Solid-state 13C-NMR studies of the effects of sodium ions on the gramicidin A ion channel

Progression of NMR studies of membrane-active peptides from lipid bilayers to live cells

Understanding the structure of membrane-active peptides faces many challenges associated with the development of appropriate model membrane systems as the peptide structure depends strongly on the lipid environment. This perspective provides a brief overview of the approach taken to study antimicrobial and amyloid peptides in phospholipid bilayers using oriented bilayers and magic angle spinning techniques. In particular, Boltzmann statistics REDOR and maximum entropy analysis of spinning side bands are used to analyse systems where multiple states of peptide or lipid molecules may co-exist. We propose that in future, rather than model membranes, structural studies in whole cells are feasible.

Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems

With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogs across the water-bilayer interface. This article is part of a Special Issue entitled: Membrane protein structure and function.

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.

Solid-state C NMR spectroscopy of a C carbonyl-labeled polypeptide

High resolution structural elucidation of macromolecular structure by solid-state nuclear magnetic resonance requires the preparation of uniformly aligned samples that are isotopically labeled. In addition, to use the chemical shift interaction as a high resolution constraint requires an in situ tensor characterization for each site of interest. For (13)C in the peptide backbone, this characterization is complicated by the presence of dipolar coupled (14)N from the peptide bond. Here the (13)C(1)-Gly(2) site in gramicidin A is studied both as a dry powder and in a fully hydrated lipid bilayer environment. Linewidths reported for the oriented samples are a factor of five narrower than those reported elsewhere, and previous misinterpretations of the linewidths are corrected. The observed frequency from oriented samples is shown to be consistent with the recently determined structure for this site in the gramicidin backbone. It is also shown that, whereas a dipolar coupling between (13)C and (14)N is apparent in dry preparations of the polypeptide, in a hydrated bilayer the dipolar coupling is absent, presumably due to a ;self-decoupling' mechanism.

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.

Monitoring gramicidin conformations in membranes: a fluorescence approach

We have monitored the membrane-bound channel and nonchannel conformations of gramicidin utilizing red-edge excitation shift (REES), and related fluorescence parameters. In particular, we have used fluorescence lifetime, polarization, quenching, chemical modification, and membrane penetration depth analysis in addition to REES measurements to distinguish these two conformations. Our results show that REES of gramicidin tryptophans can be effectively used to distinguish conformations of membrane-bound gramicidin. The interfacially localized tryptophans in the channel conformation display REES of 7 nm whereas the tryptophans in the nonchannel conformation exhibit REES of 2 nm which highlights the difference in their average environments in terms of localization in the membrane. This is supported by tryptophan penetration depth measurements using the parallax method and fluorescence lifetime and polarization measurements. Further differences in the average tryptophan microenvironments in the two conformations are brought out by fluorescence quenching experiments using acrylamide and chemical modification of the tryptophans by N-bromosuccinimide. In summary, we report novel fluorescence-based approaches to monitor conformations of this important ion channel peptide. Our results offer vital information on the organization and dynamics of the functionally important tryptophan residues in gramicidin.

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).

Sequence specific stabilization of a linear analog of the antifungal lipopeptide iturin A2 by sodium during low energy electrospray ionization mass spectrometry conditions

The structures and stability of sodiated species of 8-Beta, a linear lipopeptide analog (beta-aminotetradecanoyl-NYNQPNS) of the antifungal peptide iturin A2, were evaluated by electrospray ionization mass spectrometry (ESI-MS). Association of the lipopeptide, 8-Beta, with sodium afforded protection from fragmentation at high cone voltages and increasing collision energy conditions in the ESI-MS. The order of decreasing stability was found as 8-Beta 1Na > 8-Beta 2Na > 8-Beta 3Na > 8-Beta. Substantial differences were found between fragmentation patterns of the free and sodiated molecular species. Breakage of the N-terminal peptide bond of L-Pro generated the major product ions of the free 8-Beta parent ion. Impaired fragmentation of the sodium adducts of 8-Beta, indicated that this bond is protected by sodium complexation. Fragmentation patterns of the sodiated lipopeptide further revealed two specific binding sites for a nonsolvated sodium ion within the two type II beta-turn sequences (beta-aminotetradecanoyl-NYN and QPNS) of the natural iturin A2. It is proposed that specific interaction with sodium takes place with most of the peptide bond oxygens in these turns, and with the Gln sidechain. This interaction leads to stabilized structures in which the peptide backbone, specifically the peptide bonds in which L-Pro participates, is protected against low-energy fragmentation during ESI-MS.

The structure, dynamics and orientation of antimicrobial peptides in membranes by multidimensional solid-state NMR spectroscopy

Linear peptide antibiotics have been isolated from amphibians, insects and humans and used as templates to design cheaper and more potent analogues for medical applications. Peptides such as cecropins or magainins are < or = 40 amino acids in length. Many of them have been prepared by solid-phase peptide synthesis with isotopic labels incorporated at selected sites. Structural analysis by solid-state NMR spectroscopy and other biophysical techniques indicates that these peptide antibiotics strongly interact with lipid membranes. In bilayer environments they exhibit amphipathic alpha-helical conformations and alignments of the helix axis parallel to the membrane surface. This contrasts the transmembrane orientations observed for alamethicin or gramicidin A. Models that have been proposed to explain the antibiotic and pore-forming activities of membrane-associated peptides, as well as other experimental results, include transmembrane helical bundles, wormholes, carpets, detergent-like effects or the in-plane diffusion of peptide-induced bilayer instabilities.

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.

Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure

Solid-state nuclear magnetic resonance (NMR) is rapidly emerging as a successful and important technique for protein and peptide structural elucidation from samples in anisotropic environments. Because of the diversity of nuclei and nuclear spin interactions that can be observed, and because of the broad range of sample conditions that can be studied by solid-state NMR, the potential for gaining structural constraints is great. Structural constraints in the form of orientational, distance, and torsional constraints can be obtained on proteins in crystalline, liquid-crystalline, or amorphous preparations. Great progress in the past few years has been made in developing techniques for obtaining these constraints, and now it has also been clearly demonstrated that these constraints can be assembled into uniquely defined three-dimensional structures at high resolution. Although much progress toward the development of solid-state NMR as a routine structural tool has been documented, the future is even brighter with the continued development of the experiments, of NMR hardware, and of the molecular biological methods for the preparation of labeled samples.

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.

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.

Heterodimer formation and crystal nucleation of gramicidin D

The linear pentadecapeptide antibiotic gramicidin D is a heterogeneous mixture of six components. Precise refinements of 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 that acts as a template for gramicidin folding and nucleation of 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 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.

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.

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.

Boundary conditions for- single-ion diffusion

We have constructed a theory for diffusion through the pore of a single-ion channel by taking a limit of a random walk around a cycle of states. Similar to Levitt's theory of single-ion diffusion, one obtains boundary conditions for the Nernst-Planck equation that guarantee that the pore is occupied by at most one ion. Two of the terms in the boundary conditions are identical to those given by Levitt. However, the construction gives rise to a third term not found in Levitt's theory. With this term, the channel spends exponentially distributed intervals in the empty state. Ion sample paths have been simulated to help visualize trajectories near the channel entrances, with and without the new term. We use the modified Levitt theory to fit several potential profiles to the conductance data of Russell et al. In particular, we have analyzed the profile for Na+ in gramicidin calculated by Roux and Karplus. The peak-to-peak amplitude of their result must be reduced to at most 35% of its original value to fit the data. But with this reduction, excellent fits are obtained.

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.

Membrane protein structure: the contribution and potential of novel solid state NMR approaches

Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.

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.

Sodium ion binding in the gramicidin A channel. Solid-state NMR studies of the tryptophan residues

Gramicidin A analogs, labeled with 13C in the backbone carbonyl groups and the C-2 indole carbons of the tryptophan-11 and tryptophan-13 residues, were synthesized using t-Boc-protected amino acids. The purified analogs were incorporated into phosphatidylcholine bilayers at a 1:15 molar ratio and macroscopically aligned between glass coverslips. The orientations of the labeled groups within the channel were investigated using solid-state NMR and the effect of a monovalent ion (Na+) on the orientation of these groups determined. The presence of sodium ions did not perturb the 13C spectra of the tryptophan carbonyl groups. These results contrast with earlier results in which the Leu-10, Leu-12, and Leu-14 carbonyl groups were found to be significantly affected by the presence of sodium ions and imply that the tryptophan carbonyl groups are not directly involved in ion binding. The channel form of gramicidin A has been demonstrated to be the right-handed form of the beta 6.3 helix: consequently, the tryptophan carbonyls would be directed away from the entrance to the channel and take part in internal hydrogen bonding, so that the presence of cations in the channel would have less effect than on the outer leucine residues. Sodium ions also had no effect on the C-2 indole resonance of the tryptophan side chains. However, a small change was observed in Trp-11 when the ether lipid, ditetradecylphosphatidylcholine, was substituted for the ester lipid, dimyristoylphosphatidylcholine, indicating some sensitivity of the gramicidin side chains to the surrounding lipid.

Influence of the nature of the aromatic side-chain on the conductance of the channel of linear gramicidin: study of a series of 9,11,13,15-Tyr(O-protected) derivatives

This paper describes the single channel properties of a series of synthetic analogues of gramicidin A, where all four tryptophans are replaced either by tyrosine or by several O-protected (benzyl, methyl, ethyl or t-butyl) derivatives. It is shown that, although all analogues bear similar dipole moment on their side-chains, the conductance depends on the hydrophobicity of these protecting groups. An analysis of the conductance data suggests that the conductance is governed by the binding process and a possible explanation, based on conformational considerations, is proposed.

Model ion channels: gramicidin and alamethicin

We have discussed in some detail a variety of experimental studies which were designed to elucidate the conformational and dynamic properties of gramicidin and alamethicin. Although the behavior of these peptides is by no means fully characterized, these studies have already permitted aspects of ion channel activity to be understood in molecular terms. Studies with gramicidin in a variety of organic solutions have revealed conformational heterogeneity of this peptide; at least five major isomers exist, several of which have been characterized in detail using NMR spectroscopy and X-ray crystallography. When added to lipid membranes gramicidin undergoes a further conformational conversion. Although the conformation of gramicidin in membranes is not as well characterized as the solution conformation(s) and an X-ray structure is not yet available, detailed data, particularly from solid-state NMR studies, continue to become available and a right-handed beta 6.3 helical conformation of the peptide backbone is now generally accepted. Two of these beta 6.3 helices joined at their N-termini are believed to form the conducting channel. The conformational behavior of the side-chains of gramicidin in the membrane-bound form is not well established and several NMR, CD, fluorescence and theoretical studies are now focussed on this. Although the side-chains do not directly contact the permeating ions, they can have distinct effects on conductance and selectivity by altering the electrostatic environment sensed by the ion. The dynamics of both side-chain and backbone conformations of gramicidin appear critical to a detailed understanding of the ion transport process in this channel. As the description of the membrane-bound conformation of gramicidin becomes more detailed, simulations of ion transport using computational methods are likely to improve and will further our understanding of the processes of ion transport. As well as internal motion of the backbone and side-chains, gramicidin undergoes rotational and translational motion in the plane of the membrane. These motions do not appear to be essential for the process of ion transport but can affect channel lifetime since lifetime is determined by the rate of association and dissociation of gramicidin monomers. Gramicidin-membrane interactions are also likely to be involved in the frequency of occurrence of channel subconductance states, the frequency of channel flickering and fundamentally in the stability of the membrane-bound gramicidin conformation. Alamethicin forms channels in membranes which are strongly voltage-dependent. The molecular origin of voltage-dependent conductances has been a fundamental problem in biophysics for many years.(ABSTRACT TRUNCATED AT 400 WORDS)