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When modelling biological ion channels using Brownian dynamics (BD) or Poisson–Nernst–Planck theory, the force encountered by permeant ions is calculated by solving Poisson’s equation. Two free parameters needed to solve this equation are the dielectric constant of water in the pore and the dielectric constant of the protein forming the channel. Although these values can in theory be deduced by various methods, they do not give a reliable answer when applied to channel-like geometries that contain charged particles. To determine the appropriate values of the dielectric constants, here we solve the inverse problem. Given the structure of the MthK channel, we attempt to determine the values of the protein and pore dielectric constants that minimize the discrepancies between the experimentally-determined current–voltage curve and the curve obtained from BD simulations. Two different methods have been applied to determine these values. First, we use all possible pairs of the pore dielectric constant of water, ranging from 20 to 80 in steps of 10, and the protein dielectric constant of 2–10 in steps of 2, and compare the simulated results with the experimental values. We find that the best agreement is obtained with experiment when a protein dielectric constant of 2 and a pore water dielectric constant of 60 is used. Second, we employ a learning-based stochastic optimization algorithm to pick out the optimum combination of the two dielectric constants. From the algorithm we obtain an optimum value of 2 for the protein dielectric constant and 64 for the pore dielectric constant. [ABSTRACT FROM AUTHOR]

We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel. [ABSTRACT FROM AUTHOR]

The members of the RCK family of cloned voltage-dependent K channels are quite homologous in primary structure, but they are highly diverse in functional properties. RCK4 channels differ from RCK1 and RCK2 channels in inactivation and permeation properties, the sensitivity to external TEA, and to current modulation by external K ions. Here we show several other interesting differences: While RCK1 and RCK2 are blocked in a voltage and concentration dependent manner by internal Mg ions, RCK4 is only weakly blocked at very high potentials. The single-channel current-voltage relations of RCK4 are rather linear while RCK2 exhibits an inwardly rectifying single-channel current in symmetrical K solutions. The deactivation of the channels, measured by tail current protocols, is faster in RCK4 by a factor of two compared with RCK2. In a search for the structural motif responsible for these differences, point mutants creating homology between RCK2 and RCK4 in the pore region were tested. The single-point mutant K533Y in the background of RCK4 conferred the properties of Mg block, tail current kinetics, and inward ion permeation of RCK2 to RCK4. This mutant was previously shown to be responsible for the alterations in external TEA sensitivity and channel regulation by external K ions. Thus, this residue is expected to be located at the external side of the pore entrance. The data are consistent with the idea that the mutation alters the channel occupancy by K and thereby indirectly affects internal Mg block and channel closing. [ABSTRACT FROM AUTHOR]

Anion-selective channels from apical membranes of cultured CFPAC-1 cells were isolated and incorporated into giant liposomes for patch clamp recording. Liposomes were formed from L-α-lecithin by a dehydration-hydration method. Ion channels were characterized using the excised inside-out patch clamp configuration. The most commonly observed anion channels were similar to those observed in native epithelial tissues. The linear 20 pS Cl channel had the halide permeability sequence Cl > I ≥ Br > F, and showed anomalous mole-fraction behavior in solutions containing different proportions of Cl and F, ions. The autwardly rectifying Cl channel had the halide permeability sequence I > Br > Cl > F, and also showed anomalous molefraction behavior, indicating that both these channels probably contain multi-ion pores. The third, voltage-dependent anion channel showed at least five different substrates, had a conductance of 390 pS in the main state, and showed two types of kinetics, fast (openings and closings < 1 ms), and slow (openings and closings > 1 s). The channel was seen more frequently after reconstitution into giant liposomes than in intact cells. It was not selective amongst the halides, and there was no deviation from a linear dependence of relative current on molar fractions, indicating relatively simple permeation through the pore. Differences in halide permeabilities suggest that different anion channels may be related to different membrane proteins. Comparison with the chloride channel proteins isolated biochemically from epithelial cell membranes is discussed. [ABSTRACT FROM AUTHOR]

A functional model for the S4/IV α-helix of the action potential sodium channel is described by means of a thermodynamic approach. The model is based on a phase transition between the α-helix and an ion conducting channel-helix which is similar to the well established helix-coil transition in solution. The right hand channel-helix is a peptide chain with an alternating sequence of torsional angles (φψ)=(87°, 315°) and (φψ)=(22°, 107°) which yields a helix of 13.5 Å per turn. The axial dipole moments of the peptide bonds of this chain of l-amino acids nearly cancel each other out in similar way to those in the gramicidin A channel, which is formed by alternating d-and l-amino acids. The helix, which does not contain any H-bonds, is stabilized by a helical file of water molecules which includes the permeating ion(s). This file turns around the channel-helix to form a relatively stable 'double helix' structure which corresponds to the open channel. Since every third side chain in the S4/IV helix carries a positive charge their environments must be polarized. These polarized regions form a left hand screening-helix around the α-helix are broken and the internal α-carbon atom is considered as fixed, the outer ten residues leave the membrane while the internal ten residues form the channel-helix. In this configuration every positively charged side chain matches nearly exactly every second polarized region of the screening-helix leaving the three regions in-between exposed to the water file containing the ion(s). This further stabilizes the channel and agrees nicely with the idea of cationic selectivity. An analysis of the energetics of the α-helix-channel-helix transition showed that the voltage-independent part of the free energy per helix residue could well be close to 0 kcal/mol and thus be in the range where a transition could occur. Two voltage-dependent contributions were included: the break down of the considerable dipole of the α-helix and the outward shift of the positive charges of the side chains upon channel-helix formation. Taking into account the fact that the formation of an α-helix is a highly cooperative process the degree of voltage dependence of the probability of formation of a channel-helix proved to be in the same range as experimental values for the open probability of modified Na channels whose inactivation had been removed. With regard to gating currents, the model predicts that 2.74 positive charges are moved in an outward direction. Consequences of the model for other experimental findings are discussed. [ABSTRACT FROM AUTHOR]