Alamethicin channels - modelling via restrained molecular dynamics simulations

Multi-oligomeric states of alamethicin ion channel: Assemblies and conductance

Transmembrane assemblies of the peptaibol alamethicin (ALM) are among the most extensively studied ion channels not only because of their antimicrobial activity but also as models for channel structure and aggregation. In this study, several oligomeric states of ALM are investigated with molecular dynamics simulations to establish properties of the channel and obtain free energy profiles for ion transport and the corresponding values of conductance. The hexamer, heptamer, and octamer of ALM in phospholipid membrane are found to be stable but highly dynamic in barrel-stave structures, with calculated conductance equal to 18, 195, and 1270 pS, respectively, in 1 M KCl ion solution. The corresponding free energy profiles, reported for the first time, are reconstructed from simulations at applied voltage of 200 mV with the aid of the electrodiffusion model both with and without the knowledge of diffusivity. The calculated free energy barriers are equal to 2.5, 1.5, and 0.5 kcal/mol for K+ and 4.0, 2.2, and 1.5 kcal/mol for Cl-, for hexamer, heptamer, and octamer, respectively. The calculated conductance and the ratio between conductance in consecutive states are in good agreement with those measured experimentally. This suggests that the hexamer is the lowest conducting state, with measured conductance equal to 19 pS. The selectivity of K+ over Cl- is calculated as 1.5 and 2.3 for the octameric and heptameric channels, close to the selectivity measured for high-conductance states. Selectivity increases to 13 in the hexameric channel in which the narrowest Gln7 site has a pore radius of only ∼1.6 Å, again in accord with experiment. A good agreement found between calculated and measured conductance through a hexamer templated on cyclodextrin lands additional support for the results of our simulations, and the comparison with ALM reveals the dependence of conductance on the nature of phospholipid membrane.

Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion

An all-atom molecular dynamics simulation of the archetype barrel-stave alamethicin (alm) pore in a 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayer at 313 K indicates that ∼7 μs is required for equilibration of a preformed 6-peptide pore; the pore remains stable for the duration of the remaining 7 μs of the trajectory, and the structure factors agree well with experiment. A 5 μs simulation of 10 surface-bound alm peptides shows significant peptide unfolding and some unbinding, but no insertion. Simulations at 363 and 413 K with a -0.2 V electric field yield peptide insertion in 1 μs. Insertion is initiated by the folding of residues 3-11 into an α-helix, and mediated by membrane water or by previously inserted peptides. The stability of five alm pore peptides at 413 K with a -0.2 V electric field demonstrates a significant preference for a transmembrane orientation. Hence, and in contrast to the cationic antimicrobial peptide described in the following article, alm shows a strong preference for the inserted over the surface-bound state.

A thermodynamic approach to alamethicin pore formation

The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.

Cyclodextrin-scaffolded alamethicin with remarkably efficient membrane permeabilizing properties and membrane current conductance

Bacterial resistance to classical antibiotics is a serious medical problem, which continues to grow. Small antimicrobial peptides represent a potential solution and are increasingly being developed as novel therapeutic agents. Many of these peptides owe their antibacterial activity to the formation of trans-membrane ion-channels resulting in cell lysis. However, to further develop the field of peptide antibiotics, a thorough understanding of their mechanism of action is needed. Alamethicin belongs to a class of peptides called peptaibols and represents one of these antimicrobial peptides. To examine the dynamics of assembly and to facilitate a thorough structural evaluation of the alamethicin ion-channels, we have applied click chemistry for the synthesis of templated alamethicin multimers covalently attached to cyclodextrin-scaffolds. Using oriented circular dichroism, calcein release assays, and single-channel current measurements, the α-helices of the templated multimers were demonstrated to insert into lipid bilayers forming highly efficient and remarkably stable ion-channels.

Characterization of channel-forming peptide nanostructures

We have prepared fluorescent analogs of known ion-channel-forming synthetic peptide nanostructures. These analogs were designed as probes to gain insight about the mechanism by which self-assembling amphiphilic peptides interact with lipid membranes. Conformational studies demonstrated that the labeled analogs retain their propensity to adopt a strong helical conformation in 2,2,2-trifluoroethanol and lipid bilayers. Attenuated total reflectance results indicated that the fluorescent peptide nanostructures are under an incorporation equilibrium between two forms, adsorbed at the surface or incorporated within the bilayer, similar to their unlabeled counterparts. However, when using a HeLa mimicking membrane, the proportion of peptide nanostructures in the transmembrane orientation decreases significantly. Finally, we were able to show by confocal microscopy studies that fluorescent analogs internalized into HeLa cells and localized into both the membranes of inner organelles and the cell membrane.

Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance

Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K⁺ and Cl⁻ with their first solvation shells intact. The free energy barrier encountered by K⁺ is only 2.2 kcal/mol whereas Cl⁻ encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.

Antimicrobial peptides in toroidal and cylindrical pores

Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize biological membranes. Their mechanism of action is still not well understood. Here we investigate the preference of alamethicin and melittin for pores of different shapes, using molecular dynamics (MD) simulations of the peptides in pre-formed toroidal and cylindrical pores. When an alamethicin hexamer is initially embedded in a cylindrical pore, at the end of the simulation the pore remains cylindrical or closes if glutamines in the N-termini are not located within the pore. On the other hand, when a melittin tetramer is embedded in toroidal pore or in a cylindrical pore, at the end of the simulation the pore is lined both with peptides and lipid headgroups, and, thus, can be classified as a toroidal pore. These observations agree with the prevailing views that alamethicin forms barrel-stave pores whereas melittin forms toroidal pores. Both alamethicin and melittin form amphiphilic helices in the presence of membranes, but their net charge differs; at pH approximately 7, the net charge of alamethicin is -1 whereas that of melittin is +5. This gives rise to stronger electrostatic interactions of melittin with membranes than those of alamethicin. The melittin tetramer interacts more strongly with lipids in the toroidal pore than in the cylindrical one, due to more favorable electrostatic interactions.

Antimicrobial peptides bind more strongly to membrane pores

Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize bacterial membranes. Understanding their mechanism of action might help design better antibiotics. Using an implicit membrane model, modified to include pores of different shapes, we show that four AMPs (alamethicin, melittin, a magainin analogue, MG-H2, and piscidin 1) bind more strongly to membrane pores, consistent with the idea that they stabilize them. The effective energy of alamethicin in cylindrical pores is similar to that in toroidal pores, whereas the effective energy of the other three peptides is lower in toroidal pores. Only alamethicin intercalates into the membrane core; MG-H2, melittin and piscidin are located exclusively at the hydrophobic/hydrophilic interface. In toroidal pores, the latter three peptides often bind at the edge of the pore, and are in an oblique orientation. The calculated binding energies of the peptides are correlated with their hemolytic activities. We hypothesize that one distinguishing feature of AMPs may be the fact that they are imperfectly amphipathic which allows them to bind more strongly to toroidal pores. An initial test on a melittin-based mutant seems to support this hypothesis.

Backbone dynamics of alamethicin bound to lipid membranes: spin-echo electron paramagnetic resonance of TOAC-spin labels

Alamethicin F50/5 is a hydrophobic peptide that is devoid of charged residues and that induces voltage-dependent ion channels in lipid membranes. The peptide backbone is likely to be involved in the ion conduction pathway. Electron spin-echo spectroscopy of alamethicin F50/5 analogs in which a selected Aib residue (at position n = 1, 8, or 16) is replaced by the TOAC amino-acid spin label was used to study torsional dynamics of the peptide backbone in association with phosphatidylcholine bilayer membranes. Rapid librational motions of limited angular amplitude were observed at each of the three TOAC sites by recording echo-detected spectra as a function of echo delay time, 2tau. Simulation of the time-resolved spectra, combined with conventional EPR measurements of the librational amplitude, shows that torsional fluctuations of the peptide backbone take place on the subnanosecond to nanosecond timescale, with little temperature dependence. Associated fluctuations in polar fields from the peptide could facilitate ion permeation.

Channel-Forming Activity of Alamethicin: Effects of Covalent Tethering

In this short review article, the effects of covalent tethering of alamethicin molecules on channel-forming behavior are described. Broadly speaking, these chemical modifications have provided insight into all three aspects of channel behavior: the structure of the conducting state, the ion-selectivity and ion-permeation properties, and the voltage dependence. Each of these aspects are discussed in turn.

Interaction of alamethicin pores in DMPC bilayers

We have investigated the x-ray scattering signal of highly aligned multilayers of the zwitterionic lipid 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine containing pores formed by the antimicrobial peptide alamethicin as a function of the peptide/lipid ratio. We are able to obtain information on the structure factor of the pore fluid, which then yields the interaction potential between pores in the plane of the bilayers. Aside from a hard core with a radius corresponding to the geometric radius of the pore, we find a repulsive lipid-mediated interaction with a range of approximately 30 A and a contact value of 2.4 k(B)T. This result is in qualitative agreement with recent theoretical models.

Surface Tension Effect on Transmembrane Channel Stability in a Model Membrane

The effect of surface tension on the lipid bilayer membrane is a question that has drawn considerable research effort. This interest has been driven both by the desire to determine the surface tension effects on the lipid bilayer and from the suggestion that adding finite surface tension to a small membrane system may provide more realistic lipid properties in molecular dynamics simulations. Here, the effect of surface tension on a palmitololelylphosphatidylcholine (POPC) bilayer membrane containing a four-helix transmembrane alamethicin peptide bundle is investigated. Simulations of 10 ns were undertaken for two different ensembles, NPT and NP(z)gammaT with a surface tension, gamma, of 20 mN m(-1) per interface, which is near the pore-forming region. The significance of differences between the tension-free and surface tension simulations was determined using nonparametric statistical analysis on replicate simulations with different initial conditions. The results suggest that, when the membrane is under surface tension, the peptide helical structure is perturbed from that in the tension-free state but that the bundle conformation is more stable than that in the tension-free state, with hydrogen bonding playing an important stabilizing role. Surface tension counteracts the influence of the transmembrane helix bundle on nearby lipid order, making the lipid order more uniform throughout the membrane in the tension state. Conversely, the lipid mobility was less uniform in the tension state, with lipids far from the bundle being significantly more mobile than those near the bundle. One general implication of the results is that surface tension can affect the membrane nonuniformly, in that the properties of lipids near the peptide are different from those further away.

Analysis and evaluation of channel models: simulations of alamethicin

Alamethicin is an antimicrobial peptide that forms stable channels with well-defined conductance levels. We have used extended molecular dynamics simulations of alamethicin bundles consisting of 4, 5, 6, 7, and 8 helices in a palmitoyl-oleolyl-phosphatidylcholine bilayer to evaluate and analyze channel models and to link the models to the experimentally measured conductance levels. Our results suggest that four helices do not form a stable water-filled channel and might not even form a stable intermediate. The lowest measurable conductance level is likely to correspond to the pentamer. At higher aggregation numbers the bundles become less symmetrical. Water properties inside the different-sized bundles are similar. The hexamer is the most stable model with a stability comparable with simulations based on crystal structures. The simulation was extended from 4 to 20 ns or several times the mean passage time of an ion. Essential dynamics analyses were used to test the hypothesis that correlated motions of the helical bundles account for high-frequency noise observed in open channel measurements. In a 20-ns simulation of a hexameric alamethicin bundle, the main motions are those of individual helices, not of the bundle as a whole. A detailed comparison of simulations using different methods to treat long-range electrostatic interactions (a twin range cutoff, Particle Mesh Ewald, and a twin range cutoff combined with a reaction field correction) shows that water orientation inside the alamethicin channels is sensitive to the algorithms used. In all cases, water ordering due to the protein structure is strong, although the exact profile changes somewhat. Adding an extra 4-nm layer of water only changes the water ordering slightly in the case of particle mesh Ewald, suggesting that periodicity artifacts for this system are not serious.

Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants

A new simulation method, dissipative particle dynamics, is applied to model biological membranes. In this method, several atoms are united into a single simulation particle. The solubility and compressibility of the various liquid components are reproduced by the simulation model. When applied to a bilayer of phosphatidylethanolamine, the membrane structure obtained matches quantitatively with full atomistic simulations and with experiments reported in the literature. The method is applied to investigate the cause of cell death when bacteria are exposed to nonionic surfactants. Mixed bilayers of lipid and nonionic surfactant were studied, and the diffusion of water through the bilayer was monitored. Small transient holes are seen to appear at 40% mole-fraction C(9)E(8), which become permanent holes between 60 and 70% surfactant. When C(12)E(6) is applied, permanent holes only arise at 90% mole-fraction surfactant. Some simulations have been carried out to determine the rupture properties of mixed bilayers of phosphatidylethanolamine and C(12)E(6). These simulations indicate that the area of a pure lipid bilayer can be increased by a factor 2. The inclusion of surfactant considerably reduces both the extensibility and the maximum stress that the bilayer can withstand. This may explain why dividing cells are more at risk than static cells.

Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations

We have performed simulations of both a single potassium ion and a single sodium ion within the pore of the bacterial potassium channel KcsA. For both ions there is a dehydration energy barrier at the cytoplasmic mouth suggesting that the crystal structure is a closed conformation of the channel. There is a potential energy barrier for a sodium ion in the selectivity filter that is not seen for potassium. Radial distribution functions for both ions with the carbonyl oxygens of the selectivity filter indicate that sodium may interact more tightly with the filter than does potassium. This suggests that the key to the ion selectivity of KcsA is the greater dehydration energy of Na(+) ions, and helps to explain the block of KcsA by internal Na(+) ions.

Protonation of lysine residues inverts cation/anion selectivity in a model channel

A dimeric alamethicin analog with lysine at position 18 in the sequence (alm-K18) was previously shown to form stable anion-selective channels in membranes at pH 7.0 [Starostin, A. V., R. Butan, V. Borisenko, D. A. James, H. Wenschuh, M. S. Sansom, and G. A. Woolley. 1999. Biochemistry. 38:6144-6150]. To probe the charge state of the conducting channel and how this might influence cation versus anion selectivity, we performed a series of single-channel selectivity measurements at different pH values. At pH 7.0 and below, only anion-selective channels were found with P(K(+))/P(Cl(-)) = 0. 25. From pH 8-10, a mixture of anion-selective, non-selective, and cation-selective channels was found. At pH > 11 only cation-selective channels were found with P(K(+))/P(Cl(-)) = 4. In contrast, native alamethicin-Q18 channels (with Gln in place of Lys at position 18) were cation-selective (P(K(+))/P(Cl(-)) = 4) at all pH values. Continuum electrostatics calculations were then carried out using an octameric model of the alm-K18 channel embedded in a low dielectric slab to simulate a membrane. Although the calculations can account for the apparent pK(a) of the channel, they fail to correctly predict the degree of selectivity. Although a switch from cation- to anion-selectivity as the channel becomes protonated is indicated, the degree of anion-selectivity is severely overestimated, suggesting that the continuum approach does not adequately represent some aspect of the electrostatics of permeation in these channels. Side-chain conformational changes upon protonation, conformational changes, and deprotonation caused by permeating cations and counterion binding by lysine residues upon protonation are considered as possible sources of the overestimation.

The NMR solution structure of the ion channel peptaibol chrysospermin C bound to dodecylphosphocholine micelles

Chrysospermin C is a 19-residue peptaibol capable of forming transmembrane ion channels in phospholipid bilayers. The conformation of chrysospermin C bound to dodecylphosphocholine micelles has been solved using heteronuclear NMR spectroscopy. Selective 15N-labeling and 13C-labeling of specific alpha-aminoisobutyric acid residues was used to obtain complete stereospecific assignments for all eight alpha-aminoisobutyric acid residues. Structures were calculated using 339 distance constraints and 40 angle constraints obtained from NMR data. The NMR structures superimpose with mean global rmsd values to the mean structure of 0. 27 A (backbone heavy atoms) and 0.42 A (all heavy atoms). Chrysospermin C bound to decylphosphocholine micelles displays two well-defined helices at the N-terminus (residues Phe1-Aib9) and C-terminus (Aib13-Trp-ol19). A slight bend preceding Pro14, i.e. encompassing residues 10-12, results in an angle of approximately 38 degrees between the mean axes of the two helical regions. The bend structure observed for chrysospermin C is compatible with the sequences of all 18 long peptaibols and may represent a common 'active' conformation. The structure of chrysospermin C shows clear hydrophobic and hydrophilic surfaces which would be appropriate for the formation of oligomeric ion channels.

The mechanism of channel formation by alamethicin as viewed by molecular dynamics simulations

Alamethicin is a 20-residue channel-forming peptide that forms a stable amphipathic alpha-helix in membrane and membrane-mimetic environments. This helix contains a kink induced by a central Gly-X-X-Pro sequence motif. Alamethicin channels are activated by a cis positive transbilayer voltage. Channel activation is suggested to correspond to voltage-induced insertion of alamethicin helices in the bilayer. Alamethicin forms multi-conductance channels in lipid bilayers. These channels are formed by parallel bundles of transmembrane helices surrounding a central pore. A change in the number of helices per bundle switches the single channel conductance level. Molecular dynamics simulations of alamethicin in a number of different environments have been used to explore its channel-forming properties. These simulations include: (i) alamethicin in solution in water and in methanol; (ii) a single alamethicin helix at the surface of a phosphatidylcholine bilayer; (iii) single alamethicin helices spanning a phosphatidylcholine bilayer; and (iv) channels formed by bundles of 5, 6, 7 or 8 alamethicin helices spanning a phosphatidylcholine bilayer. The total simulation time is c. 30 ns. Thus, these simulations provide a set of dynamic snapshots of a possible mechanism of channel formation by this peptide.

Engineering charge selectivity in alamethicin channels

The peptide alamethicin provides a system for engineering ion channel charge selectivity. To define alamethicin charge selectivity experimentally, we measured single-channel current-voltage relationships in KCl gradients using covalently linked peptide dimers. Two factors were found to contribute to the charge selectivity of these channels: (i) the ionic strength of the surrounding solutions; and (ii) the distribution of fixed charge on the peptide. Native alamethicin channels exhibited either cation selectivity or anion selectivity depending on which end of the channel was at the low salt side of the membrane. When the glutamine residue at position 18 in the sequence was replaced with a lysine residue, an anion-selective channel was obtained regardless of which end of the channel was at the low salt side of the membrane.

Effective diffusion coefficients of K+ and Cl- ions in ion channel models

We have used molecular dynamics simulations, corresponding to a total simulation time of 11 ns, to investigate the effective short-time local diffusion coefficient of potassium and chloride ions in a series of model ion channels. These models, which include channels formed by the fungal peptide alamethicin, by a synthetic leucine-serine peptide, and by the pore-lining M2 helix bundle of the nicotinic acetylcholine receptor, have a range of different secondary structures, diameters and hydrophobicities. We find that the diffusion coefficients of both ions are appreciably reduced in the narrower channels, the extent of the reduction being similar for both the anionic and cationic species. This suggests that a difference in mobility cannot be the source of the ion selectivity exhibited by some of the channels (for example, the leucine-serine peptide). We find no evidence for a reduction in mobility of either ion in the nAChR model. These results are broadly in line with a previous similar study of Na+ ions, and may be useful in Poisson-Nernst-Planck, Eyring rate theory or Brownian dynamics calculations of channel conductance.

An alamethicin channel in a lipid bilayer: molecular dynamics simulations

We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle.

Two models of the influenza A M2 channel domain: verification by comparison

BACKGROUND

The influenza M2 protein is a simple membrane protein, containing a single transmembrane helix. It is representative of a very large family of single-transmembrane helix proteins. The functional protein is a tetramer, with the four transmembrane helices forming a proton-permeable channel across the bilayer. Two independently derived models of the M2 channel domain are compared, in order to assess the success of applying molecular modelling approaches to simple membrane proteins.

RESULTS

The Calpha RSMD between the two models is 1.7 A. Both models are composed of a left-handed bundle of helices, with the helices tilted roughly 15 degrees relative to the (presumed) bilayer normal. The two models have similar pore radius profiles, with a pore cavity lined by the Ser31 and Gly34 residues and a pore constriction formed by the ring of His37 residues.

CONCLUSIONS

Independent studies of M2 have converged on the same structural model for the channel domain. This model is in agreement with solid state NMR data. In particular, both model and NMR data indicate that the M2 helices are tilted relative to the bilayer normal and form a left-handed bundle. Such convergence suggests that, at least for simple membrane proteins, restraints-directed modelling might yield plausible models worthy of further computational and experimental investigation.

Viral ion channels: molecular modeling and simulation

In a number of membrane-bound viruses, ion channels are formed by integral membrane proteins. These channel proteins include M2 from influenza A, NB from influenza B, and, possibly, Vpu from HIV-1. M2 is important in facilitating uncoating of the influenza A viral genome and is the target of amantadine, an anti-influenza drug. The biological roles of NB and Vpu are less certain. In all cases, the protein contains a single transmembrane alpha-helix close to its N-terminus. Channels can be formed by homo-oligomerization of these proteins, yielding bundles of transmembrane helices that span the membrane and surround a central ion-permeable pore. Molecular modeling may be used to integrate and interpret available experimental data concerning the structure of such transmembrane pores. This has proved successful for the M2 channel domain, where two independently derived models are in agreement with one another, and with solid-state nuclear magnetic resonance (NMR) data. Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms.

Dynamic properties of Na+ ions in models of ion channels: a molecular dynamics study

We present simulation results for the effective diffusion coefficients of a sodium ion in a series of model ion channels of different diameters and hydrophobicities, including models of alamethicin, a leucine-serine peptide, and the M2 helix bundle of the nicotinic acetylcholine receptor. The diffusion coefficient, which in the simulations has a value of 0.15(2) A2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) A2ps-1 in the narrower channels, and to about 0.10(5) A2ps-1 in wider channels such as the nicotinic acetylcholine receptor. It is anticipated that this work will be useful in connection with calculations of channel conductivity using such techniques as the Poisson-Nernst-Planck equation, Eyring rate theory, or Brownian dynamics.

Functional modifications of alamethicin ion channels by substitution of glutamine 7, glycine 11 and proline 14

Alamethicin is a 20 amino acid, potentially helical peptaibol which forms voltage-dependent ion channels in bilayer systems. Two aspects of alamethicin structure have been suggested to be of particular functional significance for stabilization of alamethicin channels. (i) Proline 14 inducing a helix kink is together with glycine at position 11 responsible for an appropriate orientation of the molecules in the conducting associates. (ii) Glutamine 7 lining the channel interior is assumed to stabilize the channel structure by forming inter-helix hydrogen bonds. The functional importance of these residues was probed in macroscopic and single-channel experiments with alamethicin analogs containing polar, side chain bearing residues at position 11 (glutamine, asparagine) or at position 14 (glutamine). In order to investigate the crucial role of glutamine 7 for the stabilization of channel aggregates, this residue was substituted by alanine. The conformation of the lipid bound peptides was determined by circular dichroism spectroscopy. The results show that glutamine 7, glycine 11 and proline 14 are not essential for channel formation but substitution of any residue reduced the number of conductance levels and significantly reduced their lifetimes. Channel stabilization by the introduction of residues with potential hydrogen bonding capacity at positions 11 and 14 was not observed. Differences in the conformation of the lipid bound peptides, their orientation in the bilayer and their affinity for the lipid membrane appear thus to contribute to the modulation of functional properties.

A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1 643-1 661; Sansom et al. 1997. Biophys. J. 73:2404-241 5) and discuss implications for further theoretical work.

Models and simulations of ion channels and related membrane proteins

The past year has seen major advances in our understanding of ion channels, resulting from molecular dynamics simulations and modelling studies. Simulations of gramicidin have revealed that proton conduction along a water wire is limited by the dynamics of water reorientation. Plausible models are now available for a number of other channels, including alamethicin, the influenza A virus M2 protein, and the pore domains of the nicotinic acetylcholine receptor and Kv channels. Molecular dynamics simulations and continuum calculations have revealed some of the subtleties of the interactions between transmembrane helices and their lipid bilayer environment.

Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues

Several analogues of the channel-forming peptaibol alamethicin have been demonstrated to exhibit faster switching between channel substates than does unmodified alamethicin. Molecular modelling studies are used to explore the possible molecular basis of these differences. Models of channels formed by alamethicin analogues were generated by restrained molecular dynamics in vacuo and refined by short molecular dynamics simulations with water molecules within and at either mouth of the channel. A decrease in backbone solvation was found to correlate with a decrease in open channel stability between alamethicin and an analogue in which all alpha-amino-isobutyric acid residues of alamethicin were replaced by leucine. A decrease in the extent of hydrogen-bonding at residue 7 correlates with lower open channel stabilities of analogues in which the glutamine at position 7 was replaced by smaller polar sidechains. These two observations indicate the importance of alamethicin/water H-bonds in stabilizing the open channel.

The dielectric properties of water within model transbilayer pores

Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation.

The pore-lining region of shaker voltage-gated potassium channels: comparison of beta-barrel and alpha-helix bundle models

Although there is a large body of site-directed mutagenesis data that identify the pore-lining sequence of the voltage-gated potassium channel, the structure of this region remains unknown. We have interpreted the available biochemical data as a set of topological and orientational restraints and employed these restraints to produce molecular models of the potassium channel pore region, H5. The H5 sequence has been modeled either as a tetramer of membrane-spanning beta-hairpins, thus producing an eight-stranded beta-barrel, or as a tetramer of incompletely membrane-spanning alpha-helical hairpins, thus producing an eight-staved alpha-helix bundle. In total, restraints-directed modeling has produced 40 different configurations of the beta-barrel model, each configuration comprising an ensemble of 20 structures, and 24 different configurations of the alpha-helix bundle model, each comprising an ensemble of 24 structures. Thus, over 1300 model structures for H5 have been generated. Configurations have been ranked on the basis of their predicted pore properties and on the extent of their agreement with the biochemical data. This ranking is employed to identify particular configurations of H5 that may be explored further as models of the pore-lining region of the voltage-gated potassium channel pore.