Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.     

TRANSFORMATION OF A BOP-HOP-SOP-I-SOP-II-Halobacterium halobium MUTANT TO BOP+: EFFECTS OF BACTERIORHODOPSIN PHOTOACTIVATION ON CELLULAR PROTON FLUXES AND SWIMMING BEHAVIOR

We have transformed Pho81, a Halobacterium halobium mutant strain which does not contain any of the four retinylidene proteins known in this species, with the bop gene cluster to create Pho81BR, a BR+HR-SR-I-SR-II-strain. The absorption spectrum, pigment reconstitution process, light-dark adaptation and photochemical reaction cycle of the expressed protein are indistinguishable from those of native bacteriorhodopsin (BR) in purple membrane of wild type strains. Strain Pho81BR permits for the first time characterization of effects of BR photoactivation alone on cell swimming behavior and energetics in the absence of the spectrally similar phototaxis receptor sensory rhodopsin I (SR-I) and electrogenic chloride pump halorhodopsin (HR). A non-adaptive upward shift in spontaneous swimming reversal frequency occurs following 3 s of continuous illumination of Pho81BR cells with green light (550 +/- 20 nm). This effect is abolished by low concentrations of the proton ionophore carbonylcyanide m-chlorophenylhydrazone. Although BR does not mediate phototaxis responses in energized Pho81BR cells under our culture conditions, proton pumping by BR in Pho81BR cells partially deenergized by inhibitors of respiration and adenosine triphosphate synthesis results in a small attractant response. Based on our measurements, we attribute the observed effects of BR photoactivation on swimming behavior to secondary consequences of electrogenic proton pumping on metabolic or signal transduction pathways, rather than to primary sensory signaling such as that mediated by SR-I. Proton extrusion by BR activates gated proton influx ports resulting in net proton uptake in wild-type cells.(ABSTRACT TRUNCATED AT 250 WORDS)     

Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping across the inner-mitochondrial membrane, a process that results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping remains unknown. In the present paper, continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine heart cytochrome c oxidase for different redox states of the enzyme along its catalytic cycle. Three different computational models of the enzyme were employed to test the stability of the results. The energetics and pH dependence of the P-->F, F-->O, and O-->E steps of the cycle have been investigated. On the basis of electrostatic calculations, two possible schemes of redox-linked proton pumping are discussed. The first scheme involves His291 as a pump element, whereas the second scheme involves a group linked to propionate D of heme a(3). In both schemes, loading of the pump site is coupled to ET between the two hemes of the enzyme, while transfer of a chemical proton is accompanied by ejection of the pumped H(+). The two models, as well as the energetics results are compared with recent experimental kinetic data. The proton pumping across the membrane is an endergonic process, which requires a sufficient amount of energy to be provided by the chemical reaction in the active site. In our calculations, the conversion of OH(-) to H(2)O provides 520 meV of energy to displace pump protons from a loading site and overall about 635 meV for each electron passing through the system. Assuming that the two charges are translocated per electron against the membrane potential of 200 meV, the model predicts an overall efficiency of 63%.     

Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case

The Density functional theory (B3LYP) has been used to study the mechanisms of O--O bond cleavage and proton pumping in cytochrome c oxidase. To understand how the energy from the exergonic reduction of molecular oxygen is used to pump protons across the mitochondrial membrane, the energetics of all steps in the catalytic cycle have to be evaluated. For this purpose, models have to be designed that can accurately reproduce relative redox potentials and pKa values within the active site. The present study shows that it is possible to construct such models and to calculate energy profiles which, to a large extent, agree with experimental information. However, the energy profiles point out a problem with an unbalanced partitioning of the energy between the reductive and oxidative half cycles, which is in disagreement with the experimental observation that the proton pumping is evenly distributed between the two half cycles. A conclusion from the present study is, therefore, that something is probably still missing in the modeling of the active site.     

Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interaction and potential energy surfaces

The energetics of proton transfer in liquid water investigated by using ab initio calculation. The molecular electronic interaction of hydrated proton clusters in classified into many-body interaction elements by a new energy decomposition method. It is found that up to three-body molecular interaction is essential to describe the potential energy surface. The three-body effect mainly arises from the (non-classical) charge transfer and strongly depends on their configuration. Higher than three-body effects are small enough to be neglected. To simulate the liquid state reactions, two cluster models including all water molecules up to the second shell in the proton transfer reactions are employed. It is shown that these proton transfer reactions only involve small potential energy barriers of a few kcal/mol or less when structural rearrangement of the solvent is induced along the proton movement.     

BIOSYNTHESIS AND ASSEMBLY OF PURPLE MEMBRANE OF HALOBACTERIUM HALOBIUM S9: LIGHT STIMULATION OF BACTERIORHODOPSIN FORMATION

Abstract— The effect of light on purple membrane biogenesis in Halobacterium halobium S9 strain was investigated. When bacteria were grown in the dark, the 570nm absorption due to bacteriorhodopsin increased more slowly than under illumination, but eventually after longer incubation, reached the same level as that seen in the illuminated culture.
Analysis of membrane fractions by sucrose density gradient centrifugation revealed that two different membrane fractions, containing purple and brown membrane could be detected in the exponential growth phase. Another fraction whose density was higher than that of purple membrane, disappeared concomitantly with the increase in purple membrane and brown membrane, indicating that it may be related to purple membrane formation.
HPLC analysis of membrane proteins showed that there was no significant difference in de novo synthesis of bacterio–opsin between dark and illuminated cultures. This led us to conclude that light stimulated retinal binding to bacterio–opsin and/or retinal biosynthesis rather than bacterio–opsin synthesis. Bacteriorhodopsin seemed to form the brown membrane fraction first, which then spontaneously reorganized into purple membrane.
When incorporated in liposomes, bacteriorhodopsin in brown membrane was found to have rather higher proton pump activity than that in purple membrane. The H⁺ pumping activity was quite heat labile. This and the CD spectra indicated that bacteriorhodopsin in brown membrane might exist without forming normal timer unit.     

Light‐Gated Synthetic Protocells for Plasmon‐Enhanced Chemiosmotic Gradient Generation and ATP Synthesis

Herein, we present a light‐gated protocell model made of plasmonic colloidal capsules (CCs) assembled with bacteriorhodopsin for converting solar energy into electrochemical gradients to drive the synthesis of energy‐storage molecules. This synthetic protocell incorporated an important intrinsic property of noble metal colloidal particles, namely, plasmonic resonance. In particular, the near‐field coupling between adjacent metal nanoparticles gave rise to strongly localized electric fields and resulted in a broad absorption in the whole visible spectra, which in turn promoted the flux of photons to bacteriorhodopsin and accelerated the proton pumping kinetics. The cell‐like potential of this design was further demonstrated by leveraging the outward pumped protons as “chemical signals” for triggering ATP biosynthesis in a coexistent synthetic protocell population. Hereby, we lay the ground work for the engineering of colloidal supraparticle‐based synthetic protocells with higher‐order functionalities.     

A quantum theory atoms in molecules investigation of Lewis base protonation

This investigation uses atomic properties derived from the quantum theory of atoms in molecules formalism to rationalize the infrared intensity of the stretching vibration that arises as a Lewis base (B) is protonated (B‐H mode). Moreover, the interacting quantum atom (IQA) partition is employed to evaluate the energetics of protonation. All calculations are performed at the CCSD/cc‐pVQZ level except by the IQA analysis, which is carried out by means of the B3LYP/cc‐pVQZ//CCSD/cc‐pVQZ treatment. First, an efficiency scale is established for Lewis bases in terms of the electronic charge transfer potential. Next, this study shows that the intensity of the B‐H stretching depends mostly on the electronic charge amount transferred to the proton. Thus, intensity data provide empirical assessment of Lewis base charge transfer efficiency. Finally, the group separation observed during correlation of proton affinities and electronic charge transfer potential is explained by the interaction energy between fragments of the protonated system.     

Model for proton transport coupled to protein conformational change: application to proton pumping in the bacteriorhodopsin photocycle

A modeling method is presented for protein systems in which proton transport is coupled to conformational change, as in proton pumps and in motors driven by the proton-motive force. Previously developed methods for calculating pKa values in proteins using a macroscopic dielectric model are extended beyond the equilibrium case to a master-equation model for the time evolution of the system through states defined by ionization microstate and a discrete set of conformers. The macroscopic dielectric model supplies free energy changes for changes of protonation microstate, while the method for obtaining the energetics of conformational change and the relaxation rates, the other ingredients needed for the master equation, are system dependent. The method is applied to the photoactivated proton pump, bacteriorhodopsin, using conformational free energy differences from experiment and treating relaxation rates through three adjustable parameters. The model is found to pump protons with an efficiency relatively insensitive to parameter choice over a wide range of parameter values, and most of the main features of the known photocycle from very early M to the return to the resting state are reproduced. The boundaries of these parameter ranges are such that short-range proton transfers are faster than longer-range ones, which in turn are faster than conformational changes. No relaxation rates depend on conformation. The results suggest that an "accessibility switch", while not ruled out, is not required and that vectorial proton transport can be achieved through the coupling of the energetics of ionization and conformational states.     

Bacteriorhodopsin as an Example of a Light-Driven Proton Pump

Apart from the long known visual pigments, another retinal protein complex exists in nature, viz. bacteriorhodopsin from halobacteria. In contrast to the visual pigments such as the rhodopsins, which act as light sensors in the eye, bacteriorhodopsin actually transforms light energy. This energy conversion is connected with the asymmetric incorporation of bacteriorhodopsin in the lattice structure of the purple membrane which forms patches on the cell surface of halobacteria. Alongside the chlorophyll system, the purple membrane system represents the second light energy conversion principle to be discovered in living nature. Bacteriorhodopsin acts as a light-driven proton pump or as the main component of such a pump system. Absorption of light triggers off a cycle of reactions coupled with the spatially oriented uptake and release of a proton. In the intact cell an electrochemical gradient is thus built up across the cell membrane of the bacterium in which part of the absorbed light energy is stored and which is not dependent upon redox processes as in the case of respiration or photosynthesis. This electrochemical gradient can supply the energy required for ATP synthesis in the cell; a reversible proton-translocating ATPase serves as catalyst system.     

Interface energetics and engineering of organic heterostructures in organic photovoltaic cells

The reliable information about interface energetics of organic materials, especially the energy level alignment at organic heterostructures is of pronounced importance for unraveling the photon harvesting and charge separation process in organic photovoltaic(OPV) cells. This article provides an overview of interface energetics at typical planar and mixed donor-acceptor heterostructures, perovskite/organic hybrid interfaces, and their contact interfaces with charge collection layers. The substrate effect on energy level offsets at organic heterostructures and the processes that control and limit the OPV operation are presented. Recent efforts on interface engineering with electrical doping are also discussed.     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions

The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.     

THE EFFECT OF CROSS-LINKING ON PHOTOCYCLING ACTIVITY OF BACTERIORHODOPSIN

Abstract— Purple membrane preparations from Halobacterium halobium were chemically modified with imidoesters. Dimethyl adipimidate (8.3 Å chain length) amidinates about five of the six free lysine residues whereas dimethyl suberimidate (11.3 Å) under the same conditions reacts with only 2–3 residues. Gel electrophoresis showed that the shorter chain length imidoesters were less effective than dimethyl suberimidate in oligomer formation. However, dimethyl adipimidate resulted in a more marked inhibition of the photoreaction activity. Monofunctional imidates, methyl acetimidate and methyl butyrimi-date, at comparable degrees of amidination, did not appreciably affect activity indicating that the presence of bulky groups on the exposed lysine residues does not cause the effects observed. Hence, the introduction of molecular mobility constraints by intramolecular cross-linking slows photocycling, and, therefore, inhibits proton pumping activity of bacteriorhodopsin. This indicates that conforma-tional changes of the protein moiety of bacteriorhodopsin occur during photocycling activity.     

ENERGY LEVELS IN CHLOROPHYLL AND ELECTRON TRANSFER PROCESSES*,†

Abstract— A brief account of the localized model for charge carrier generation in solid dyes is given, and generalized to include transfers of electrons and holes between unlike molecules. A part of the experimental basis for the localized model is the finding that the dye molecule sees its environment as a classical dielectric medium, even when it is composed of like molecules; since the effects of the environment on the ionization energy of chlorophyll are small, a close relationship can be inferred between laboratory energy levels and those effective in the chloro-plast. The measured energy diagrams suggest a very low yield of charge carriers in either pure chlorophyll, but leave open the possibility of a substantial yield at an interface between chlorophylls a and b . The energy levels are consistent with the idea that charge carrier transfers between excited chlorophyll molecules and acceptors take place in the primary process.     

Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin

The membrane protein bacteriorhodopsin contains all-trans-retinal in a binding site lined by amino acid side groups and water molecules that guide the photodynamics of retinal. Upon absorption of light, retinal undergoes a subpicosecond all-trans-->13-cis phototransformation involving torsion around a double bond. The main reaction product triggers later events in the protein that induce pumping of a proton through bacteriorhodopsin. Quantum-chemical calculations suggest that three coupled electronic states, the ground state and two closely lying excited states, are involved in the motion along the torsional reaction coordinate phi. The evolution of the protein-retinal system on these three electronic surfaces has been modelled using the multiple spawning method for non-adiabatic dynamics. We find that, although most of the population transfer occurs on a timescale of 300 fs, some population transfer occurs on a longer timescale, occasionally extending well beyond 1 ps.     

ADENOSINE 5-TRIPHOSPHATE CONTENT AND ENERGY CHARGE DURING PHOTOMORPHOGENESIS OF THE MUSTARD SEEDLING SIN APIS ALBA L.

Abstract— The contents of ATP, ADP and AMP (enzymatic assay) and the rate of respiration (output of CO₂ per h, continuously measured with an infrared CO₂ analyzer) were determined in long-term experiments with intact dark-grown and far-red-light-grown mustard ( Sinapis alba L.) seedlings. While there is a strong effect of far-red light treatment on the respiratory rate (inhibition as well as promotion, depending on the onset of light), an effect on the contents of adenosine nucleotides, and therewith on energy charge, is hardly detectable. At most, there is a tendency that long-term far-red light slightly lowers ATP levels and energy charge. The results suggest that the adenylate system (and therewith the energy charge) in the mustard seedling is controlled by endogenous homoeostasis even under intense phytochrome-mediated photomorphogenesis. It is unlikely that the levels of adenosine nucleotides or the energy charge are links in any causal chain originating from P_fr and leading to phenomena of photomorphogenesis.     

PROPERTIES OF SYNTHETIC BACTERIORHODOPSIN PIGMENTS. FURTHER PROBES OF THE CHROMOPHORE BINDING SITE

Abstract— A series of retinals with specific structural alterations have been synthesized to probe the bacteriorhodopsin binding site. The 4-chloro-, 4-bromo- and 4-iodoretinals all form pigments with bacterioopsin but undergo an in situ displacement of the allylic halogen to form the 4-hydroxyretinal pigment. Several naphthyl retinals were prepared which effectively extend the polyene chain and/or add bulk to the ring portion of the chromophore. All the naphthyl retinals form pigments with bacterioopsin but only the pigment containing the derivative with a polyene side chain identical to that of retinal pumps protons efficiently. The 12-butyl-13-desmethylretinal was also synthesized but this analogue did not form a pigment with bacterioopsin. These results confirm the nonspecificity at the ring portion of the chromophore binding site and the importance of the role of the polyene chain in the proton pumping function of bacteriorhodopsin.