Monovalent cation transport: lack of structural deformation upon cation binding

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.

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.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations

Gramicidin A (gA) channels provide an ideal system to test molecular dynamics (MD) simulations of membrane proteins. The peptide backbone lines a cation-selective pore, and due to the small channel size, the average structure and extent of fluctuations of all atoms in the peptide will influence ion permeation. This raises the question of how well molecular mechanical force fields used in MD simulations and potential of mean force (PMF) calculations can predict structure and dynamics as well as ion permeation. To address this question, we undertook a comparative study of nuclear magnetic resonance (NMR) observables predicted by fully atomistic MD simulations on a gA dimer embedded in a sodium dodecyl sulfate (SDS) micelle with measurements of the gA dimer backbone and tryptophan side chain dynamics using solution-state (15)N NMR on gA dimers in SDS micelles (Vostrikov, V. V.; Gu, H.; Ingólfsson, H. I.; Hinton, J. F.; Andersen, O. S.; Roux, B.; Koeppe, R. E., II. J. Phys. Chem. B2011, DOI 10.1021/jp200906y , accompanying article). This comparison enables us to examine the robustness of the MD simulations done using different force fields as well as their ability to predict important features of the gA channel. We find that MD is able to predict NMR observables, including the generalized order parameters (S(2)), the (15)N spin-lattice (T(1)) and spin-spin (T(2)) relaxation times, and the (1)H-(15)N nuclear Overhauser effect (NOE), with remarkable accuracy. To examine further how differences in the force fields can affect the channel conductance, we calculated the PMF for K(+) and Na(+) permeation through a gA channel in a dimyristoylphosphatidylcholine (DMPC) bilayer. In this case, we find that MD is less successful in quantitatively predicting the single-channel conductance.

Gramicidin channels are internally gated

Gramicidin channels are archetypal molecular subjects for solid-state NMR studies and investigations of single-channel or cation conductance. Until now, the transitions between on and off conductance states have been thought, based on multichannel studies, to represent monomer <--> dimer reactions. Here we use a single-molecule deposition method (vesicle fusion to a planar bilayer) to show that gramicidin dimer channels do not normally dissociate when conductance terminates. Furthermore, the observation of two 13C peaks in solid-state NMR indicates very stable dichotomous conformations for both the first and second peptide bonds in the monomers, and a two-dimensional chemical exchange spectrum with a 12-s mixing time demonstrates that the Val1 carbonyl conformations exchange slowly, with lifetimes of several seconds. It is proposed that gramicidin channels are gated by small conformational changes in the channel near the permeation pathway. These studies demonstrate how regulation of conformations governing closed <--> open transitions may be achieved and studied at the molecular level.

Use of reverse micelles in membrane protein structural biology

Membrane protein structural biology is a rapidly developing field with fundamental importance for elucidating key biological and biophysical processes including signal transduction, intercellular communication, and cellular transport. In addition to the intrinsic interest in this area of research, structural studies of membrane proteins have direct significance on the development of therapeutics that impact human health in diverse and important ways. In this article we demonstrate the potential of investigating the structure of membrane proteins using the reverse micelle forming surfactant dioctyl sulfosuccinate (AOT) in application to the prototypical model ion channel gramicidin A. Reverse micelles are surfactant based nanoparticles which have been employed to investigate fundamental physical properties of biomolecules. The results of this solution NMR based study indicate that the AOT reverse micelle system is capable of refolding and stabilizing relatively high concentrations of the native conformation of gramicidin A. Importantly, pulsed-field-gradient NMR diffusion and NOESY experiments reveal stable gramicidin A homodimer interactions that bridge reverse micelle particles. The spectroscopic benefit of reverse micelle-membrane protein solubilization is also explored, and significant enhancement over commonly used micelle based mimetic systems is demonstrated. These results establish the effectiveness of reverse micelle based studies of membrane proteins, and illustrate that membrane proteins solubilized by reverse micelles are compatible with high resolution solution NMR techniques.

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.

Probing Hydrogen Bonding and Ion−Carbonyl Interactions by Solid-State 17O NMR Spectroscopy: G-Ribbon and G-Quartet

We report solid-state 17O NMR determination of the 17O NMR tensors for the keto carbonyl oxygen (O6) of guanine in two 17O-enriched guanosine derivatives: [6-17O]guanosine (G1) and 2',3',5'-O-triacetyl-[6-17O]guanosine (G2). In G1.2H2O, guanosine molecules form hydrogen-bonded G-ribbons where the guanine bases are linked by O6...H-N2 and N7...H-N7 hydrogen bonds in a zigzag fashion. In addition, the keto carbonyl oxygen O6 is also weakly hydrogen-bonded to two water molecules of hydration. The experimental 17O NMR tensors determined for the two independent molecules in the asymmetric unit of G1.2H2O are: Molecule A, CQ=7.8+/-0.1 MHz, etaQ=0.45+/-0.05, deltaiso=263+/-2, delta11=460+/-5, delta22=360+/-5, delta33=-30+/-5 ppm; Molecule B, CQ=7.7+/-0.1 MHz, etaQ=0.55+/-0.05, deltaiso=250+/-2, delta11=440+/-5, delta22=340+/-5, delta33=-30+/-5 ppm. In G1/K+ gel, guanosine molecules form extensively stacking G-quartets. In each G-quartet, four guanine bases are linked together by four pairs of O6...H-N1 and N7...H-N2 hydrogen bonds in a cyclic fashion. In addition, each O6 atom is simultaneously coordinated to two K+ ions. For G1/K+ gel, the experimental 17O NMR tensors are: CQ=7.2+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2, delta11=400+/-5, delta22=300+/-5, delta33=-20+/-5 ppm. In the presence of divalent cations such as Sr2+, Ba2+, and Pb2+, G2 molecules form discrete octamers containing two stacking G-quartets and a central metal ion, that is, (G2)4-M2+-(G2)4. In this case, each O6 atom of the G-quartet is coordinated to only one metal ion. For G2/M2+ octamers, the experimental 17O NMR parameters are: Sr2+, CQ=6.8+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm; Ba2+, CQ=7.0+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2 ppm; Pb2+, CQ=7.2+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm. We also perform extensive quantum chemical calculations for the 17O NMR tensors in both G-ribbons and G-quartets. Our results demonstrate that the 17O chemical shift tensor and quadrupole coupling tensor are very sensitive to the presence of hydrogen bonding and ion-carbonyl interactions. Furthermore, the effect from ion-carbonyl interactions is several times stronger than that from hydrogen-bonding interactions. Our results establish a basis for using solid-state 17O NMR as a probe in the study of ion binding in G-quadruplex DNA and ion channel proteins.

Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels

Gramicidin A/gramicidin M heterodimer conductances were measured in planar lipid bilayers and found to form two distinguishable populations about halfway between the gramicidin A and gramicidin M homodimer conductances. This implies that the principle difference in the gramicidin A and gramicidin M transport free-energy profiles occurs at the channel center, where it would produce similar effects on the rate-limiting barrier for the two heterodimers. Kinetic analysis based on this and nearly all previously published homodimer conductance data for both gramicidin A and gramicidin M channels confirms this conclusion, indicating that the translocation step is approximately 100-fold slower in gramicidin M homodimers than in gramicidin A homodimers and that first- and second-ion exit-rate constants are higher by factors of 24 and 10, respectively. Assuming that the ratios of rate constants are related to the free-energy difference between gramicidin A and gramicidin M, we construct an effective ion-Trp free-energy interaction profile that has a minimum at the channel center.

Steered Molecular Dynamics Simulations of Na+ Permeation across the Gramicidin A Channel

The potential of mean forces (PMF) governing Na+ permeation through gramicidin A (gA) channels with explicit water and membrane was characterized using steered molecular dynamics (SMD) simulations. Constant-force SMD with a steering force parallel to the channel axis revealed at least seven energy wells in each monomer of the channel dimer. Except at the channel dimer interface, each energy well is associated with at least three and at most four backbone carbonyl oxygens and two water oxygens in a pseudo-hexahedral or pseudo-octahedral coordination with the Na+ ion. Repeated constant-velocity SMD by dragging a Na+ ion from each energy well in opposite directions parallel to the channel axis allowed the computation of the PMF across the gA channel, revealing a global minimum corresponding to Na+ binding sites near the entrance of gA at +/-9.3 A from the geometric center of the channel. The effect of volatile anesthetics on the PMF was also analyzed in the presence of halothane molecules. Although the accuracy of the current PMF calculation from SMD simulations is not yet sufficient to quantify the PMF difference with and without anesthetics, the comparison of the overall PMF profiles nevertheless confirms that the anesthetics cause insignificant changes to the structural makeup of the free energy wells along the channel and the overall permeation barrier. On average, the PMF appears less rugged in the outer part of the channel in the presence of anesthetics, consistent with our earlier finding that halothane interaction with anchoring residues makes the gA channel more dynamic. A causal relationship was observed between the reorientation of the coordinating backbone carbonyl oxygen and Na+ transit from one energy well to another, suggesting the possibility that even minute changes in the conformation of pore-lining residues due to dynamic motion could be sufficient to trigger the ion permeation. Because some of the carbonyl oxygens contribute to Na+ coordination in two adjacent energy wells, our SMD results reveal that the atomic picture of ion "hopping" through a gA channel actually involves a Na+ ion being carried in a relay by the coordinating oxygens from one energy well to the next. Steered molecular dynamics complements other computational approaches as an attractive means for the atomistic interpretation of experimental permeation studies.

Proton transfer in gramicidin water wires in phospholipid bilayers: attenuation by phosphoethanolamine

The transfer of protons in water wires was studied in native gramicidin A (gA), and in the SS- and RR-diastereoisomers of dioxolane-linked gA channels (SS and RR channels). These peptides were incorporated into membranes comprised of distinct combinations of phospholipid headgroups and acyl chains. Quantitative relationships between single channel conductances to H+ (g(H)) and [H+] were determined in distinct phospholipid membranes, and are in remarkable contrast with results previously obtained in monoglyceride membranes. In particular: 1), g(H)-[H+] relationships for the various gA channels in distinct phospholipid membranes are well fitted by single adsorption isotherms. A simple kinetic model assuming mono-occupancy of channels by protons fits said relationships. This does not occur with monoglyceride membranes. 2), Under nonsaturating [H+], g(H) is approximately 1 order of magnitude larger in phospholipid than in monoglyceride membranes. 3), Differences between rates of H+ transfer in various gA channels are still present but considerably attenuated in phospholipid relative to monoglyceride membranes. 4), Charged phospholipid headgroups affect g(H) via changes in [H+] at the membrane/solution interfaces. 5), Phosphoethanolamine groups caused a marked attenuation of g(H) relative to membranes with other phospholipid headgroups. This attenuation is voltage-dependent and tends to saturate H+ currents at voltages larger than 250 mV. This effect is likely to occur by limiting the access and exit of H+ in and out of the channel due to relatively strong oriented H-bonds between waters and phosphoethanolamine groups at channel interfaces. The differential effects of phospholipids on proton transfer could be reasoned by considering solvation effects of side chain residues of gramicidin channels by double acyl chains and by the presence of polar headgroups facilitating the entrance/exit of protons through the channel mouths.

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.

Role of protein flexibility in ion permeation: a case study in gramicidin A

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason--besides the well-known problem with the description of single file pore water--why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model.

On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation

Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficulties. We illustrate this using simple model calculations based on the gramicidin A and KcsA potassium channels, which show that thermal atomic fluctuations lead to energy profiles that vary by tens of kcal/mol. Consequently, within the framework of a rigid pore model, ion-channel energetics is extremely sensitive to the choice of experimental structure and how the space-dependent dielectric constant is assigned. Given these observations, the significance of any description based on a rigid structure appears limited. Creating a conducting channel model from one single structure requires substantial and arbitrary engineering of the model parameters, making it difficult for such approaches to contribute to our understanding of ion permeation at a microscopic level.

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.

Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation

The dissociation of gramicidin A (gA) channels into monomers is the simplest example of a channel gating process. The initial steps in this process are studied via a computational model that simulates the reaction coordinate for dimer-monomer dissociation. The nonbonded interaction energy between the monomers is determined, allowing for their free relative translational and rotational motion. Lowest energy pathways and reaction coordinates of the gating process are determined. Partial rupture of the six hydrogen bonds (6HB) at the dimer junction takes place by coupling monomer rotation and lateral displacement. Coupling rotation with axial separation is far more expensive energetically. The transition state for channel dissociation occurs when monomers are displaced laterally by approximately 4-6 A, separated by approximately 1.6-2 A, and rotated by approximately 120 degrees, breaking two hydrogen bonds. In membranes with significant hydrophobic mismatch there is a much greater likelihood of forming 4HB and possibly even 2HB states. In the 4HB state the pore remains fully open and conductive. However, transitions from the 6HB to 4HB and 4HB to 2HB states take place via intermediates in which the gA pore is closed and nonconductive. These lateral monomer displacements give rise to transitory pore occlusion at the dimer junction, which provides a rationale for fast closure events (flickers). Local dynamics of gA monomers also leads to lateral and rotational diffusion of the whole gA dimer, giving rise to diffusional rotation of the dimer about the channel axis.

Gramicidin A channel as a test ground for molecular dynamics force fields

We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K(+) ion is calculated along the channel axis using the umbrella sampling method. Calculations are performed using two of the most common force fields in MD simulations: CHARMM and GROMACS. Both force fields lead to large central barriers for K(+) ion permeation, that are substantially higher than those deduced from the physiological data by inverse methods. In long MD simulations lasting over 60 ns, several ions are observed to enter the binding site but none of them crossed the channel despite the presence of a large driving field. The present results, taken together with many earlier studies, highlights the shortcomings of the standard force fields used in MD simulations of ion channels and calls for construction of more appropriate force fields for this purpose.

Recent advances in ion channel research

The field of ion channels has entered into a rapid phase of development in the last few years, partly due to the breakthroughs in determination of the crystal structures of membrane proteins and advances in computer simulations of biomolecules. These advances have finally enabled the long-dreamed goal of relating function of a channel to its underlying molecular structure. Here we present simplified accounts of the competing permeation theories and then discuss their application to the potassium, gramicidin A and calcium channels.

Continuum electrostatics fails to describe ion permeation in the gramicidin channel

We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure. The potential and electric field acting on ions in and around the channel are computed by solving Poisson's equation. These are then used in Brownian dynamics simulations to obtain concentration profiles and the current passing through the channel. We show that regardless of the effective dielectric constant used for water in the channel or the channel protein, it is not possible to reproduce all the experimental data on gramicidin A; thus, continuum electrostatics cannot provide a valid framework for the description of ion dynamics in gramicidin channels. Using experimental data and molecular dynamics simulations as guides, we have constructed potential energy profiles that can satisfactorily describe the available physiological data. These profiles provide useful benchmarks for future potential of mean force calculations of permeating ions from molecular dynamics simulations of gramicidin A. They also offer a convenient starting point for studying structure-function relationships in modified gramicidin channels.

Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles

Gramicidins A, B, and C are the three most abundant, naturally occurring analogues of this family of channel-forming antibiotic. GB and GC differ from the parent pentadecapeptide, GA, by single residue mutations, W11F and W11Y, respectively. Although these mutations occur in the cation binding region of the channel, they do not affect monovalent cation specificity, but are known to alter cation-binding affinities, thermodynamic parameters of cation binding, conductance and the activation energy for ion transport. The structures of all three analogues incorporated into deuterated sodium dodecyl sulfate micelles have been obtained using solution state 2D-NMR spectroscopy and molecular modeling. For the first time, a rigorous comparison of the 3D structures of these analogues reveals that the amino acid substitutions do not have a significant effect on backbone conformation, thus eliminating channel differences as the cause of variations in transport properties. Variable positions of methyl groups in valine and leucine residues have been linked to molecular motions and are not likely to affect ion flow through the channel. Thus, it is concluded that changes in the magnitude and orientation of the dipole moment at residue 11 are responsible for altering monovalent cation transport.

Noncontact dipole effects on channel permeation. V. Computed potentials for fluorinated gramicidin

Experimental and theoretical calculations indicate that the dipole moment of the four Trp side chains in gramicidin A (gA) channels modify channel conductance through long-range electrostatic interactions. Electrostatic ion/side-chain interaction energies along the channel were computed with CHARMM using ab initio atom charges for native and 4-, 5-, or 6-fluorinated Trp side chains. The bulk water reaction to the polar side chains was included using the method of images as implemented by, and channel waters in idealized structures were included. Ion/Trp interaction energies were approximately -0.6 kcal/mol throughout the channel for all four of the native Trp pairs. Channel waters produced a modest reduction in the magnitude of interactions, essentially offsetting images representing the bulk water outside the channel. The effects of side-chain fluorination depended on ring position and, to a lesser extent, residue number. Compared with native Trp, 5-fluorination reduces the translocation barrier with minor effects on the exit barrier. In contrast, 6-fluorination primarily reduces exit barrier. 4-Fluorination produces a more complex double-well energy profile. Effects of measured side-chain movements resulting from fluorination or change in lipid bilayer were negligible whereas thermal side chain librations cause large effects, especially in the region of the ion-binding sites.

The binding site of sodium in the gramicidin A channel

The available information concerning the structure and location of the main binding site for sodium in the gramicidin A channel is reviewed and discussed. Results from molecular dynamics simulations using an atomic model of the channel embedded in a lipid bilayer are compared with experimental observations. The combined information from experiment and simulation suggests that the main binding sites for sodium are near the channel's mouth, approximately 9.2 A from the centre of the dimer channel, although the motion along the axis could be as large as 1 to 2 A. In the binding site, the sodium ion is lying off axis, making contact with two carbonyl oxygens and two single-file water molecules. The main channel ligand is provided by the carbonyl group of the Leu10-Trp11 peptide linkage, which exhibits the largest deflection from the ion-free channel structure.

13C selective polarization and spin diffusion in a lipid bilayer-bound polypeptide by solid-state NMR

While (15)N solid-state NMR has proven to be very advantageous for the development of structural biological methods, (13)C spectroscopy has increased sensitivity and spectral dispersion. However, large natural abundance signals and homonuclear dipolar interactions pose significant problems. Here we have used a pair of (13)C-labeled sites in a lipid-solubilized polypeptide to show the selective polarization can be used in combination with spin diffusion to achieve simplified spectra. Both unoriented and oriented samples have been used, with the latter providing a well-resolved homonuclear dipolar splitting.

Gramicidin D conformation, dynamics and membrane ion transport

The linear pentadecapeptide antibiotic, gramicidin D, a heterogeneous mixture of six components, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The conformation of gramicidin A in the solid state, in organic solvents, and in planar lipid bilayers and the relationship between the composition and the conformation of gramicidin and its selective transport of ions across membranes has been the subject of intense investigation for over 50 years. The x-ray crystal structure and nmr solution spectroscopy agree fully with one another and reveal that entirely different conformations of gramicidin are present in uncomplexed and ion complexed forms. Precise refinements of the three-dimensional structures of naturally occurring gramicidin D in crystals obtained from methanol, ethanol, and n-propanol demonstrate the unexpected presence of stable left-handed antiparallel double-helical heterodimers that vary with the crystallization solvent. The side chains of Trp residues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor beta ribbon formation and stabilization of the antiparallel double helix. This conformation acts as a template for gramicidin folding and nucleation of the different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation and crystal nucleation has potential applications to other systems in which anomalous behavior is exhibited by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins. The crystallographically determined structures of cesium, potassium, rubidium, and hydronium ion complexes of gramicidin A are in excellent agreement with the nmr structure determination of the cesium ion gramicidin complex in a methanol chloroform mixture (50 : 50). The right-handed antiparallel double stranded double helical structures (DSDHR) also exhibit geometric features compatible with the solid-state 15N and 2H nmr data recorded for gramicidin in planar lipid bilayers and attributed to the active form of gramicidin A. The DSDHR crystal structures reveal an ion channel with a single partially solvated cation distributed over three ion binding sites. The channel lumen is relatively smooth and electrostatically negative as required for cation passage, while the exterior is electrostatically neutral, a requirement for membrane insertion. The "coordination" of the Cs+ ion is achieved by interaction with the pi orbitals of the carbonyls which do not point toward the ions. The K+ binding sites, which are similar in position to Cs+ binding sites, are shifted off center slightly toward the wall of the channel.

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.

Solid-state NMR and hydrogen-deuterium exchange in a bilayer-solubilized peptide: structural and mechanistic implications

Hydrogen-deuterium exchange has been monitored by solid-state NMR to investigate the structure of gramicidin M in a lipid bilayer and to investigate the mechanisms for polypeptide insertion into a lipid bilayer. Through exchange it is possible to observe 15N-2H dipolar interactions in oriented samples that yield precise structural constraints. In separate experiments the pulse sequence SFAM was used to measure dipolar distances in this structure, showing that the dimer is antiparallel. The combined use of orientational and distance constraints is shown to be a powerful structural approach. By monitoring the hydrogen-deuterium exchange at different stages in the insertion of peptides into a bilayer environment it is shown that dimeric gramicidin is inserted into the bilayer intact, i.e., without separating into monomer units. The exchange mechanism is investigated for various sites and support for a relayed imidic acid mechanism is presented. Both acid and base catalyzed mechanisms may be operable. The nonexchangeable sites clearly define a central core to which water is inaccessible or hydroxide or hydronium ion is not even momentarily stable. This provides strong evidence that this is a nonconducting state.

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.

Cation binding induced changes in 15N CSA in a membrane-bound polypeptide

Cation binding to the monovalent cation selective channel, gramicidin A, is shown to induce changes in the dipolar and chemical shift observables from uniformly aligned samples. While these changes could be the result of structural or dynamic changes, they are shown to be primarily induced by through-bond polarizability effects when cations are solvated by the carbonyl oxygens of the peptide backbone. Upon cation binding partial charges are changed throughout the peptide plane, inducing large changes in the 13C1 chemical shifts, smaller changes in the 15N chemical shifts, and even smaller effects for the 15N-13C1 and 15N-2H dipolar interactions. These conclusions are substantiated by characterizing the 15N chemical shift tensors in the presence and absence of cations in fast-frozen lipid bilayer preparations of gramicidin A.

The conducting form of gramicidin A is a right-handed double-stranded double helix

The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDH) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDH as the major conformer responsible for ion transport in membranes.

Single potassium ion seeks open channel for transmembrane travels: tales from the KcsA structure

Potassium channels selectively catalyze potassium transport across cell membranes. Over the past five decades, a multitude of potassium channel models have been proposed. The recent crystal structure determination of the KcsA potassium channel confirms, corrects and expands our understanding of a fundamental biological catalyst, revealing the basis of exquisite selectivity and near diffusion-limited throughput.

Raman linear intensity difference of membrane-bound peptides: indole ring orientations of tryptophans 11 and 13 in the gramicidin A transmembrane channel

A Raman linear intensity difference (RLID) method has been developed to determine orientations of chromophores in membrane-bound peptides and proteins. The method involves orientation of the peptide or protein in lipid bilayer membranes and measurement of intensity differences between Raman spectra excited with two orthogonal laser polarizations. Analysis of the RLID spectrum is simplified when the chromophore exhibits a vibrational mode for which the Raman band is enhanced through resonance with a single molecular electronic transition. To examine the indole ring orientations of Trp residues in the gramicidin A transmembrane channel, we have prepared analogues of gramicidin A, in which one of four Trp residues is replaced by deuterated Trp (Trp-2,4,5,6,7-d5). Two vibrational Raman bands omega(d)3 and omega(d)2 of deuterated Trp have been shown to gain intensity predominantly through resonance with the Bb and La electronic transitions, respectively, when excited at 244 and 257 nm. By examining the RLID spectra of the omega(d)3 and omega(d)2 bands of gramicidin A channels oriented in phospholipid bilayer membranes, we have determined the inclination angles of the Bb and La transition moments with respect to the channel axis in the absence and presence of Na+. The orientations of the Trp-11 and Trp-13 indole rings in the gramicidin channel structure have been derived from the inclination angles of the transition moments. The indole rings of Trp-11 and Trp-13, which are known to shift along the channel axis upon binding of Na+, do not reorient during their positional shifts.

Recent Advances in the High Resolution Structures of Bacterial Channels: Gramicidin A

Gramicidin is a polypeptide antibiotic which forms dimeric channels specific for the transport of monovalent cations across membranes. It adopts several different conformations, most notably double helical (pore) and helical dimer (channels) forms, which have very different structural and functional characteristics. This review focuses on recent high resolution structure determinations of both the pore and channel forms of the molecule by X-ray crystallographic and/or NMR spectroscopic techniques. It discusses the structural consequences of binding ions and the location of ion binding sites and how the structures are related to the conductance properties of the molecule. This relatively simple molecule is probably the best characterized ion channel (both structurally and functionally) and has, to date, been the principal proving-ground for many of our ideas about the molecular nature of ion conduction in membranes. Copyright 1998 Academic Press.

Using theory and simulation to understand permeation and selectivity in ion channels

It is clear that the function of ion channels must flow from their structure. With recent advances in computational power and methodology, it appears feasible to correlate structure to ion channel permeation at an atomistically detailed level of description. The overall strategy is to structure the calculations in a hierarchy, ranging from coarse-grained thermodynamic and kinetic descriptions to fine-grained molecular dynamics descriptions with atomic detail. Each level of description is connected to the others by appropriate statistical mechanical theory. The coarse-grained descriptions can be correlated directly with electrophysiological experiment. The fine-grained descriptions are used to parameterize the coarse-grained descriptions and to describe the permeation process at the most detailed level. This strategy has so far had varying degrees of success. It has successfully described water permeation through lipid bilayers and gramicidin channels. It has revealed the essential events of ion permeation through gramicidin channels at an atomistically detailed level. The role of channel protein motions in permeation has been elucidated. However, it appears that force fields used to describe molecular dynamics must be refined further to achieve completely accurate predictions of the permeation of such small ions as sodium. Channels with more complex structure and more multiion occupancy than gramicidin pose major computational challenges with respect to sampling protein conformations and ion distributions involved in the permeation process. Possible approaches to meeting these challenges are discussed.

High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

BACKGROUND

Solid-state nuclear magnetic resonance (NMR) spectroscopy provides novel structural constraints from uniformly aligned samples. These orientational constraints orient specific atomic sites with respect to the magnetic field direction and the unique molecular axis of alignment. Solid-state NMR is uniquely and ideally suited for providing such structural constraints on polypeptides and proteins in a lamellar phase lipid environment. Membrane protein structure represents a great challenge for structural biologists; a new approach for characterizing high resolution three-dimensional structure in such an environment is needed.

RESULTS

The optimal use of orientational constraints for defining three-dimensional structures is demonstrated with the elucidation of the gramicidin A channel structure at high resolution. Initial structures are refined against both the experimental constraints and the CHARMM energy using a novel simulated-annealing protocol to define torsion angle solutions with an error bar of approximately +/- 5 degrees.

CONCLUSIONS

This analysis results in the determination of a high-resolution, time averaged structure of gramicidin A obtained in a lipid bilayer environment above the gel-to-liquid crystalline phase transition temperature. It is demonstrated that solid-state NMR can be used to establish polypeptide, and potentially protein, structures in such an environment. Furthermore, this high-resolution structure is demonstrated to provide new insights into polypeptide function. For the gramicidin A channel the roles of the indole groups that facilitate ion transport and details of the cation solvation environment provided by the amide oxygens are characterized.

Solid-state nuclear magnetic resonance characterization of gramicidin channel structure

The method of using orientational constraints derived from solid-state NMR for structural characterization of polypeptides in heterogeneous environments has now been demonstrated. A very high resolution structure has been achieved that has led to greater functional understanding of this channel. Much can be done to improve this structural technique to make it more efficient and more generally applicable. Others as well as ourselves are applying this approach to membrane proteins. Although solid-phase synthesis and specific site isotopic labeling has been essential for the development described here, one of the primary challenges is to be able to use amino acid-specific and uniform labeling of peptides and proteins by biosynthetic means for isotopic incorporation. This will allow for the study of many more proteins and significantly large proteins. Unlike solution NMR structural methods, there are no intrinsic molecular weight limitations. In fact, as the molecular weight increases the molecular motion will become less and the spectroscopic properties will improve. The major limitation will be sensitivity: as the molecular weight increases the number of moles will decrease in the samples, causing sensitivity to decrease. Advances in field strength and NMR technology help to address this problem. With larger molecules and more isotopically labeled sites resolution could also be a problem; however, the two- and three-dimensional methods demonstrated by Opella and co-workers clearly show the potential for enormous resolving power. In the 15N dimension alone it is shown that the resolution is greater than in solution NMR. Although challenges such as spectral assignments have yet to be completely solved, several approaches have been described, and the prospects are excellent for solving this and other problems facing the development of this novel approach for structural elucidation. Although there is an attempt to get away from solid-phase synthesis to solve larger molecular weight structures, peptide synthesis will continue to be important for generating single- and double-site labeled model compounds for characterizations of spin interaction tensors. Such characterizations will continue to be a very important aspect of this structural approach.

The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data

The location of the main binding site for sodium in the gramicidin A (GA) channel was investigated with molecular dynamics simulations, using an atomic model of the channel embedded in a fully hydrated dimyristoyl phosphatidycholine (DMPC) bilayer. Twenty-four separate simulations in which a sodium was restrained at different locations along the channel axis were generated. The results are compared with carbonyl 13C chemical shift anisotropy solid-state NMR experimental data previously obtained with oriented GA:DMPC samples. Predictions are made for other solid-state NMR properties that could be observed experimentally. The combined information from experiment and simulation strongly suggests that the main binding sites for sodium are near the channel's mouth, approximately 9.2 A from the center of the dimer channel. The 13C chemical shift anisotropy of Leu10 is the most affected by the presence of a sodium ion in the binding site. In the binding site, the sodium ion is lying off-axis, making contact with two carbonyl oxygens and two single-file water molecules. The main channel ligand is provided by the carbonyl group of the Leu10-Trp11 peptide linkage, which exhibits the largest deviation from the ion-free channel structure. Transient contacts with the carbonyl group of Val8 and Trp15 are also present. The influence of the tryptophan side chains on the channel conductance is examined based on the current information about the binding site.

Crystal structure of the gramicidin/potassium thiocyanate complex

The hydrophobic channel-forming polypeptide gramicidin adopts a left-handed antiparallel double helix conformation with 6.4 residues per turn when in complex with monovalent cation salts in a methanol environment. The crystal structure of the gramicidin/potassium thiocyanate complex (a = 32.06 A, b = 51.80 A, and c = 31.04 A; space group P2(1)2(1)2(1)) has been solved to 2.5 A with an R-factor of 0.193. In the structure, binding sites for the cations are formed by the polypeptide backbone carbonyl groups tilting away from the helix axis toward the ions located in the central lumen. The polypeptide backbone conformations and the side-chain orientations in this potassium complex are significantly different from those in the previously solved gramicidin/caesium chloride crystal complex, due to the requirements for interactions with the smaller sized potassium cation. The locations and numbers of potassium binding sites also differ considerably from the locations and numbers of caesium binding sites in the other structure. Combining information from all the cation binding sites in the two gramicidin/ion complexes produces different views of the three-dimensional structures of a cation as it is transported along a transmembrane pore, and provides an experimental structural basis for modeling the dynamics of peptide-ion binding and ion transport.