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.

Electrostatics and the ion selectivity of ligand-gated channels

The nicotinic acetylcholine receptor (nAChR) is a cation-selective ion channel that opens in response to acetylcholine binding. The related glycine receptor (GlyR) is anion selective. The pore-lining domain of each protein may be modeled as a bundle of five parallel M2 helices. Models of the pore-lining domains of homopentameric nAChR and GlyR have been used in continuum electrostatics calculations to probe the origins of ion selectivity. Calculated pKA values suggest that "rings" of acidic or basic side chains at the mouths of the nAChR or GlyR M2 helix bundles, respectively, may not be fully ionized. In particular, for the nAChR the ring of glutamate side chains at the extracellular mouth of the pore is predicted to be largely protonated at neutral pH, whereas those glutamate side chains in the intracellular and intermediate rings (at the opposite mouth of the pore) are predicted to be fully ionized. Inclusion of the other domains of each protein represented as an irregular cylindrical tube in which the M2 bundles are embedded suggests that both the M2 helices and the extramembrane domains play significant roles in determining ion selectivity.

The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics

The pore domain of the nicotinic acetylcholine receptor has been modeled as a bundle of five kinked M2 helices. Models were generated via molecular dynamics simulations incorporating restraints derived from 9-A resolution cryoelectron microscopy data (Unwin, 1993; 1995), and from mutagenesis data that identify channel-lining side chains. Thus, these models conform to current experimental data but will require revision as higher resolution data become available. Models of the open and closed states of a homopentameric alpha 7 pore are compared. The minimum radius of the closed-state model is less than 2 A; the minimum radius of the open-state models is approximately 6 A. It is suggested that the presence of "bound" water molecules within the pore may reduce the effective minimum radii below these values by up to approximately 3 A. Poisson-Boltzmann calculations are used to obtain a first approximation to the potential energy of a monovalent cation as it moves along the pore axis. The differences in electrostatic potential energy profiles between the open-state models of alpha 7 and of a mutant of alpha 7 are consistent with the experimentally observed change in ion selectivity from cationic to anionic. Models of the open state of the heteropentameric Torpedo nicotinic acetylcholine receptor pore domain are also described. Relatively small differences in pore radius and electrostatic potential energy profiles are seen when the Torpedo and alpha 7 models are compared.

Modelling and simulation of ion channels: applications to the nicotinic acetylcholine receptor

Molecular dynamics simulations with experimentally derived restraints have been used to develop atomic models of M2 helix bundles forming the pore-lining domains of the nicotinic acetylcholine receptor and related ligand-gated ion channels. M2 helix bundles have been used in microscopic simulations of the dynamics and energetics of water and ions within an ion channel. Translational and rotational motion of water are restricted within the pore, and water dipoles are aligned relative to the pore axis by the surrounding helix dipoles. Potential energy profiles for translation of a Na+ ion along the pore suggest that the protein and water components of the interaction energy exert an opposing effect on the ion, resulting in a relatively flat profile which favors cation permeation. Empirical conductance calculations based on a pore radius profile suggest that the M2 helix model is consistent with a single channel conductance of ca. 50 pS. Continuum electrostatics calculations indicate that a ring of glutamate residues at the cytoplasmic mouth of the alpha 7 nicotinic receptor M2 helix bundle may not be fully ionized. A simplified model of the remainder of the channel protein when added to the M2 helix bundle plays a significant role in enhancing the ion selectivity of the channel.

Shock-transformation of whitlockite to merrillite and the implications for meteoritic phosphate

Meteorites represent the only samples available for study on Earth of a number of planetary bodies. The minerals within meteorites therefore hold the key to addressing numerous questions about our solar system. Of particular interest is the Ca-phosphate mineral merrillite, the anhydrous end-member of the merrillite–whitlockite solid solution series. For example, the anhydrous nature of merrillite in Martian meteorites has been interpreted as evidence of water-limited late-stage Martian melts. However, recent research on apatite in the same meteorites suggests higher water content in melts. One complication of using meteorites rather than direct samples is the shock compression all meteorites have experienced, which can alter meteorite mineralogy. Here we show whitlockite transformation into merrillite by shock-compression levels relevant to meteorites, including Martian meteorites. The results open the possibility that at least part of meteoritic merrillite may have originally been H⁺-bearing whitlockite with implications for interpreting meteorites and the need for future sample return.

Quantifying the amount of water in meteorites remains challenging, with minerals the key to understanding water contents. Here, Adcock et al. perform shock experiments on H⁺-bearing whitlockite demonstrating that it may transform into anhydrous merrillite, which is commonly found in Martian meteorites.

The nicotinic acetylcholine receptor: from molecular model to single-channel conductance

The nicotinic acetylcholine receptor (nAChR) is the archetypal ligand-gated ion channel. A model of the alpha7 homopentameric nAChR is described in which the pore-lining M2 helix bundle is treated atomistically and the remainder of the molecule is treated as a "low resolution" cylinder. The surface charge on the cylinder is derived from the distribution of charged amino acids in the amino acid sequence (excluding the M2 segments). This model is explored in terms of its predicted single-channel properties. Based on electrostatic potential profiles derived from the model, the one-dimensional Poisson-Nernst-Planck equation is used to calculate single-channel current/voltage curves. The predicted single-channel conductance is three times higher (ca. 150 pS) than that measured experimentally, and the predicted ion selectivity agrees with the observed cation selectivity of nAChR. Molecular dynamics (MD) simulations are used to estimate the self-diffusion coefficients (D) of water molecules within the channel. In the narrowest region of the pore, D is reduced ca. threefold relative to that of bulk water. Assuming that the diffusion of ions scales with that of water, this yields a revised prediction of the single-channel conductance (ca. 50 pS) in good agreement with the experimental value. We conclude that combining atomistic (MD) and continuum electrostatics calculations is a promising approach to bridging the gap between structure and physiology of ion channels.

Protein-water-ion interactions in a model of the pore domain of a potassium channel: a simulation study

A model of the selectivity filter of a voltage-gated K+ (Kv) channel formed by an eight-stranded beta-barrel is compared with physiological properties of the channel. Continuum electrostatic calculations suggest that only two of the eight Asp sidechains at the extracellular mouth of the pore will ionise. A ring of four Tyr sidechains forms the narrowest region of the pore. Molecular dynamic simulations of the potential energy of a K+ ion as translated along the model pore indicate that the two ionised Asp sidechains and the hydroxyl groups of the Tyr sidechains stabilise the partially desolvated ion as it passes through the narrowest region.

Functional characterization of a mutated chicken alpha7 nicotinic acetylcholine receptor subunit with a leucine residue inserted in transmembrane domain 2

1. Site-directed mutagenesis was used to create an altered form of the chicken alpha7 nicotinic acetylcholine (ACh) receptor subunit (alpha7x61) in which a leucine residue was inserted between residues Leu9' and Ser10' in transmembrane domain 2. The properties of alpha7x61 receptors are distinct from those of the wild-type receptor. 2. Oocytes expressing wild-type alpha7 receptors responded to 10 microM nicotine with rapid inward currents that desensitized with a time-constant of 710+/-409 ms (mean+/-s.e.mean, n=5). However in alpha7x61 receptors 10 microM nicotine resulted in slower onset inward currents that desensitized with a time-constant of 5684+/-3403 ms (mean+/-s.e.mean, n = 4). No significant difference in the apparent affinity of nicotine or acetylcholine between mutant and wild-type receptors was observed. Dihydro-beta-erythroidine (DHbetaE) acted as an antagonist on both receptors. 3. Molecular modelling of the alpha7x61 receptor channel pore formed by a bundle of M2 alpha-helices suggested that three of the channel lining residues would be altered by the leucine insertion i.e.; Ser10 would be replaced by the leucine insertion, Val13' and Phe14' would be replaced, by Thr and Val, respectively. 4 When present in the LEV-1 nicotinic ACh receptor subunit from Caenorhabditis elegans the same alteration conferred resistance to levamisole anthelmintic drug. Levamisole blocked responses to nicotine of wild-type and alpha7x61 receptors. However, block was more dependent on membrane potential for the alpha7x61 receptors. 5. We conclude that the leucine insertion in transmembrane domain 2 has the unusual effect of slowing desensitization without altering apparent agonist affinity.

An extensive and diverse gene family of nicotinic acetylcholine receptor alpha subunits in Caenorhabditis elegans

Using reverse transcription-polymerase chain reactions the transcription of eight novel candidate nicotinic acetylcholine receptor (nAChR) alpha subunit genes has been demonstrated in the nematode Caenorhabditis elegans. Together with five other alpha subunit genes described elsewhere by ourselves (unc-38) and other workers (deg-3, acr-4, Ce21 and acr-6), this is now the largest known family of nAChR alpha subunit genes in a single species. By homology we have identified four groups of alpha subunits: DEG-3-like; ACR-16[Ce21]-like; UNC-38-like and ACR-8-like. Five C. elegans nAChR alpha subunits contain a modification in loop C of the ACh binding site in which the normally conserved Tyr-x-Cys-Cys, is replaced by a distinct motif (Tyr-x-x-Cys-Cys). Variation is also found in the channel lining M2 regions, including the replacement in four subunits of the highly conserved leucine at the 9' position by valine and most notably, the replacement in all ACR-8-like subunits of the highly conserved glutamic acid at the -1' position by histidine. Restrained molecular dynamics simulations have been used to generate homo-pentameric M2 helix bundle models for alpha subunits and possible functional implications examined. The calculated electrostatic potential energy profile for the M2 region of ACR-8 differs strikingly from that of ACR-16[Ce21] largely due to the presence of histidine at the -1' position, suggesting a possible perturbation of nAChR channel action permeability in the presence of this subunit type.