biologic oxygen consumption on earth done by aerobic organisms. During the catalytic reaction, CcO reduces dioxygen to water and uses the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-linked proton pump. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. Thus, additional extensive studies of CcO by varieties of biophysical and biochemical approaches are involved to shed light on the mechanism of proton translocation. In this review, we summarize the current level of knowledge about CcO, including the latest model developed to explain the CcO proton-pumping mechanism.