Proton translocation by bacteriorhodopsin and heme-copper oxidases

Computer simulations of ABC transporter componentsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease

Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.

Membrane topology mapping of the Na+-pumping NADH: quinone oxidoreductase from Vibrio cholerae by PhoA-green fluorescent protein fusion analysis

The membrane topologies of the six subunits of Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae were determined by a combination of topology prediction algorithms and the construction of C-terminal fusions. Fusion expression vectors contained either bacterial alkaline phosphatase (phoA) or green fluorescent protein (gfp) genes as reporters of periplasmic and cytoplasmic localization, respectively. A majority of the topology prediction algorithms did not predict any transmembrane helices for NqrA. A lack of PhoA activity when fused to the C terminus of NqrA and the observed fluorescence of the green fluorescent protein C-terminal fusion confirm that this subunit is localized to the cytoplasmic side of the membrane. Analysis of four PhoA fusions for NqrB indicates that this subunit has nine transmembrane helices and that residue T236, the binding site for flavin mononucleotide (FMN), resides in the cytoplasm. Three fusions confirm that the topology of NqrC consists of two transmembrane helices with the FMN binding site at residue T225 on the cytoplasmic side. Fusion analysis of NqrD and NqrE showed almost mirror image topologies, each consisting of six transmembrane helices; the results for NqrD and NqrE are consistent with the topologies of Escherichia coli homologs YdgQ and YdgL, respectively. The NADH, flavin adenine dinucleotide, and Fe-S center binding sites of NqrF were localized to the cytoplasm. The determination of the topologies of the subunits of Na+-NQR provides valuable insights into the location of cofactors and identifies targets for mutagenesis to characterize this enzyme in more detail. The finding that all the redox cofactors are localized to the cytoplasmic side of the membrane is discussed.

Proton transfers in the bacteriorhodopsin photocycle

The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's CuB center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from delta-nitrogen of His291 ligand of CuB center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pKa of His291 for an extended model in which the whole Fe(a3)-CuB center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pKa units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.

Improved Density Functional Theory/Electrostatic Calculation of the His291 Protonation State in Cytochrome c Oxidase: Self-Consistent Charges for Solvation Energy Calculation

The protonation state of His291 in cytochrome c oxidase (CcO), a ligand to the Cu(B) center of the enzyme, has been recently studied in this group by using combined density functional theory (DFT)/electrostatic (QM/MM) calculations. On the basis of these calculations, a model of the proton pumping mechanism of CcO has been proposed. Due to certain technical difficulties, the procedure used in the previous calculation to find partial atomic charges of the QM system for the solvation energy evaluation was not entirely satisfactory; i.e., it was not self-consistent. Here, we describe a procedure that resolves the problem and report on the improved calculations of the protonation state of the His residue. The new procedure fits the protein and reaction field potentials in the region of the QM system with artificial point charges placed on a surface of a sphere surrounding the QM system and a few charges inside the sphere and allows one to perform DFT calculations that involve an inhomogeneous dielectric environment in a self-consistent way. The procedure improves the accuracy of calculations in comparison with previous work. The improved results show, however, that although the absolute energies change significantly the relative energies of the protonated and deprotonated states of His291 remain close to the previously reported ones and therefore do not change significantly the pK(a) values reported earlier. Therefore, our new improved calculations support for the proposed His291 model of the CcO pump.

Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase

Electron transfer in cell respiration is coupled to proton translocation across mitochondrial and bacterial membranes, which is a primary event of biological energy transduction. The resulting electrochemical proton gradient is used to power energy-requiring reactions, such as ATP synthesis. Cytochrome c oxidase is a key component of the respiratory chain, which harnesses dioxygen as a sink for electrons and links O2 reduction to proton pumping. Electrons from cytochrome c are transferred sequentially to the O2 reduction site of cytochrome c oxidase via two other metal centres, Cu(A) and haem a, and this is coupled to vectorial proton transfer across the membrane by a hitherto unknown mechanism. On the basis of the kinetics of proton uptake and release on the two aqueous sides of the membrane, it was recently suggested that proton pumping by cytochrome c oxidase is not mechanistically coupled to internal electron transfer. Here we have monitored translocation of electrical charge equivalents as well as electron transfer within cytochrome c oxidase in real time. The results show that electron transfer from haem a to the O2 reduction site initiates the proton pump mechanism by being kinetically linked to an internal vectorial proton transfer. This reaction drives the proton pump and occurs before relaxation steps in which protons are taken up from the aqueous space on one side of the membrane and released on the other.

Protons @ interfaces: implications for biological energy conversion

The review focuses on the anisotropy of proton transfer at the surface of biological membranes. We consider (i) the data from "pulsed" experiments, where light-triggered enzymes capture or eject protons at the membrane surface, (ii) the electrostatic properties of water at charged interfaces, and (iii) the specific structural attributes of proton-translocating enzymes. The pulsed experiments revealed that proton exchange between the membrane surface and the bulk aqueous phase takes as much as about 1 ms, but could be accelerated by added mobile pH-buffers. Since the accelerating capacity of the latter decreased with the increase in their electric charge, it was concluded that the membrane surface is separated from the bulk aqueous phase by a barrier of electrostatic nature. The barrier could arise owing to the water polarization at the negatively charged membrane surface. The barrier height depends linearly on the charge of penetrating ions; for protons, it has been estimated as about 0.12 eV. While the proton exchange between the surface and the bulk aqueous phase is retarded by the interfacial barrier, the proton diffusion along the membrane, between neighboring enzymes, takes only microseconds. The proton spreading over the membrane is facilitated by the hydrogen-bonded networks at the surface. The membrane-buried layers of these networks can eventually serve as a storage/buffer for protons (proton sponges). As the proton equilibration between the surface and the bulk aqueous phase is slower than the lateral proton diffusion between the "sources" and "sinks", the proton activity at the membrane surface, as sensed by the energy transducing enzymes at steady state, might deviate from that measured in the adjoining water phase. This trait should increase the driving force for ATP synthesis, especially in the case of alkaliphilic bacteria.

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.

Two conformational states of Glu242 and pKas in bovine cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme in the respiratory electron transport chain of aerobic organisms. It catalyses the reduction of atmospheric oxygen to water, and couples this reaction to proton pumping across the membrane; this process generates the electrochemical gradient that subsequently drives the synthesis of ATP. The molecular details of the mechanism by which electron transfer is coupled to proton pumping in CcO is poorly understood. Recent calculations from our group indicate that His291, a ligand of the Cu(B) center of the enzyme, may play the role of the pumping element. In this paper we describe calculations in which a DFT/continuum electrostatic method is used to explore the coupling of the conformational changes of Glu242 residue, the main proton donor of both chemical and pump protons, to its pKa, and the pKa of His291, a putative proton loading site of our pumping model. The computations are done for several redox states of metal centers, different protonation states of Glu242 and His291, and two well-defined conformations of the Glu242 side chain. Thus, in addition to equilibrium redox/protonation states of the catalytic cycle, we also examine the transient and intermediate states. Different dielectric models are employed to investigate the robustness of the results, and their viability in the light of the proposed proton pumping mechanism of CcO. The main results are in agreement with the experimental measurements and support the proposed pumping mechanism. Additionally, the present calculations indicate a possibility of gating through conformational changes of Glu242; namely, in the pumping step, we find that Glu242 needs to be reprotonated before His291 can eject a proton to the P-site of membrane. As a result, the reprotonation of Glu can control proton release from the proton loading site.

Sulfate anion helices formed by the assistance of a flip-flop water chain

A flip-flop extended water structure assists the formation of sulfate anion helices (both left- and right-handed) in a crystalline hydrate of a simple organic-inorganic compound [C6H10N2]SO4. 1.5H2O (1).

Proton transfer pathways in the mutant His-64–Ala of human carbonic anhydrase II

We have investigated the possible proton transfer pathways from the surface of the protein to the zinc-bound water molecule in the mutant His-64-Ala of human carbonic anhydrase II. Starting with an input of known crystallographic structures of the mutant, we model the proton pathways as hydrogen-bonded networks of proton conducting groups and bound solvent molecules. No proton path is detected in the mutant, in close agreement with the experimental observation of a 20-fold decrease in its catalytic efficiency compared to the wild-type enzyme. We also investigate in detail changes in hydration structure at the active site of the mutant and the resulting proton paths in the presence of an exogenous proton donor 4-methylimidazole (4-MI). The proton transfer pathways thus detected are correlated to the observed chemical rescue of catalytic activity by 4-MI.

Acidity of a Cu-Bound Histidine in the Binuclear Center of CytochromecOxidase

Cytochrome c oxidase (CcO) is a crucial enzyme in the respiratory chain. Its function is to couple the reduction of molecular oxygen, which takes place in the Fea3-CuB binuclear center, to proton translocation across the mitochondrial membrane. Although several high-resolution structures of the enzyme are known, the molecular basis of proton pumping activation and its mechanism remain to be elucidated. We examine a recently proposed scheme (J. Am. Chem. Soc. 2004, 126, 1858; FEBS Lett. 2004, 566, 126) that involves the deprotonation of the CuB-bound imidazole ring of a histidine (H291 in mammalian CcO) as a key element in the proton pumping mechanism. The central feature of that proposed mechanism is that the pKa values of the imidazole vary significantly depending on the redox state of the metals in the binuclear center. We use density functional theory in combination with continuum electrostatics to calculate the pKa values, successively in bulk water and within the protein, of the Cu-bound imidazole in various Cu- and Cu-Fe complexes. From pKas in bulk water, we derived a value of -266.34 kcal.mol(-1) for the proton solvation free energy (Delta). This estimate is in close agreement with the experimental value of -264.61 kcal.mol(-1) (J. Am. Chem. Soc. 2001, 123, 7314), which reinforces the conclusion that Delta is more negative than previous values used for pKa calculations. Our approach, on the basis of the study of increasingly more detailed models of the CcO binuclear center at different stages of the catalysis, allows us to examine successively the effect of each of the two metals' redox states and of solvation on the acidity of imidazole, whose pKa is approximately 14 in bulk water. This analysis leads to the following conclusions: first, the effect of Cu ligation on the imidazole acidity is negligible regardless of the redox state of the metal. Second, results obtained for Cu-Fe complexes in bulk water indicate that Cu-bound imidazole pKa values lie within the range of 14.8-16.6 throughout binuclear redox states corresponding to the catalytic cycle, demonstrating that the effect of the Fe oxidation states is also negligible. Finally, the low-dielectric CcO proteic environment shifts the acid-base equilibrium toward a neutral imidazole, further increasing the corresponding pKa values. These results are inconsistent with the proposed role of the Cu-bound histidine as a key element in the pumping mechanism. Limitations of continuum solvation models in pKa calculations are discussed.

The timing of proton migration in membrane-reconstituted cytochrome c oxidase

In mitochondria and aerobic bacteria energy conservation involves electron transfer through a number of membrane-bound protein complexes to O2. The reduction of O2, accompanied by the uptake of substrate protons to form H2O, is catalyzed by cytochrome c oxidase (CcO). This reaction is coupled to proton translocation (pumping) across the membrane such that each electron transfer to the catalytic site is linked to the uptake of two protons from one side and the release of one proton to the other side of the membrane. To address the mechanism of vectorial proton translocation, in this study we have investigated the solvent deuterium isotope effect of proton-transfer rates in CcO oriented in small unilamellar vesicles. Although in H2O the uptake and release reactions occur with the same rates, in D2O the substrate and pumped protons are taken up first (tau(D) congruent with 200 micros, "peroxy" to "ferryl" transition) followed by a significantly slower proton release to the other side of the membrane (tau(D) congruent with 1 ms). Thus, the results define the order and timing of the proton transfers during a pumping cycle. Furthermore, the results indicate that during CcO turnover internal electron transfer to the catalytic site is controlled by the release of the pumped proton, which suggests a mechanism by which CcO orchestrates a tight coupling between electron transfer and proton translocation.

Effect of flexibility on hydrophobic behavior of nanotube water channels

Carbon nanotubes can serve as simple nonpolar water channels. Here we report computer simulations exploring the relationship between the mechanical properties of such channels and their interaction with water. We show that on one hand, increasing the flexibility of the carbon nanotubes increases their apparent hydrophobic character, while on the other hand the presence of water inside the channel makes them more resistant to radial collapse. We quantify the effect of increasing flexibility on the hydrophobicity of the nanotube water channel. We also show that flexibility impedes water transport across the nanotube channel by increasing the free-energy barriers to such motion. Conversely, the presence of water inside the nanotube is shown to affect the energetics of radial collapse in a water nanotube, an ostensibly mechanical property. We quantify the magnitude of the effect and show that it arises from the formation of energetically favorable low-dimensional water structures inside the nanotube such as one-dimensional wires and two-dimensional sheets.

Structural Character and Energetics of Tyrosyl Radical Formation by Electron/Proton Transfers of a Covalently Linked Histidine-Tyrosine: A Model for Cytochrome c Oxidase

The structural, energetic, and electronic and IR spectroscopic properties for a model of the cross-linked histidine-tyrosine (His-Tyr) residues as found in cytochrome c oxidase (CcO) are investigated by ab initio methods. The formation of a His-Tyr radical is studied by two paths: proton release followed by electron release and vice versa. The energetics for the proton/electron releases of the Tyr depend modestly on the cross-linked His substituent and, more sensitively, on the charge of the cation attached to the imino N site of the His residue. Protonation of the imino N site significantly increases the electron ionization potential and decreases the proton dissociation energy, making them competitive processes. A positive charge placed at the imino N site, whose value is scanned from zero to one, shows a continuous increase in ionization potential and a decrease in proton dissociation energy, with the +1 limit agreeing well with the protonated imino N site result, indicating a dominant electrostatic effect. The charge populations and the spin density distributions of the His-Tyr model, the radical cation formed by electron ionization, the anion formed by proton dissociation, and the final His-Tyr radical depend sensitively on the substituents, implying a modulation role on the charge transfer between the phenol and imidazole rings, especially for the charged species. His-Tyr and protonated His-Tyr exhibit differences among their respective structural isomers with consequences on their IR absorptions. Small barriers between their pseudo-cis and pseudo-trans rotamers demonstrate the relative flexibility between the two rings, and these may facilitate proton release and charge transfer. The cation effect demonstrates that the cationized cross-linked His-Tyr should be the best candidate to mimic the covalently ring-linked histidine-tyrosine structure in CcO.

Direct determination of reaction paths and stationary points on potential of mean force surfaces

A simulation approach is introduced for directly determining reaction paths and stationary points on potential of mean force (PMF) surfaces associated with molecular events that occur in complex environments. The nudged elastic band approach was employed to search for steepest descent paths on the PMF surface using the relevant PMF derivatives from a series of local simulations. The steepest descent path on the PMF surface corresponds to the minimum PMF path (i.e. the path with the lowest local PMF barrier), which contains important information about stationary points (e.g. saddle points) on the PMF surface, which in turn can provide useful insights into the thermodynamics and kinetics for the process of interest. By working with the PMF defined in a low-dimensional sub-space rather than a potential energy function of full molecular dimensionality, the main features of the process under study are concisely represented and the orthogonal degrees of freedom are adequately sampled with the appropriate canonical distribution at the desired temperature (e.g. 300 K). Therefore, minimum PMF paths carry statistically meaningful mechanistic information and are complementary to reaction paths of full molecular dimensionality proposed in previous studies. The NEB based path optimization method is direct in the sense that no information regarding the global PMF surface is necessary for the determination of the local reaction path and stationary points along this path. Since only low-dimensional quantities (paths) are searched for, the PMF-path method is expected to scale better in terms of dimension of the PMF sub-space than those aims to fully explore multi-dimensional PMF surfaces. Test applications on simple molecular systems, the alanine di-peptide in vacuum and in solution and a micro-solvated proton-wire, indicate that reliable PMF paths can be determined for both conformational isomerization and chemical reaction processes. However, highly accurate PMF derivatives are required for determining more quantitative observables, such as the free energy profile along the minimum PMF path. Therefore, effective numerical algorithms for calculating local PMF derivatives and systematic protocols for defining the relevant sub-space are the main focus in the near future. Finally, we emphasize that the minimum PMF path defined here includes thermal (e.g. entropic) effects associated with the orthogonal degrees of freedom, but finite kinetic energies associated with the PMF degrees of freedom are not included; this can be improved by adopting a different definition of the reaction path, such as the maximum flux path, on the PMF surface, or thermally sampling all degrees of freedom orthogonal to the one-dimensional path.

Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations

Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to approximately 1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore.

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

Proton transport (PTR) processes play a major role in bioenergetics and thus it is important to gain a molecular understanding of these processes. At present the detailed description of PTR in proteins is somewhat unclear and it is important to examine different models by using well-defined experimental systems. One of the best benchmarks is provided by carbonic anhydrase III (CA III), because this is one of the few systems where we have a clear molecular knowledge of the rate constant of the PTR process and its variation upon mutations. Furthermore, this system transfers a proton between several water molecules, thus making it highly relevant to a careful examination of the "proton wire" concept. Obtaining a correlation between the structure of this protein and the rate of the PTR process should help to discriminate between alternative models and to give useful clues about PTR processes in other systems. Obviously, obtaining such a correlation requires a correct representation of the "chemistry" of PTR between different donors and acceptors, as well as the ability to evaluate the free energy barriers of charge transfer in proteins, and to simulate long-time kinetic processes. The microscopic empirical valence bond (Warshel, A., and R. M. Weiss. 1980. J. Am. Chem. Soc. 102:6218-6226; and Aqvist, J., and A. Warshel. 1993. Chem. Rev. 93:2523-2544) provides a powerful way for representing the chemistry and evaluating the free energy barriers, but it cannot be used with the currently available computer times in direct simulation of PTR with significant activation barriers. Alternatively, one can reduce the empirical valence bond (EVB) to the modified Marcus' relationship and use semimacroscopic electrostatic calculations plus a master equation to determine the PTR kinetics (Sham, Y., I. Muegge, and A. Warshel. 1999. Proteins. 36:484-500). However, such an approximation does not provide a rigorous multisite kinetic treatment. Here we combine the useful ingredients of both approaches and develop a simplified EVB effective potential that treats explicitly the chain of donors and acceptors while considering implicitly the rest of the protein/solvent system. This approach can be used in Langevin dynamics simulations of long-time PTR processes. The validity of our new simplified approach is demonstrated first by comparing its Langevin dynamics results for a PTR along a chain of water molecules in water to the corresponding molecular dynamics simulations of the fully microscopic EVB model. This study examines dynamics of both models in cases of low activation barriers and the dependence of the rate on the energetics for cases with moderate barriers. The study of the dependence on the activation barrier is next extended to the range of higher barriers, demonstrating a clear correlation between the barrier height and the rate constant. The simplified EVB model is then examined in studies of the PTR in carbonic anhydrase III, where it reproduces the relevant experimental results without the use of any parameter that is specifically adjusted to fit the energetics or dynamics of the reaction in the protein. We also validate the conclusions obtained previously from the EVB-based modified Marcus' relationship. It is concluded that this approach and the EVB-based model provide a reliable, effective, and general tool for studies of PTR in proteins. Finally in view of the behavior of the simulated result, in both water and the CA III, we conclude that the rate of PTR in proteins is determined by the electrostatic energy of the transferred proton as long as this energy is higher than a few kcal/mol.

Proton pathways in green fluorescence protein

Proton pathways in green fluorescent protein (GFP) are more extended than previously reported. In the x-ray data of wild-type GFP, a two-step exit pathway exists from the active site to the protein surface, controlled by a threonine switch. A proton entry pathway begins at a glutamate-lysine cluster around Glu-5, and extends all the way to the buried Glu-222 near the active site. This structural evidence suggests that GFP may function as a portable light-driven proton-pump, with proton emitted in the excited state through the switchable exit pathway, and replenished from Glu-222 and the Glu-5 entry pathway in the ground state.

Proton Exit Channels in Bovine Cytochrome c Oxidase

Cytochrome c oxidase (CcO) is the terminal transmembrane enzyme of the respiratory electron transport chain in aerobic cells. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping, a process which 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 and proton exit pathways remain unknown. In our previous work, the continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine cytochrome c oxidase for different redox states of the enzyme. A possible mechanism of oxygen reduction and proton pumping via His291 was proposed. In this paper, using electrostatic calculations, we examine the proton exit pathways in the enzyme. By monitoring the changes of the protonation states, proton affinities, and energies of electrostatic interactions between the titratable groups in different redox states of CcO, we identified the clusters of strongly interacting residues. Using these data, we detected four possible proton exit points on the periplasmic side of the membrane (Lys171B/Asp173B, His24B/Asp25B, Asp51, and Asp300). We then were able to trace the proton exit pathways and to evaluate the energy profiles along the paths. On the basis of energetic considerations and the conservation of the residues in a protein sequence, the most likely exit pathway is one via the Lys171B/Asp173B site. The obtained results are fully consistent with our His291 model of proton pumping, and provide a rationale for the absence of proton leaking in CcO between the pumping strokes.

Realistic Simulations of Proton Transport along the Gramicidin Channel: Demonstrating the Importance of Solvation Effects

The nature of proton transduction (PTR) through a file of water molecules, along the gramicidin A (gA) channel, has long been considered as being highly relevant to PTR in biological systems. Previous attempts to model this process implied that the so-called Grotthuss mechanism and the corresponding orientation of the water file plays a major role. The present work reexamines the PTR in gA by combining a fully microscopic empirical valence bond (EVB) model and a recently developed simplified EVB-based model with Langevin dynamics (LD) simulations. The full model is used first to evaluate the free energy profile for a stepwise PTR process. The corresponding results are then used to construct the effective potential of the simplified EVB. This later model is then used in Langevin dynamics simulations, taking into account the correct physics of possible concerted motions and the effect of the solvent reorganization. The simulations reproduce the observed experimental trend and lead to a picture that is quite different from that assumed previously. It is found that the PTR in gA is controlled by the change in solvation energy of the transferred proton along the channel axis. Although the time dependent electrostatic fluctuations of the channel and water dipoles play their usual role in modulating the proton-transfer process (Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 444), the PTR rate is mainly determined by the free energy profile. Furthermore, the energetics of the reorientation of the unprotonated water file do not appear to provide a consistent way of assessing the activation barrier for the PTR process. It seems to us that in the case of gA, and probably other systems with significant electrostatic barriers for the transfer of the proton charge, the PTR rate is controlled by the electrostatic barrier. This finding has clear consequences with regards to PTR processes in biological systems.

Thermodynamic Properties of Internal Water Molecules in the Hydrophobic Cavity around the Catalytic Center of Cytochrome c Oxidase

Cytochrome c oxidase is a redox-driven proton pump that creates a membrane proton gradient responsible for driving ATP synthesis in aerobic cells. The crystal structure of the enzyme has been recently solved; however, the details of the mechanism of its proton pumping remain unknown. The enzyme internal water molecules play a key role in proton translocation through the enzyme. Here, we examine the thermodynamic properties of internal water in a hydrophobic cavity around the catalytic center of the enzyme. The crystal structure does not show any water molecules in this region; it is believed, however, that, since protons are delivered to the catalytic center, where the reduction of molecular oxygen occurs, at least some water molecules must be present there. The goal of the present study was to examine how many water molecules are present in the catalytic center cavity and why these water molecules are not observed in the crystal structure of the enzyme. The behavior of water molecules is discussed in the context of redox-coupled proton translocation in the enzyme.

Water clusters in nonpolar cavities

We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities can be filled at equilibrium with highly structured water clusters. The structural and thermodynamic properties of these encapsulated water clusters are similar to those observed experimentally in the gas phase. Water filling is highly sensitive to the size of the cavity and the strength of the interactions with the cavity wall. Water penetration into pores can thus be modulated by small changes in the polarity and structure of the cavity. Implications on water penetration into proteins are discussed.

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

The nature of the control of water/proton selectivity in biological channels is a problem of a fundamental importance. Most studies of this issue have proposed that an interference with the orientational requirements of the so-called proton wire is the source of selectivity. The elucidation of the structures of aquaporins, which have evolved to prevent proton transfer (PT), provided a clear benchmark for exploring the selectivity problem. Previous simulations of this system have not examined, however, the actual issue of PT, but only considered the much simpler task of the transfer of water molecules. Here we take aquaporin as a benchmark and quantify the origin of the water/proton selectivity in this and related systems. This is done by evaluating in a consistent way the free energy profile for transferring a proton along the channel and relating this profile to the relevant PT rate constants. It is found that the water/proton selectivity is controlled by the change in solvation free energy upon moving the charged proton from water to the channel. The reason for the focus on the elegant concept of the proton wire and the related Grotthuss-type mechanism is also considered. It is concluded that these mechanisms are clearly important in cases with flat free energy surfaces (e.g., in bulk water, in gas phase water chains, and in infinitely long channels). However, in cases of biological channels, the actual PT mechanism is much less important than the energetics of transferring the proton charge from water to different regions in the channels.

Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating

Using electrostatic calculations, we have examined the dependence of the protonation state of cytochrome c oxidase from bovine heart on its redox state. Based on these calculations, we propose a possible scheme of redox-linked proton pumping. The scheme involves His291 - one of the ligands of the Cu(B) redox center - which plays the role of the proton loading site (PLS) of the pump. The mechanism of pumping is based on ET reaction between two hemes of the enzyme, which is coupled to a transfer of two protons. Upon ET, the first proton (fast reaction) is transferred to the PLS (His291), while subsequent transfer of the second "chemical" proton to the binuclear center (slow reaction) is accompanied by the ejection of the first (pumped) proton. Within the proposed model, we discuss the catalytic cycle of the enzyme.

Thermodynamic and choreographic constraints for energy transduction by cytochrome c oxidase

Cooperative effects are fundamental for electroprotonic energy transduction processes, crucial to sustain much of life chemistry. However, the primary cooperative mechanism by which transmembrane proteins couple the downhill transfer of electrons to the uphill activation (acidification) of protic groups is still a matter of great controversy. To understand cooperative processes fully, it is necessary to obtain the microscopic thermodynamic parameters of the functional centres and relate them to the relevant structural features, a task difficult to achieve for large proteins. The approach discussed here explores how this may be done by extrapolation from mechanisms used by simpler proteins operative in similar processes. The detailed study of small, soluble cytochromes performing electroprotonic activation has shown how they use anti-electrostatic effects to control the synchronous movement of charges. These include negative e(-)/H(+) (redox-Bohr effect) cooperativities. This capacity is the basis to discuss an unorthodox mechanism consistent with the available experimental data on the process of electroprotonic energy transduction performed by cytochrome c oxidase (CcO).

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%.

Bacteriorhodopsin

Fourier transform infrared and Raman spectroscopy, solid-state NMR, and X-ray crystallography have contributed detailed information about the structural changes in the proton transport cycle of the light-driven pump, bacteriorhodopsin. The results over the past few years add up to a step-by-step description of the configurational changes of the photoisomerized retinal, how these changes result in internal proton transfers and the release of a proton to the extracellular surface and uptake on the other side, as well as the conservation and transformation of excess free energy during the cycle.

Solution 1H, 15N NMR spectroscopic characterization of substrate-bound, cyanide-inhibited human heme oxygenase: water occupation of the distal cavity

A solution NMR spectroscopic study of the cyanide-inhibited, substrate-bound complex of uniformly (15)N-labeled human heme oxygenase, hHO, has led to characterization of the active site with respect to the nature and identity of strong hydrogen bonds and the occupation of ordered water molecules within both the hydrogen bonding network and an aromatic cluster on the distal side. [(1)H-(15)N]-HSQC spectra confirm the functionalities of several key donors in particularly robust H-bonds, and [(1)H-(15)N]HSQC-NOESY spectra lead to the identification of three additional robust H-bonds, as well as the detection of two more relatively strong H-bonds whose identities could not be established. The 3D NMR experiments provided only a modest, but important, extension of assignments because of the loss of key TOCSY cross-peaks due to the line broadening from a dynamic heterogeneity in the active site. Steady-state NOEs upon saturating the water signal locate nine ordered water molecules in the immediate vicinity of the H-bond donors, six of which are readily identified in the crystal structure. The additional three are positioned in available spaces to account for the observed NOEs. (15)N-filtered steady-state NOEs upon saturating the water resonances and (15)N-filtered NOESY spectra demonstrate significant negative NOEs between water molecules and the protons of five aromatic rings. Many of the NOEs can be rationalized by water molecules located in the crystal structure, but strong water NOEs, particularly to the rings of Phe47 and Trp96, demand the presence of at least an additional two immobilized water molecules near these rings. The H-bond network appears to function to order water molecules to provide stabilization for the hydroperoxy intermediate and to serve as a conduit to the active site for the nine protons required per HO turnover.

Redox-driven proton pumping by heme-copper oxidases

One of the key problems of molecular bioenergetics is the understanding of the function of redox-driven proton pumps on a molecular level. One such class of proton pumps are the heme-copper oxidases. These enzymes are integral membrane proteins in which proton translocation across the membrane is driven by electron transfer from a low-potential donor, such as, e.g. cytochrome c, to a high-potential acceptor, O(2). Proton pumping is associated with distinct exergonic reaction steps that involve gradual reduction of oxygen to water. During the process of O(2) reduction, unprotonated high pK(a) proton acceptors are created at the catalytic site. Initially, these proton acceptors become protonated as a result of intramolecular proton transfer from a residue(s) located in the membrane-spanning part of the enzyme, but removed from the catalytic site. This residue is then reprotonated from the bulk solution. In cytochrome c oxidase from Rhodobacter sphaeroides, the proton is initially transferred from a glutamate, E(I-286), which has an apparent pK(a) of 9.4. According to a recently published structure of the enzyme, the deprotonation of E(I-286) is likely to result in minor structural changes that propagate to protonatable groups on the proton output (positive) side of the protein. We propose that in this way, the free energy available from the O(2) reduction is conserved during the proton transfer. On the basis of the observation of these structural changes, a possible proton-pumping model is presented in this paper. Initially, the structural changes associated with deprotonation of E(I-286) result in the transfer of a proton to an acceptor for pumped protons from the input (negative) side of the membrane. After reprotonation of E(I-286) this acceptor releases a proton to the output side of the membrane.

Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam

Proton-transfer reactions form an integral part of bioenergetics and enzymatic catalysis. The identification of proton-conducting pathways inside a protein is a key to understanding the mechanisms of biomolecular proton transfer. Proton pathways are modeled here as hydrogen bonded networks of proton-conducting groups, including proton-exchanging groups of amino acid side chains and bound water molecules. We focus on the identification of potential proton-conducting pathways inside a protein of known structure. However, consideration of the static structure alone is often not sufficient to detect suitable proton-transfer paths, leading, for example, from the protein surface to the active site buried inside the protein. We include dynamic fluctuations of amino acid side chains and water molecules into our analysis. To illustrate the method, proton transfer into the active site of cytochrome P450cam is studied. The cooperative rotation of amino acids and motion of water molecules are found to connect the protein surface to the molecular oxygen. Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups.

Voltage-gated proton channels and other proton transfer pathways

Proton channels exist in a wide variety of membrane proteins where they transport protons rapidly and efficiently. Usually the proton pathway is formed mainly by water molecules present in the protein, but its function is regulated by titratable groups on critical amino acid residues in the pathway. All proton channels conduct protons by a hydrogen-bonded chain mechanism in which the proton hops from one water or titratable group to the next. Voltage-gated proton channels represent a specific subset of proton channels that have voltage- and time-dependent gating like other ion channels. However, they differ from most ion channels in their extraordinarily high selectivity, tiny conductance, strong temperature and deuterium isotope effects on conductance and gating kinetics, and insensitivity to block by steric occlusion. Gating of H(+) channels is regulated tightly by pH and voltage, ensuring that they open only when the electrochemical gradient is outward. Thus they function to extrude acid from cells. H(+) channels are expressed in many cells. During the respiratory burst in phagocytes, H(+) current compensates for electron extrusion by NADPH oxidase. Most evidence indicates that the H(+) channel is not part of the NADPH oxidase complex, but rather is a distinct and as yet unidentified molecule.

Proton transport through water-filled carbon nanotubes

Proton transfer along 1D chains of water molecules inside carbon nanotubes is studied by simulations. Ab initio molecular dynamics and an empirical valence bond model yield similar structures and time scales. The proton mobility along 1D water chains exceeds that in bulk water by a factor of 40, but is reduced if orientational defects are present. Excess protons interact with hydrogen-bonding defects through long-range electrostatics, resulting in coupled motion of protons and defects.

Computer simulation of water in cytochrome c oxidase

Statistical mechanics and molecular dynamics simulations have been carried out to study the distribution and dynamics of internal water molecules in bovine heart cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of water, which in subunit I alone amounts to about 165 molecules. The dynamic characterization of these water molecules is carried out. The nascent water molecules produced in the redox reaction at the heme a(3)-CuB binuclear site form an intriguing chain structure. The chain begins at the position of Glu242 at the end of the D channel, and has a fork structure, one branch of which leads to the binuclear center, and the other to the propionate d of heme a(3). The branch that leads to the binuclear center has dynamic access both to the site where the formation of water occurs, and to delta-nitrogen of His291. From the binuclear center, the chain continues to run into the K channel. The stability of this hydrogen bond network is examined dynamically. The catalytic site is located at the hydrophobic region, and the nascent water molecules are produced at the top of the energy hill. The energy gradient is utilized as the mechanism of water removal from the protein. The water exit channels are explored using high-temperature dynamics simulations. Two putative channels for water exit from the catalytic site have been identified. One is leading directly toward Mg(2+) site. However, this channel is only open when His291 is dissociated from CuB. If His291 is bound to CuB, the only channel for water exit is the one that originates at E242 and leads toward the middle of the membrane. This is the same channel that is presumably used for oxygen supply.

Determination of the orientation of the axial ligands and of the magnetic properties of the haems in the tetrahaem ferricytochrome from Shewanella frigidimarina

The unambiguous assignment of the nuclear magnetic resonance (NMR) signals of the alpha-substituents of the haems in the tetrahaem cytochrome isolated from Shewanella frigidimarina NCIMB400, was made using a combination of homonuclear and heteronuclear experiments. The paramagnetic (13)C shifts of the nuclei directly bound to the porphyrin of each haem group were analysed in the framework of a model for the haem electronic structure. The analysis yields g-tensors for each haem, which allowed the assignment of some electron paramagnetic resonance (EPR) signals to specific haems, and the orientation of the magnetic axes relative to each haem to be established. The orientation of the axial ligands of the haems was determined semi-empirically from the NMR data, and the structural results were compared with those of the homologous tetrahaem cytochrome from Shewanella oneidensis MR-1 showing significant similarities between the two proteins.

Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport

Recent 3-D structures of several intermediates in the photocycle of bacteriorhodopsin (bR) provide a detailed structural picture of this molecular proton pump in action. In this review, we describe the sequence of conformational changes of bR following the photoisomerization of its all-trans retinal chromophore, which is covalently bound via a protonated Schiff base to Lys216 in helix G, to a 13-cis configuration. The initial changes are localized near the protein's active site and a key water molecule is disordered. This water molecule serves as a keystone for the ground state of bR since, within the framework of the complex counter ion, it is important both for stabilizing the structure of the extracellular half of the protein, and for maintaining the high pK(a) of the Schiff base (the primary proton donor) and the low pK(a) of Asp85 (the primary proton acceptor). Subsequent structural rearrangements propagate out from the active site towards the extracellular half of the protein, with a local flex of helix C exaggerating an early movement of Asp85 towards the Schiff base, thereby facilitating proton transfer between these two groups. Other coupled rearrangements indicate the mechanism of proton release to the extracellular medium. On the cytoplasmic half of the protein, a local unwinding of helix G near the backbone of Lys216 provides sites for water molecules to order and define a pathway for the reprotonation of the Schiff base from Asp96 later in the photocycle. A steric clash of the photoisomerized retinal with Trp182 in helix F drives an outward tilt of the cytoplasmic half of this helix, opening the proton transport channel and enabling a proton to be taken up from the cytoplasm. Although bR is the first integral membrane protein to have its catalytic mechanism structurally characterized in detail, several key results were anticipated in advance of the structural model and the general framework for vectorial proton transport has, by and large, been preserved.

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides

The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures. A comparative study of the wild-type and the EQ(I-286) mutant enzyme revealed structural rearrangements around E(I-286) that could be crucial for proton transfer in this enzyme. In the structure of the mutant enzyme, EQ(I-286), which cannot transfer protons during oxygen reduction, the side-chain of Q(I-286) does not have the hydrogen bond to the carbonyl oxygen of M(I-107) that is seen in the wild-type structure. Furthermore, the Q(I-286) mutant has a different arrangement of water molecules and residues in the vicinity of the Q side-chain. These differences between the structures could reflect conformational changes that take place upon deprotonation of E(I-286) during turnover of the wild-type enzyme, which could be part of the proton-pumping machinery of the enzyme.

Plasticity of proton pathways in haem-copper oxygen reductases

Oxygen reductases are the final enzymes in the aerobic respiratory chains catalysing the reduction of dioxygen to water, with the concomitant translocation of protons through the bacterial cytoplasmatic or mitochondrial membranes. Most of these enzymes belong to the family of haem-copper oxygen reductases. Intraprotein proton-conducting pathways are needed for the chemical reaction and for the translocated protons. Based on sequence and structural analyses, and site-directed mutagenesis, two proton channels were established for the mitochondrial-like oxygen reductases. However, the amino acid residues forming these channels are not conserved among the family members. Most importantly, many oxygen reductases do not contain ionisable amino acid residues in the putative proton pathways nor in alternative positions. The diversity of channels in haem-copper oxygen reductases exemplifies the plasticity of proton pathways that occurred throughout evolution, and strongly suggests a substantial role for water as the main proton carrier.

Proton transport via the membrane surface

Some proton pumps, such as cytochrome c oxidase (C(c)O), translocate protons across biological membranes at a rate that considerably exceeds the rate of proton transport to the entrance of the proton-conducting channel via bulk diffusion. This effect is usually ascribed to a proton-collecting antenna surrounding the channel entrance. In this paper, we consider a realistic phenomenological model of such an antenna. In our model, a homogeneous membrane surface, which can mediate proton diffusion toward the channel entrance, is populated with protolytic groups that are in dynamic equilibrium with the solution. Equations that describe coupled surface-bulk proton diffusion are derived and analyzed. A general expression for the rate constant of proton transport via such a coupled surface-bulk diffusion mechanism is obtained. A rigorous criterion is formulated of when proton diffusion along the surface enhances the transport. The enhancement factor is found to depend on the ratio of the surface and bulk diffusional constants, pK(a) values of surface protolytic groups, and their concentration. A capture radius for a proton on the surface and an effective size of the antenna are found. The theory also predicts the effective distance that a proton can migrate on the membrane surface between a source (such as CcO) and a sink (such as ATP synthase) without fully equilibrating with the bulk. In pure aqueous solutions, protons can travel over long distances (microns). In buffered solutions, the travel distance is much shorter (nanometers); still the enhancement effect of the surface diffusion on the proton flow to a target on the surface can be tens to hundreds at physiological buffer concentrations. These results are discussed in a general context of chemiosmotic theory.

Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel

The conduction of protons in the hydrogen-bonded chain of water molecules (or "proton wire") embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a "hop-and-turn" or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H+) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H+ is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H+, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.

An inverting basket model for AE1 transport

We describe an "inverting basket" model for transport in the erythrocyte anion exchanger, AE1. The inverting basket is formed by the side chains of three putative key residues, two positively (Lys 826 and Arg 730) and one negatively (Glu 681) charged residue. We have tentatively chosen seven transmembrane helices, TM1, TM2, TM4, TM8, TM10, TM12 and TM13 to form a conical channel using the well-established Glu 681 of TM8 and candidates Lys 826 and Arg 730 of TM12-13 and TM10, respectively, to form the inverting basket. We assume that these residues bind to an anion and shift from outward facing (C(o)) to inward facing (C(i)) conformation without significant backbone movements to transport an anion across the membrane. The transition of the complex (residues and ion) from outward facing (C(o)) to inward facing (C(i)) constitutes one "basket" inversion. The barrier to inversion is composed of two major components: that of the anhydrous complex, which we refer to as a steric energy barrier and a dehydration effect due to the removal of charges in the complex from water in the channel. The steric barrier is dependent on the side chain charge and configuration and on the ion charge and size. The dehydration effect, for our model, ameliorates the steric barrier, in the case of the empty complex but less so for the monovalent and divalent ions. We conclude, that it is possible for a seven-helix bundle to have a steric barrier to basket inversion, but that hydration effects in thin hydrophobic barrier models may be more complex than usually envisioned.