Equilibrium binding constants for the group I metal cations with gramicidin-A determined by competition studies and T1+-205 nuclear magnetic resonance spectroscopy

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Despite the progress in modeling complex molecular systems of ever-increasing complexity, a quantitatively accurate computational treatment of ion permeation through narrow membrane channels remains challenging. An important factor to reach this goal is induced electronic polarization, which is likely to impact the permeation rate of small ions through narrow molecular pores. In this work, we extended the recently developed polarizable force field based on the classical Drude oscillators to assess the role of induced polarization effects on the energetics of sodium and potassium ion transport across the gramicidin A (gA) ion channel. The inclusion of induced polarization lowers barriers present in 1D potential of mean force (PMF) for cation permeation by ∼50% compared to those obtained with the additive force field. Conductance properties calculated with 1D PMFs from Drude simulations are in better agreement with experimental results. Polarization of single-file water molecules and protein atoms forming the narrow pore has a direct impact on the free-energy barriers and cation-specific solid-state NMR chemical shifts. Sensitivity analysis indicates that small changes to water-channel interactions can alter the free energy barrier for ion permeation. These results, illustrating polarization effects present in the complex electrostatic environment of the gA channel, have broad implications for revising proposed mechanisms of ion permeation and selectivity in a variety of ion channels.

The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity

Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.

Measurements of Ion Binding to Lipid-Hosted Ionophores by Affinity Chromatography

The binding affinity between antibiotic ionophores and alkali ions within supported lipid bilayers was evaluated using affinity chromatography. We used zonal elution and frontal analysis methods in nanovolume liquid chromatography to characterize the binding selectivity of the carrier and channel ionophores valinomycin and gramicidin A within different phosphatidylcholine bilayers. Distinct binding sensitivity to the lipid phase, both in affinity and selectivity, is observed for valinomycin, whereas gramicidin is less sensitive to changes in a membrane environment, behavior that is consistent with ion binding occurring within the interior of an established channel. There is good agreement between the chromatographic retention and the reported binding selectivity measured by other techniques. Surface potential near the binding site affects ion retention and the apparent association binding constants, but not the binding selectivity or enthalpy measurements. A model accounting for the surface potential contributions of retained ions during frontal analyses yields values close to intrinsic binding constants for gramicidin A (K_A for K⁺ between 70 and 120 M^-1) using reasonable estimates of the initial potential that is postulated to arise from the underlying silica.

Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K ions

Guanine quadruplex (G-quadruplex) structures play a vital role in stabilizing the DNA genome and in protecting healthy cells from transforming into cancer cells. The structural stability of G-quadruplexes is greatly enhanced by the binding of monovalent cations such as Na⁺ or K⁺ into the interior axial channel. We computationally study the free energy of binding of Na⁺ and K⁺ ions to two intramolecular G-quadruplexes that differ considerably in their degree of rigidity and the presence or absence of terminal nucleotides. The goal of our study is two-fold. On the one hand, we study the free energy of binding every ion, which complements the experimental findings that report the average free energy for replacing Na⁺ with K⁺ ions. On the other hand, we examine the role of the G-quadruplex structure in the binding free energy. In the study, we employ all-atom molecular dynamics simulations and the alchemical transformation method for the computation of the free energies. To compare the cation-dependent contribution to the structural stability of G-quadruplexes, we use a two-step approach to calculate the individual free energy difference ΔG of binding two Na⁺ and two K⁺ to two G-quadruplexes: the unimolecular DNA d[T₂GT₂(G₃T)₃] (Protein Data Bank ID 2M4P) and the human telomeric DNA d[AGGG(TTAGGG)₃] (PDB ID 1KF1). In contrast to the experimental studies that estimate the average free energy of binding, we find a varying difference of approximately 2-9 kcal/mol between the free energy contribution of binding the first and second cation, Na⁺ or K⁺. Furthermore, we found that the free energy of binding K⁺ is not affected by the chemical nature of the two quadruplexes. By contrast, Na⁺ showed dependency on the G-quadruplex structure; the relatively small size allows Na⁺ to explore larger configurational space than K⁺. Numerical results presented here may offer reference values for future design of cationic drug-like ligands that replace the metal ions in G-quadruplexes.

Does cation break the cyano bond? A critical evaluation of nitrile-cation interaction

DFT and G4 results reveal that cations display the following trends in imparting its positive charge to acrylonitrile; H⁺ > Li⁺ > Na⁺ > K⁺ for group I and Be²⁺ > Mg²⁺ > Ca²⁺ for group II. Solvation by water molecules and interaction with cation make the cyano bond more polarized and exhibits ketene-imine character. Bond order in nitrile-cation complexes has been predicted based on the s character of the covalent bond orbitals. Mulliken, CHELPG, and NPA charges are in good agreement in predicting positive charge buildup and GIAO nuclear deshileding on C1. G4 enthalpies show that Mg²⁺ is more strongly bound to acrylonitrile than to acetonitrile by 3 kcal mol⁻¹, and the proton affinity of the former is higher by 0.8 kcal mol⁻¹. G4 enthalpies of reductions support prior experimental observation that metalated conjugated nitriles show enhanced reactivity toward weak nucleophiles to afford Michael addition products.

Atomic-level simulation of current-voltage relationships in single-file ion channels

The difficulty in characterizing ion conduction through membrane channels at the level of individual permeation events has made it challenging to elucidate the mechanistic principles underpinning this fundamental physiological process. Using long, all-atom simulations enabled by special-purpose hardware, we studied K⁺ permeation across the K_V1.2/2.1 voltage-gated potassium channel. At experimentally accessible voltages, which include the physiological range, the simulated permeation rate was substantially lower than the experimentally observed rate. The current–voltage relationship was also nonlinear but became linear at much higher voltages. We observed permeation consistent with a “knock-on” mechanism at all voltages. At high voltages, the permeation rate was in accordance with our previously reported K_V1.2 pore-only simulations, after the simulated voltages from the previous study were recalculated using the correct method, new insight into which is provided here. Including the voltage-sensing domains in the simulated channel brought the linear current–voltage regime closer to the experimentally accessible voltages. The simulated permeation rate, however, still underestimated the experimental rate, because formation of the knock-on intermediate occurred too infrequently. Reducing the interaction strength between the ion and the selectivity filter did not increase conductance. In complementary simulations of gramicidin A, similar changes in interaction strength did increase the observed permeation rate. Permeation nevertheless remained substantially below the experimental value, largely because of infrequent ion recruitment into the pore lumen. Despite the need to apply large voltages to simulate the permeation process, the apparent voltage insensitivity of the permeation mechanism suggests that the direct simulation of permeation at the single-ion level can provide fundamental physiological insight into ion channel function. Notably, our simulations suggest that the knock-on permeation mechanisms in K_V1.2 and KcsA may be different.

Binding of Organic Cations to Gramicidin A Channel Studied with AutoDock and Molecular Dynamics Simulations

The accurate description of protein-ligand binding energies and configurations is an important problem in molecular biology with many applications in medicine and pharmacology. Molecular dynamics (MD) simulations provide the required accuracy but they are too slow for searching binding positions. Conversely, docking methods are much faster but have limited accuracy. An appropriate combination of the two methods could avoid the shortcomings associated with each, thus offering a better approach to the protein-ligand binding problem. Here we investigate the feasibility of such a combined docking-MD approach in a well-defined system: binding of organic cations to the gramicidin A channel. We use the AutoDock program to generate a set of protein-ligand binding configurations, which are then refined in MD simulations. For each system, we examine the binding configuration in detail and calculate the binding free energy by constructing the potential of mean force for the ligand. Our results show that AutoDock provides suitable initial configurations, which can be used profitably in MD simulations to obtain an accurate description of protein-ligand binding with a reasonable computational effort.

Free energy simulations of single and double ion occupancy in gramicidin A

Simultaneous occupancy of the two binding sites in gramicidin A by monovalent cations is a well known property of this channel, but the energetic feasibility of this process in molecular dynamics simulations has not been established so far. Here the authors study the energetics of single and double ion occupancy in gramicidin A by constructing the potential of mean force for single and pair of cations. As representatives of small and large ions, they consider both Na+ and K+ ions in the calculations. Binding constants of ions are estimated from the free energy profiles. Comparisons with the experimental results indicate 3-4 kT discrepancy in the binding energies. They also study the coordination of the ions in their respective binding sites and the dynamic behavior of the channel water during the double ion binding process.

Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex

The crystal structure of the Tl+ form of the G-quadruplex formed from the Oxytricha nova telomere sequence, d(G4T4G4), has been solved to 1.55 A. This G-quadruplex contains five Tl+ ions, three of which are interspersed between adjacent G-quartet planes and one in each of the two thymine loops. The structure displays a high degree of similarity to the K+ crystal structure [Haider et al. (2002), J. Mol. Biol., 320, 189-200], including the number and location of the monovalent cation binding sites. The highly isomorphic nature of the two structures, which contain such a large number of monovalent binding sites (relative to nucleic acid content), verifies the ability of Tl+ to mimic K+ in nucleic acids. Information from this report confirms and extends the assignment of 205Tl resonances from a previous report [Gill et al. (2005), J. Am. Chem. Soc., 127, 16 723-16 732] where 205Tl NMR was used to study monovalent cation binding to this G-quadruplex. The assignment of these resonances provides evidence for the occurrence of conformational dynamics in the thymine loop region that is in slow exchange on the 205Tl timescale.

Chance and design—Proton transfer in water, channels and bioenergetic proteins

Proton transfer and transport in water, gramicidin and some selected channels and bioenergetic proteins are reviewed. An attempt is made to draw some conclusions about how Nature designs long distance, proton transport functionality. The prevalence of water rather than amino acid hydrogen bonded chains is noted, and the possible benefits of waters as the major component are discussed qualitatively.

Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields

We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence of the PMF, finite size effects, and lipid hydrocarbon chain polarizability. When comparing the modern all-atom force fields of CHARMM27 and AMBER94, we found that a fairly consistent picture emerges, and that both AMBER94 and CHARMM27 predict observables that are in semiquantitative agreement with both the experimental conductance and dissociation coefficient. Even small changes in the force field, however, result in significant changes in permeation energetics. Furthermore, the full two-dimensional free-energy surface describing permeation reveals the location and magnitude of the central barrier and the location of two binding sites for K(+) ion permeation near the channel entrance--i.e., an inner site on-axis and an outer site off-axis. We conclude that the MD-PMF approach is a powerful tool for understanding and predicting the function of narrow ion channels in a manner that is consistent with the atomic and thermally fluctuating nature of proteins.

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels

Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations

The rigid force fields currently used in molecular dynamics (MD) simulations of biomolecules are optimized for globular proteins. Whether they can also be used in MD simulations of membrane proteins is an important issue that needs to be resolved. Here we address this issue using the gramicidin A channel, which provides an ideal test case because of the simplicity of its structure and the availability of a wealth of functional data. Permeation properties of gramicidin A can be summarized as "it conducts monovalent cations, rejects anions, and binds divalent cations." Hence, a comprehensive test should consider the energetics of permeation for all three types of ions. To that end, we construct the potential of mean force for K(+), Cl(-), and Ca(2+) ions along the channel axis. For an independent check of the potential-of-mean-force results, we also calculate the free energy differences for these ions at the channel center and binding sites relative to bulk. We find that "rejection of anions" is satisfied but there are difficulties in accommodating the other two properties using the current MD force fields.

Ion solvation by channel carbonyls characterized by 17O solid-state NMR at 21 T

Recently available ultrahigh magnetic fields offer new opportunities for studies of quadrupole nuclei in biological solids because of the dramatic enhancement in sensitivity and resolution associated with the reduction of second-order quadrupole interactions. Here, we present a new approach for understanding the function and energetics of ion solvation in channels using solid-state 17O NMR spectroscopy of single-site 17O-labeled gramicidin A. The chemical shift and quadrupole coupling parameters obtained in powder samples of lyophilized material are similar to those shown in the literature for carbonyl oxygens. In lipid bilayers, it is found that the carbonyl 17O anisotropic chemical shift of Leu10, one of the three carbonyl oxygens contributing to the ion binding site in gramicidin A, is altered by 40 ppm when K+ ion binds to the channel, demonstrating a high sensitivity to such interactions. Moreover, considering the large breadth of the carbonyl 17O chemical shift (>500 ppm), the recording of anisotropic 17O chemical shifts in bilayers aligned with respect to magnetic field B0 offers high-quality structural restraints similar to 15N and 13C anisotropic chemical shifts.

205Tl NMR Methods for the Characterization of Monovalent Cation Binding to Nucleic Acids

Monovalent cations play an important role in many biological functions. The guanine rich sequence, d(G4T4G4), requires monovalent cations for formation of the G-quadruplex, d(G4T4G4)2. This requirement can be satisfied by thallium (Tl+), a potassium (K+) surrogate. To verify that the structure of d(G4T4G4)2 in the presence of Tl+ is similar to the K+-form of the G-quadruplex, the solution structure of the Tl+-form of d(G4T4G4)2 was determined. The 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A. Comparison of this structure to the identical G-quadruplex formed in the presence of K+ validates the isomorphous nature of Tl+ and K+. Using a 1H-205Tl spin-echo difference experiment we show that, in the Tl+-form of d(G4T4G4)2, small scalar couplings (<1 Hz) exist between 205Tl and protons in the G-quadruplex. These data comprise the first 1H-205Tl scalar couplings observed in a biological system and have the potential to provide important constraints for structure determination. These experiments can be applied to any system in which the substituted Tl+ cations are in slow exchange with the bulk ions in solution.

Ultra-wide bore 900 MHz high-resolution NMR at the National High Magnetic Field Laboratory

Access to an ultra-wide bore (105 mm) 21.1 T magnet makes possible numerous advances in NMR spectroscopy and MR imaging, as well as novel applications. This magnet was developed, designed, manufactured and tested at the National High Magnetic Field Laboratory and on July 21, 2004 it was energized to 21.1 T. Commercial and unique homebuilt probes, along with a standard commercial NMR console have been installed and tested with many science applications to develop this spectrometer as a user facility. Solution NMR of membrane proteins with enhanced resolution, new pulse sequences for solid state NMR taking advantage of narrowed proton linewidths, and enhanced spatial resolution and contrast leading to improved animal imaging have been documented. In addition, it is demonstrated that spectroscopy of single site (17)O labeled macromolecules in a hydrated lipid bilayer environment can be recorded in a remarkably short period of time. (17)O spectra of aligned samples show the potential for using this data for orientational restraints and for characterizing unique details of cation binding properties to ion channels. The success of this NHMFL magnet illustrates the potential for using a similar magnet design as an outsert for high temperature superconducting insert coils to achieve an NMR magnet with a field >25 T.

Effects of phenylalanine substitutions in gramicidin A on the kinetics of channel formation in vesicles and channel structure in SDS micelles

The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp-->Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two beta6.3 helices joined by six hydrogen bonds at their NH2-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics.

Energetics of ion conduction through the gramicidin channel

The free energy governing K(+) conduction through gramicidin A channels is characterized by using over 0.1 micros of all-atom molecular dynamics simulations with explicit solvent and membrane. The results provide encouraging agreement with experiments and insights into the permeation mechanism. The free energy surface of K(+), as a function of both axial and radial coordinates, is calculated. Correcting for simulation artifacts due to periodicity and the lack of hydrocarbon polarizability, the calculated single-channel conductance for K(+) ions is 0.8 pS, closer to experiment than any previous calculation. In addition, the estimated single ion dissociation constants are within the range of experimental determinations. The relatively small free energy barrier to ion translocation arises from a balance of large opposing contributions from protein, single-file water, bulk electrolyte, and membrane. Mean force decomposition reveals a remarkable ability of the single-file water molecules to stabilize K(+) by -40 kcal/mol, roughly half the bulk solvation free energy. The importance of the single-file water confirms the conjecture of Mackay et al. [Mackay, D. H. J., Berens, P. H., Wilson, K. R. & Hagler, A. T. (1984) Biophys. J. 46, 229-248]. Ion association with the channel involves gradual dehydration from approximately six to seven water molecules in the first shell, to just two inside the narrow pore. Ion permeation is influenced by the orientation of the single-file water column, which can present a barrier to conduction and give rise to long-range coupling of ions on either side of the pore. Small changes in the potential function, including contributions from electronic polarization, are likely to be sufficient to obtain quantitative agreement with experiments.

The structure, cation binding, transport, and conductance of Gly15-gramicidin A incorporated into SDS micelles and PC/PG vesicles

To further investigate the effect of single amino acid substitution on the structure and function of the gramicidin channel, an analogue of gramicidin A (GA) has been synthesized in which Trp(15) is replaced by Gly in the critical aqueous interface and cation binding region. The structure of Gly(15)-GA incorporated into SDS micelles has been determined using a combination of 2D-NMR spectroscopy and molecular modeling. Like the parent GA, Gly(15)-GA forms a dimeric channel composed of two single-stranded, right-handed beta(6.3)-helices joined by hydrogen bonds between their N-termini. The replacement of Trp(15) by Gly does not have a significant effect on backbone structure or side chain conformations with the exception of Trp(11) in which the indole ring is rotated away from the channel axis. Measurement of the equilibrium binding constants and Delta G for the binding of monovalent cations to GA and Gly(15)-GA channels incorporated into PC vesicles using (205)Tl NMR spectroscopy shows that monovalent cations bind much more weakly to the Gly(15)-GA channel entrance than to GA channels. Utilizing the magnetization inversion transfer NMR technique, the transport of Na(+) ions through GA and Gly(15)-GA channels incorporated into PC/PG vesicles has been investigated. The Gly(15) substitution produces an increase in the activation enthalpy of transport and thus a significant decrease in the transport rate of the Na(+) ion is observed. The single-channel appearances show that the conducting channels have a single, well-defined structure. Consistent with the NMR results, the single-channel conductances are reduced by 30% and the lifetimes by 70%. It is concluded that the decrease in cation binding, transport, and conductance in Gly(15)-GA results from the removal of the Trp(15) dipole and, to a lesser extent, the change in orientation of Trp(11).

Thallous ion movements through gramicidin channels incorporated in lipid monolayers supported by mercury

The potential independent limiting flux of hydrated Tl(+) ions through gramicidin (GR) channels incorporated in phospholipid monolayers self assembled on a hanging mercury-drop electrode is shown to be controlled both by diffusion and by a dehydration step. Conversely, the potential independent limiting flux of dehydrated Tl(+) ions stemming from Tl amalgam electro-oxidation is exclusively controlled by diffusion of thallium atoms within the amalgam. Modulating the charge on the polar heads of dioleoylphosphatidylserine (DOPS) by changing pH affects the limiting flux of hydrated Tl(+) ions to a notable extent, primarily by electrostatic interactions. The dipole potential of DOPS and dioleoylphosphatidylcholine (DOPC), positive toward the hydrocarbon tails, does not hinder the translocation step of Tl(+) ions to such an extent as to make it rate limiting. Consequently, incorporation in the lipid monolayer of phloretin, which decreases such a positive dipole potential, does not affect the kinetics of Tl(+) flux through GR channels. In contrast, the increase in the positive dipole potential produced by the incorporation of ketocholestanol causes the translocation step to contribute to the rate of the overall process. A model providing a quantitative interpretation of the kinetics of diffusion, dehydration-hydration, translocation, and charge transfer of the Tl(+)/Tl(0)(Hg) couple through GC channels incorporated in mercury-supported phospholipid monolayers is provided. A cut-off disk model yielding the profile of the local electrostatic potential created by an array of oriented dipoles located in the lipid monolayer along the axis of a cylindrical ion channel is developed.

Conducting gramicidin channel activity in phospholipid monolayers

Potential step amperometry (chronoamperometry) of the Tl(I)/Tl(Hg) electrochemical reduction process has been used to investigate the underlying mechanisms of gramicidin activity in phospholipid monolayers. The experiments were carried out at gramicidin-modified dioleoyl phosphatidylcholine (DOPC)-coated electrodes. Application of a potential step to the coated electrode system results in a current transient that can be divided into two regions. An initial exponential decay of current corresponds to the inactivation of monomer channel conductance and a longer time scale quasi-steady-state represents the diffusion of ions to a bimolecular surface reaction. Concentrations of monomer conducting channels are relatively low, and the results indicate that two or more forms of gramicidin are in equilibrium with each other in the layer. Aromatic/conjugated compounds incorporated into the monolayer increase the reduction current by decreasing the rate of channel inactivation and increasing the stability of the conducting channel. This effect is positively correlated with the degree of the compound's aromaticity. The anomalous influence of alkali metal ions on the reduction current is consistent with the model of gramicidin being speciated in the monolayer in more than one form. The results have implications on the lability of the peptide conformation in biological membranes and its dependence on lipid environment, solution composition, and applied potential.

Cation transport: an example of structural based selectivity

Through the high-resolution structure of the gramicidin A channel in lamellar phase lipids and the characterization of specific ion peptide interactions, fundamental principles for ion channel selectivity and conductance efficiency are illustrated with atomic resolution detail. Delocalized cation binding in the first turn of the helix reduces the unfavorable entropy contribution upon binding. Stepwise dehydration minimizes the energy barrier for cation entry and provides valence selectivity in this channel. Three or more water molecules in the monovalent cation binding site result in flexibility in the cation solvation environment causing weak cation size selectivity. Lack of cation induced structural modification avoids the formation of a significant energy barrier, thus permitting efficient cation transport.

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor

Metal ions are essential for the folding and activity of large catalytic RNAs. While divalent metal ions have been directly implicated in RNA tertiary structure formation, the role of monovalent ions has been largely unexplored. Here we report the first specific monovalent metal ion binding site within a catalytic RNA. As seen crystallographically, a potassium ion is coordinated immediately below AA platforms of the Tetrahymena ribozyme P4-P6 domain, including that within the tetraloop receptor. Interference and kinetic experiments demonstrate that potassium ion binding within the tetraloop receptor stabilizes the folding of the P4-P6 domain and enhances the activity of the Azoarcus group I intron. Since a monovalent ion binding site is integral to the tetraloop receptor, a tertiary structural motif that occurs frequently in RNA, monovalent metal ions are likely to participate in the folding and activity of a wide diversity of RNAs.

Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study

The valence selectivity of the gramicidin channel is examined using computer simulations based on atomic models. The channel interior is modeled using a gramicidin-like periodic poly (L,D)-alanine beta-helix. Free energy perturbation calculations are performed to obtain the relative affinity of K+ and Cl- for the channel. It is observed that the interior of the gramicidin channel provides an energetically favorable interaction site for a cation but not for an anion. Relative to solvation in bulk water, the carbonyl CO oxygens can provide a favorable interaction to stabilize K+, whereas the amide NH hydrogens are much less effective in stabilizing Cl-. The results of the calculations demonstrate that, as a consequence of the structural asymmetry of the backbone charge distribution, a K+ cation can partition spontaneously from bulk water to the interior of the gramicidin channel, whereas a Cl- anion cannot.

Monovalent cation transport: lack of structural deformation upon cation binding

Cations often deform the structure of regulatory proteins to affect a functional response, but for other protein functions a more passive effect is desired. For instance, it is shown here that in the conductance of Na+ by the gramicidin channel there appears to be no significant structural deformation of either the side chains or backbone upon Na+ binding in the channel. This is based on 15N and 13C chemical shifts, 2H quadrupolar interactions, and 15N-2H dipolar interactions obtained by solid-state NMR spectroscopy of uniformly aligned lipid bilayer preparations of the gramicidin channel in the presence and absence of Na+. This conclusion is despite some significant changes in the 15N alpha and 13C1 chemical shift values which are argued here to be the result of indirect polarization effects upon cation binding rather than reflections of structural and dynamic changes. The lack of structural deformation implies that Na+ moves to the carbonyl oxygens lining the pore of this channel for solvation rather than the carbonyl groups moving in toward the channel axis. This forces the cations onto a helical path following the positions of the carbonyl oxygens around the channel pore. Furthermore, an ideal binding site geometry for Na+ in the channel is avoided. Instead, adequate binding energy is provided by the channel to compensate for the loss of hydration energy when the cations enter the channel. The avoidance of strong binding ensures that efficient transport of the cations through the channel can be realized.

The determination of binding constants of micellar-packaged gramicidin A by 13C-and 23Na-NMR

Based on the malonyl gramicidin A structure of a single-stranded head-to-head hydrogen bonded right-handed, beta 6.3-helix in dodecyl phosphocholine (DPC) lipid micelles (Jing et al. (1994) Biophys. J. 66, A353), the determination of cation binding sites for gramicidin A (GA) in DPC micelles becomes a significant step in the study of ion transport through the model channel. First, the investigation of cation binding sites in DPC micellar packaged gramicidin A was achieved by 13C-NMR experiments at 30 degrees C using four C-13 labeled GA samples. Then, the analyses based on two different equations, one for single and one for double occupancy, were employed to evaluate the correct occupancy model for GA in DPC micelles. The results clearly indicate double occupancy to be correct for Na+ ion as well as for K+, Rb+, Cs+, and Tl+ ions. Finally, the binding constants for Na+ ion were also estimated by the measurement of the longitudinal relaxation time (T1) using 23Na-NMR of the same sample at the same ffmperature as used for the 13C-NMR study. The binding constants obtained from 23Na-NMR are essentially equivalent to those determined from the 13C-chemical shifts.

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy

The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy perturbation methods. The relative free energy of binding of all of the five common cations Li+, Na+, K+, Rb+, and Cs+ is calculated in the singly and doubly occupied channel and in bulk water. The atomic system, which includes the gramicidin channel, a model membrane made of neutral Lennard-Jones particles and 190 explicit water molecules to form the bulk region, is similar to the one used in previous work to calculate the free energy profile of a Na+ ion along the axis of the channel. In all of the calculations, the ions are positioned in the main binding sites located near the entrances of the channel. The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions. Thermodynamic decomposition is used to show that the origin of the trend observed in the calculations is due to the loss of favorable interactions between the ion and the single file water molecules inside the channel. Small ions are better solvated by the internal water molecules in the singly occupied state than in the doubly occupied state; bigger ions are solvated almost as well in both occupation states. Water-channel interactions play a role in the channel response. The observed trends are related to general thermodynamical properties of electrolyte solutions.

Ion binding constants for gramicidin A obtained from water permeability measurements

Gramicidin A pores are permeable to water and small monovalent cations. For K, Rb, and Cs there is good evidence from conductances and permeability ratios that a second ion can enter a pore already occupied by another, but for Na this evidence is inconclusive and comparison of tracer fluxes and single channel conductances suggests that second ion entries are prohibited. Partly as a result of the complications of second ion entry there have been widely differing estimates for the dissociation constants for the first ion in the channel. Dani and Levitt (1981, Biophys. J. 35: 485-499) introduced a method for calculating ion binding constants from simultaneous measurements of water fluxes and membrane conductance. They found no evidence for second ion binding and calculated dissociation constants of 115 mM for Li, 69 mM for K, and 2 mM for Tl. It is shown here that the two-ion, four-state model predicts a dependence of water permeability on ion concentration that is difficult to distinguish from the predictions of block by a single ion. Using a modified technique that allows measurement of higher conductances, the first ion dissociation constants have been determined as 80 mM for Na, 40 mM for Rb and 15 mM for Cs. These values and those of Dani and Levitt fall in a smooth sequence. The dissociation constant for Cs is consistent with single channel conductances and flux ratios. There is a discrepancy between this constant for Na and the value, 370 mM, calculated from the single channel conductances and the assumption that a second ion cannot enter or affect an occupied pore. The dissociation constant for Rb is intermediate between those for K and Cs whereas tracer flux measurements (Schagina, Grinfeldt & Lev, 1983. J. Membrane Biol. 73: 203-216) have suggested that Rb interacts much more strongly with the channel than Cs.

Thermodynamic parameters for the binding of divalent cations to gramicidin A incorporated into a lipid environment by Tl-205 nuclear magnetic resonance

Thermodynamic parameters, enthalpy and entropy, for the binding of the divalent cations, Mg+2, Ca+2, Sr+2, Ba+2, and Cd+2, to gramicidin A, incorporated into lysophosphatidylcholine, have been determined using a combination of Tl-205 nuclear magnetic resonance spectroscopy and competition binding. The binding process is thermodynamically driven by the enthalpy and not the entropy. The enthalpy values are related to the process involving the transfer of cations from an aqueous environment to an amide environment. A comparison is made between the thermodynamic parameters for the binding of monovalent and divalent cations to gramicidin A to illustrate the channel blocking ability of the divalent cations with respect to monovalent cation transport.

TI-205 nuclear magnetic resonance determination of the thermodynamic parameters for the binding of monovalent cations to gramicidins A and C

Thermodynamic parameters for the binding of the monovalent cations, Li+, Na+, K+, Rb+, Cs+, NH4+, TI+, and Ag+, to gramicidin A and for the binding of TI+ to gramicidin C, incorporated into lysophosphatidylcholine, have been determined using a combination of TI-205 nuclear magnetic resonance spectroscopy and competition binding. The thermodynamic parameters, enthalpy and entropy, are discussed in terms of a process involving the transfer of cations from an aqueous to amide environment.

Analysis of the binding of Ca2+ to gramicidin A in ethanol in terms of the dimer-monomer conformational equilibrium

This study reports the first direct observation of the binding of Ca2+ to gramicidin A in ethanol, analysed in terms of the polypeptide dimer-monomer conformational equilibrium. High performance size-exclusion chromatography has been successfully used to elucidate the binding mechanism and to determine the rate constants as well as the stoichiometry of the processes involved. In addition, fluorescence intensity and anisotropy measurements have revealed a dependence of the number of accessible Ca2+-binding sites on the peptide concentration.