Statistical mechanical equilibrium theory of selective ion channels.

A rigorous statistical mechanical formulation of the equilibrium properties of selective ion channels is developed, incorporating the influence of the membrane potential, multiple occupancy, and saturation effects. The theory provides a framework for discussing familiar quantities and concepts in the context of detailed microscopic models. Statistical mechanical expressions for the free energy profile along the channel axis, the cross-sectional area of the pore, and probability of occupancy are given and discussed. In particular, the influence of the membrane voltage, the significance of the electric distance, and traditional assumptions concerning the linearity of the membrane electric field along the channel axis are examined. Important findings are: 1) the equilibrium probabilities of occupancy of multiply occupied channels have the familiar algebraic form of saturation properties which is obtained from kinetic models with discrete states of denumerable ion occupancy (although this does not prove the existence of specific binding sites; 2) the total free energy profile of an ion along the channel axis can be separated into an intrinsic ion-pore free energy potential of mean force, independent of the transmembrane potential, and other contributions that arise from the interfacial polarization; 3) the transmembrane potential calculated numerically for a detailed atomic configuration of the gramicidin A channel embedded in a bilayer membrane with explicit lipid molecules is shown to be closely linear over a distance of 25 A along the channel axis. Therefore, the present analysis provides some support for the constant membrane potential field approximation, a concept that has played a central role in the interpretation of flux data based on traditional models of ion permeation. It is hoped that this formulation will provide a sound physical basis for developing nonequilibrium theories of ion transport in selective biological channels.     

The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations

Molecular dynamics simulations employing combined quantum mechanical and molecular mechanical (QM/MM) potentials have been carried out to investigate the reaction mechanism of the hydrolysis of paraoxon by phosphotriesterase (PTE). We used a dual-level QM/MM approach that synthesizes accurate results from high-level electronic structure calculations with computational efficiency of semiempirical QM/MM potentials for free energy simulations. In particular, the intrinsic (gas-phase) energies of the active site in the QM region are determined by using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation theory (MP2) and the molecular dynamics free energy simulations are performed by using the mixed AM1:CHARMM potential. The simulation results suggest a revised mechanism for the phosphotriester hydrolysis mechanism by PTE. The reaction free energy profile is mirrored by structural motions of the binuclear metal center in the active site. The two zinc ions occupy a compact conformation with an average zinc-zinc distance of 3.5 +/- 0.1 A in the Michaelis complex, whereas it is elongated to 5.3 +/- 0.3 A at the transition state and product state. The substrate is loosely bound to the more exposed zinc ion (Znbeta2+) at an average distance of 3.8 A +/- 0.3 A. The P=O bond of the substrate paraoxon is activated by adopting a tight coordination to the Znbeta2+, releasing the coordinate to the bridging hydroxide ion and increasing its nucleophilicity. It was also found that a water molecule enters into the binding pocket of the loosely bound binuclear center, originally occupied by the nucleophilic hydroxide ion. We suggest that the proton of this water molecule is taken up by His254 at low pH or released to the solvent at high pH, resulting in a hydroxide ion that pulls the Znbeta2+ ion closer to form the compact configuration and restores the resting state of the enzyme.     

Measurement of urinary trimethylamine and trimethylamime oxide by direct infusion electrospray quadrupole time-of-flight mass spectrometry

Urinary trimethylamine (TMA) and its oxide (TMAOx) are measured separately and as a mixture using ¹⁵N-labeled internal standards and direct infusion electrospray with a quadrupole time-of-flight (Q-ToF) instrument. TMA is quaternized with trideuteromethyl iodide to avoid inclusion of endogenous tetramethylammonium ion in the TMA measurement, whereas TMAOx is measured as the protonated molecule. Measurements reported as percentage TMA made with separate and combined samples agree within 6% of the measured values and demonstrate that both TMA and TMAOx can be measured simultaneously in a single analysis. Moreover, the analysis is simpler and less tedious and time-consuming than some earlier methods.     

Permeation and interaction of monovalent cations with the cGMP-gated channel of cone photoreceptors

We measured the ion selectivity of cGMP-dependent currents in detached membrane patches from the outer segment of cone photoreceptors isolated from the retina of striped bass. In inside-out patches excised from either single or twin cones the amplitude of these currents, under symmetric ionic solutions, changed with the concentration of cGMP with a dependence described by a Hill equation with average values, at +80 mV, of Km = 42.6 microM and n = 2.49. In the absence of divalent cations, and under symmetric ionic solutions, the I-V curves of the currents were linear over the range of -80 to +80 mV. The addition of Ca altered the form of the I-V curve to a new function well described by an empirical equation that also describes the I-V curve of the photocurrent measured in intact photoreceptors. The monovalent cation permeability sequence of the cGMP-gated channels in the absence of divalent ions was PK > PNa = PLi = PRb > PCs (1.11 > 1.0 = 0.99 = 0.96 > 0.82). The conductance selectivity sequence at +80 mV was GNa = GK > GRb > GCs > GLi (1.0 = 0.99 > 0.88 > 0.74 > 0.60). The organic cations tetramethylammonium (TMA) and arginine partially blocked the current, but the larger ion, arginine, was permeant, whereas the smaller ion, TMA, was not. The amplitude of the outward current through the channels increased with the concentration of monovalent cations on the cytoplasmic membrane surface, up to a saturating value. The increase was well described by the adsorption isotherm of a single ion binding site within the channel with average binding constants, at +80 mV, of 104 mM for Na and 37.6 mM for Li. By assuming that the ion channel contains a single ion binding site in an energy trough separated from each membrane surface by an energy barrier, and using Eyring rate theory, we simulated I-V curves that fit the experimental data measured under ionic concentration gradients. From this fit we conclude that the binding site interacts with one ion at a time and that the energy barriers are asymmetrically located within the membrane thickness. Comparison of the quantitative features of ion permeation and interaction between the cGMP-gated channels of rod and cone photoreceptors reveals that the ion binding sites are profoundly different in the two types of channels. This molecular difference may be particularly important in explaining the differences in the transduction signal of each receptor type.     

Novel urushiol derivatives as HDAC8 inhibitors: rational design,virtual screening,molecular docking and molecular dynamics studies

Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The compounds’ binding affinity toward HDAC8 was screened by Glide docking. The highest-scoring compounds were processed further with molecular docking, MD simulations, and binding free energy studies to analyze the binding modes and mechanisms. Ten compounds had Glide scores of ?8.2 to ?10.2, which revealed that introducing hydroxy, carbonyl, amino, or methyl ether groups into the alkyl side chain or addition of –F, –Cl, sulfonamide, benzamido, amino, or hydroxy substituents on the benzene ring could significantly increase binding affinity. Molecular docking studies revealed that zinc ion coordination, hydrogen bonding, and hydrophobic interactions contributed to the high calculated binding affinities of these compounds toward HDAC8. MD simulations and binding free energy studies showed that all complexes possessed good stability, as characterized by low RMSDs, low RMSFs of residues, moderate hydrogen bonding and zinc ion coordination and low values of binding free energies. Hie147, Tyr121, Phe175, Hip110, Phe119, Tyr273, Lys21, Gly118, Gln230, Leu122, Gly269, and Gly107 contributed favorably to the binding; and Van der Waals and electrostatic interactions provided major contributions to the stability of these complexes. These results show the potential of urushiol derivatives as HDAC8 binding lead compounds, which have great therapeutic potential in the treatment of various malignancies, neurological disorders, and human parasitic diseases.     

Dimensionality reduction of free energy profiles of benzene in silicalite-1: calculation of diffusion coefficients using transition state theory

This study describes the development and application of a new computational methodology for calculating the self-diffusivity of sorbate molecules strongly confined within shape-selective nanoporous materials. An umbrella sampling strategy, employing repulsive walls to confine the sorbate within specific regions of the pore space, is invoked to extract free energy profiles with respect to the sorbate degrees of freedom. Based on these profiles, it is shown how the multidimensional problem of translational diffusion of benzene in flexible silicalite-1 can be reduced first to a six-dimensional problem, then to a three-dimensional (3D) problem and finally, to a 1D problem. A 3D free energy distribution is accumulated as a function of the benzene centre of mass position and ultimately reduced to a set of 1D profiles for the benzene centre of mass along the pore axes. From these profiles, the rate constants for jumps executed by benzene between sorption sites are calculated using transition state theory; from the latter rate constants, the low-occupancy self-diffusivity is obtained using the MESoRReD method [Kolokathis PD, Theodorou DN. On solving the master equation in spatially periodic systems. J Chem Phys. 2012;137:034112]. The activation energy for diffusion and preferred orientations in the various sorption states in silicalite are in very favourable agreement with available experimental measurements.     

Magnetic resonance distinction between site bound and atmospherically bound paramagnetic counterions in polyelectrolyte solutions.

A combination of the water protons NMR chemical shifts, longitudinal and transversal relaxation rates and of the paramagnetic counterion EPR signal is shown to provide a clear distinction between site binding, atmospheric trapping and free counterions in solutions of polyelectrolyte TMA salts with increasing concentrations of the divalent counterions Co++ and Mn++. Site binding is defined by the loss of water in the counterion first hydration shell while atmospheric binding results in a change in the counterion correlation time as compared to a free ion.     

Activation, inactivation and recovery in the sodium channels of the squid giant axon dialysed with different solutions.

Comparisons were made between families of ion currents recorded in voltage-clamped squid axons dialysed with 20 mM NaF and 330 mM CsF or TMAF, and bathed in a solution in which four fifths of the Na was replaced by Tris. The permeability coefficient PNa,fast for the fast-inactivating current in the initial open state was calculated as a function of test potential from the size of the initial peak of INa. The permeability coefficient PNa,non for the non-inactivating open state was calculated from the steady-state INa that persisted until the end of the test pulse. Dialysis with TMA had no direct effect on the QV curve for gating charge. The reversal potential for INa,non was always lower than that for INa,fast, the mean difference being about -9 mV when dialysing with Cs, but only about -1 mV with TMA. Except close to threshold, PNa,fast was roughly halved by dialysis with TMA as compared with Cs, but PNa,non was substantially increased. The time constant tau h inactivation of the sodium system was slightly increased during dialysis with TMA in place of Cs, and there were small shifts in the steady-state inactivation curve, but the rate of recovery from inactivation was not measurably altered. The flattening off of the tau h curve at increasingly positive test potentials corresponded to a steady reduction of the apparent inactivation charge until a value of about 0.2e was reached for pulses to 100 mV. The instantaneous I-V relationship in the steady state was also investigated. The results have a useful bearing on the effects of dialysis with TMA, on the differences between the initial and steady open states of the sodium channel, and on the relative voltage-dependences of the transitions in each direction between the resting and inactivated states.     

Interaction of surfactants with model and biological membranes. II. Effect of N-alkyl-N,N,N-trimethylammonium ions on phosphatidylcholine bilayers as studied by spin probe ESR

The interaction of N-alkyl-N,N,N-trimethylammonium (CnTMA, n = 6-18) salts (iodides and/or bromides) with model membranes prepared by hydration of egg yolk phosphatidylcholine (EYPC) over aqueous salt solutions has been studied by m-doxyl stearic acid (m-DSA, m = 12 and 16) spin probe method. In disoriented EYPC bilayers the CnTMA salts decrease the orientational order parameter S33 of m-DSA evaluated from the powder pattern ESR spectra. This effect is maximal for C6TMA. In oriented EYPC bilayers prepared by the parallel-beam sputtering method and hydrated over saturated NaCl solution the order parameter S33 calculated from the angular dependence of the nitrogen hyperfine splitting is decreased in the presence of C6TMA. The order parameter S11 obtained from the angular dependence of line positions indicates deviation of m-DSA motion from axial symmetry. C6TMA increases the probability of gauche conformations of the lipid chains by about 13-14%, and decreases the effective energy difference between the trans and gauche conformations by about 420-480 J/mol, at molar ratio of EYPC/C6TMA = 2:1. The angular dependence of linewidths is analysed by employing a theory of spin relaxation based on the strong collision model for molecular reorientations. The correlation time tau 0 of the reorientation of an axis orthogonal to the doxyl ring of 16-DSA is decreased in the presence of C6TMA, while that of 12-DSA is not influenced by it. The ratio of tau 2/tau 0 is increased in the presence of C6TMA for the both spin probes. The results are explained using the free-volume model of the CnTMA-EYPC membrane interaction.     

Energetics of permeation of thin lipid membranes by ions

The energy of an ion in a thin hydrocarbon membrane relative to its energy in a bulk aqueous phase is considered in terms of the electrostatic and surface components that may be expected to be involved. Except when diffusion activation energies are large compared to partition free energies, the latter will control permeation rate and the state of an ion having the lowest partition energy will be critical for its permeability. This minimum is found when an ion is surrounded with a thin layer of water. All ions of the same charge will tend to be at their lowest state in a sphere of water of the same size. It is concluded, therefore, that all ions of a given charge will have about the same permeability in lipid membranes.     

Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group

The hydrophobicity of the peptide C=O ... H-N hydrogen-bonded group is an important parameter that determines the structure of proteins in water and in biological membranes, and therefore the free energy of transferring this group from water to non-polar solvents should be determined accurately. The essential work on this problem was carried out by Klotz and co-workers, and has been summarized elsewhere. Using N-methylacetamide as a model peptide, the free energies of the following processes were determined; (1) formation of the C=O ... H-N bond in water, (2) formation of the C=O ... N-N bond in CCl4, and (3) transfer of N-methylacetamide from water to CCl4. (4) From (3), the free energy of transferring the non-hydrogen bonded (C=O, H-N) group from water to CCl4 was calculated. When the free energies of (1), (2) and (4) are combined, one finds that the free energy of transferring the C=O ... H-N group from water to CCl4 is a surprising -1.4 kcal/mol (1 cal = 4.184 J). This number does not seem reasonable, since it implies that the C=O ... H-N group is about as hydrophobic as an isopropyl group, i.e. the side-chain of valine. In the present report, it is shown that this apparent hydrophobicity results from an underestimation of the free energy contribution that the methyl groups make to the transfer of N-methylacetamide from water to CCl4. When appropriate methyl group transfer free energies are used, one finds that the free energy of transferring the C=O ... H-N group from water to CCl4 is +0.62 kcal/mol. Therefore, this group is relatively insensitive to solvent polarity. A similar calculation shows that the free energy of transferring the C=O ... H-O hydrogen-bonded group from water to benzene is +0.55 kcal/mol.     

Energetics and the design principles of the Na/K-ATPase

Following on the pioneering analysis by Pickart and Jencks of the energetics of the calcium pump, the present mini review attempts a similar analysis of the somewhat more complicated sodium--and potassium--activated ATPase pump-enzyme. The analysis is based on the measurements of the rate-constants of the individual steps in the enzymic reaction which brings about pumping and uses data assembled by Stürmer et al., in the laboratory of Peter L?uger in Konstanz. The aim of such an analysis is to calculate the overall free energy released on ATP hydrolysis and to apportion this energy among the successive steps of the pump-enzyme reaction. We calculate the so-called basic free energy changes that take into account the prevailing ligand and ion concentrations, rather than the standard-state free energies that refer to 1 M concentrations of these ions and ligands. Using appropriate values of the ion and ligand concentrations in cardiac muscle, the available free energy which can be released from the hydrolysis of ATP (at 20 degrees C) comes out at 575 mV. Following a complete cycle of pumping, 371 mV of this free energy are found stored in the sodium and potassium ion gradients. The remaining 204 mV from the free energy of hydrolysis of ATP are lost to the ATP system. This part of the energy, that had been transduced into the concentration gradient of sodium, has presumably been used in the living cell to drive the co- and counter-transport (symport and antiport) of ions and metabolites in secondary transports. The free energy changes are pretty evenly apportioned along the various steps in the pumping cycle. The steps that one might naively have thought to be "powered", such as the step in which covalently bound phosphate is transformed from a high-energy to a low-energy state, or the step in which sodium is released into the phase containing a high concentration of sodium, show some of the lowest drops of free energy, 61 mV and 27 mV, respectively. The most surprising step in the overall reaction of ATP hydrolysis and synthesis is the phosphorylation of the protein from inorganic phosphate with formation of the acylphosphate bond. The stabilization of the acylphosphate bond presumably arises from ionic interactions between the covalently bound phosphate itself and appropriate groupings on the enzyme. ATP formation on the F0F1 ATPase (the F-type ATPase) is in an analogous way stabilized in the first place by phospho-ligand/enzyme interactions.     

Effects of the dietary supplements, activated charcoal and copper chlorophyllin, on urinary excretion of trimethylamine in Japanese trimethylaminuria patients

Trimethylaminuria (TMAU) is a metabolic disorder characterized by the inability to oxidize and convert dietary-derived trimethylamine (TMA) to trimethylamine N-oxide (TMAO). This disorder has been relatively well-documented in European and North American populations, but no reports have appeared regarding patients in Japan. We identified seven Japanese individuals that showed a low metabolic capacity to convert TMA to its odorless metabolite, TMAO. The metabolic capacity, as defined by the concentration of TMAO excreted in the urine divided by TMA concentration plus TMAO concentration, in these seven individuals ranged from 70 to 90%. In contrast, there were no healthy controls examined with less than 95% of the metabolic capacity to convert TMA to TMAO. The intake of dietary charcoal (total 1.5 g charcoal per day for 10 days) reduced the urinary free TMA concentration and increased the concentration of TMAO to normal values during charcoal administration. Copper chlorophyllin (total 180 mg per day for 3 weeks) was also effective at reducing free urinary TMA concentration and increasing TMAO to those of concentrations present in normal individuals. In the TMAU subjects examined, the effects of copper chlorophyllin appeared to last longer (i.e., several weeks) than those observed for activated charcoal. The results suggest that the daily intake of charcoal and/or copper chlorophyllin may be of significant use in improving the quality of life of individuals suffering from TMAU.     

Protein compressibility, dynamics, and pressure

The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure.     

Metabolism of trimethylamines in kelp bass (Paralabrax clathratus) and marine and freshwater pink salmon (Oncorhynchus gorbuscha)

Summary ³H or¹⁴C labeled tracers were used to investigate the metabolism of trimethylamine (TMA), trimethylamine oxide (TMAO), choline, and betaine in free swimming kelp bass (Paralabrax clathratus). An indwelling cannula in the ventral aorta was used to administer tracer and withdraw blood samples. The concentrations of TMA and TMAO were determined in liver, muscle, and plasma. The TMA liver content is higher than that of muscle (0.85 vs 0.01 moles/g wet tissue) while the amount of TMAO in muscle greatly exceeds its liver concentration (60 vs 0.04 moles/g wet tissue). Prolonged fasting (21 and 75 days) or feeding the fish a squid diet containing high levels of TMAO did not alter the tissue concentrations of TMA or TMAO, suggesting that these compounds are endogenous in origin and that their tissue concentrations are subject to regulation. Comparison of the radiospecific activities of TMA and TMAO, and the administered TMA tracer suggest that TMA is channled directly to TMAO in the liver without equilibration in the hepatic TMA pool. The conversion kinetics of TMA to TMAO and the distribution of these amines in liver and muscle with time suggest that labeled TMA is rapidly taken up into a sequestered pool from which it is slowly released, oxidized to TMAO in the liver, and then transported via the circulation to the muscle mass. The location of this proposed sequestered TMA pool was not determined. Experiments with labeled choline and betaine suggest that these compounds are interconverted in the liver and that enzymes are present for conversion of choline betaine TMA TMAO. Labeled dimethylamine (DMA) was not metabolized and is, therefore, probably not a precursor of TMA and TMAO. [¹⁴C]Trimethylamine (TMA) was also used to investigate the possible role of trimethylamine oxide (TMAO) as an osmoregulatory compound in migrating prespawning cannulated Pacific pink salmon (Oncorhynchus gorbuscha) taken from marine or fresh water environments. Marine and fresh water salmon oxidized administered [¹⁴C]TMA to TMAO; labeled metabolites other than TMA and TMAO were not detected. Four hours after [¹⁴C]TMA injection about 10% of the administered dose was present in muscle as labeled TMAO and about 33% as TMA. Unlike our finding in kelp bass, [¹⁴C]TMAO was not recovered in liver, although low amounts of labeled TMA were found (0.4% of administered dose). Labeled TMA and TMAO, however, were detected in liver after [¹⁴C]betaine adminstration to a marine salmon, indicating that TMA-mono-oxygenase is present in salmon liver. The presence of labeled choline indicates that choline and betaine are interconverted as in kelp bass. The amount of [¹⁴C]TMA oxidized to [¹⁴C]TMAO and then accumulated in the muscle mass is the same in marine and fresh water salmon, as is the amount of chemical TMAO present (4.6 moles/g muscle).     

Aliphatics vs. aromatics hydration thermodynamics

By comparing the hydration thermodynamics of benzene with that of a hypothetical aliphatic hydrocarbon having the same accessible surface area (ASA) of benzene, Makhatadze and Privalov concluded that the whole difference is due to the weak H-bonds that water forms with the aromatic ring. The formation of such H-bonds would be characterized by a negative Gibbs energy change, slightly increasing in magnitude with temperature, and a positive entropy change over a large temperature range. The latter thermodynamic feature is not physically reliable for the formation of H-bonds. In the present article, by using a statistical mechanical dissection scheme of hydration, a microscopic interpretation for the numbers obtained by Makhatadze and Privalov is proposed. The difference in hydration Gibbs energy should be attributed to the different strength of van der Waals interactions that benzene can do with water, owing to the larger polarizability of the aromatic ring with respect to an aliphatic hydrocarbon of equal size. In addition, the difference in hydration entropy should account for the different extent of H-bond reorganization upon the insertion of benzene and the corresponding aliphatic hydrocarbon in water.     

Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations

Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two-dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring-opening process takes place through an S(N)2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B-catalyzed cAMP hydrolysis is about 13 kcal·mol(-1) and an overall reaction free energy is about -17 kcal·mol(-1), both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol(-1). We found that the proton transfer from the general acid residue His234 to the O3' oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn(2+) and Mg(2+) in the active site as the reaction proceeds from the Michaelis complex to the transition state.     

The oxenoid model of the mechanism of activating molecular oxygen by cytochrome p450: the role of substrate structure

The arene oxides formation energy for about 30 benzene derivatives were calculated in frames of MO LCAO method. The benzene derivatives are typical substrates of cytochrome P-450 catalyzed aromatic oxidation. The relationship between the formation energy of tetrahedral type arene oxides and the relative reactivity of substrates toward microsomal hydroxylation was found. The formation energy of arene oxides correlates also with toxicity of benzene derivatives. Some limitations of the oxenoid model are discussed.     

A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity.

The influence of a gramicidin-like channel former on ion free energy barriers is studied using Monte Carlo simulation. The model explicitly describes the ion, the water dipoles, and the peptide carbonyls; the remaining degrees of freedom, bulk electrolyte, non-polar lipid and peptide regions, and electronic (high frequency) permittivity, are treated in continuum terms. Contributions of the channel waters and peptide COs are studied both separately and collectively. We found that if constrained to their original orientations, the COs substantially increase the cationic permeation free energy; with or without water present, CO reorientation is crucial for ion-CO interaction to lower cation free energy barriers; the translocation free energy profiles for potassium-, rubidium-, and cesium-like cations exhibit no broad barriers; the lipid-bound peptide interacts more effectively with anions than cations; anionic translocation free energy profiles exhibit well defined maxima. Using experimental data to estimate transfer free energies of ions and water from bulk electrolyte to a non-polar dielectric (continuum lipid), we found reasonable ion permeation profiles; cations bind and permeate, whereas anions cannot enter the channel. Cation selectivity arises because, for ions of the same size and charge, anions bind hydration water more strongly.