Entropy effects on the ion-diffusion rate in transmembrane protein channels

Conformational model for ion permeation in membrane channels: a comparison with multi-ion models and applications to calcium channel permeability

The permeation properties of ion channels existing in several conductive states were analyzed. Each state was represented by the one-ion model. A special emphasis was placed on features, assumed to be indicative of a multi-ion mode of channel occupancy such as a deviation of concentration dependence of channel conductance from the Michaelis-Menten equation, an anomalous mole fraction effect, a strong voltage dependence of ion block and coupling of unidirectional fluxes (anomalous Ussing flux ratio). The conformational model was shown to have all these properties. The ion permeation through voltage-sensitive calcium channels fulfilled all the characteristics of the model proposed.

Ion transport in a model gramicidin channel. Structure and thermodynamics

The potential of mean force for Na+ and K+ ions as a function of position in the interior of a periodic poly(L,D)-alanine model for the gramicidin beta-helix is calculated with a detailed atomic model and realistic interactions. The calculated free energy barriers are 4.5 kcal/mol for Na+ and 1.0 kcal/mol for K+. A decomposition of the free energy demonstrates that the water molecules make a significant contribution to the free energy of activation. There is an increase in entropy at the transition state associated with greater fluctuations. Analysis reveals that the free energy profile of ions in the periodic channel is controlled not by the large interaction energy involving the ion but rather by the weaker water-water, water-peptide and peptide-peptide hydrogen bond interactions. The interior of the channel retains much of the solvation properties of a liquid in its interactions with the cations. Of particular importance is the flexibility of the helix, which permits it to respond to the presence of an ion in a fluidlike manner. The distortion of the helix is local (limited to a few carbonyls) because the structure is too flexible to transmit a perturbation to large distances. The plasticity of the structure (i.e., the property to deform without generating a large energy stress) appears to be an essential factor in the transport of ions, suggesting that a rigid helix model would be inappropriate.

Ion permeation through single ACh-activated channels in denervated adult toad sartorius skeletal muscle fibres: effect of temperature

The gigaohm seal technique was used to study the effects of temperature on ion permeation through acetylcholine-activated channels. This was done in cell-attached patches of the extrajunctional membrane of chronically-denervated, enzyme-treated cells from sartorius muscle of the toad Bufo marinus. The predominant extracellular cation in the pipette solution was Na+. Single channel current-voltage curves were measured at different temperatures and electrodiffusion and three-site-four-barrier rate theory models were used to characterize ion permeation through the channels and determine the effects of temperature on permeation parameters. The fitting of the experimental data to these models suggested the presence of at least three and probably more ion-selective sites within the channel. The most frequently occurring channel type (greater than 95% of channel openings) had a chord conductance of 25 pS at 11 degrees C and -70 mV and was classified as 'extrajunctional'. The single channel conductance of this channel had a low temperature-dependence (Q10 approximately equal to 1.3). The apparent activation enthalpy, Ea, for the conductance between 11 degrees C and 20 degrees C, did not appear to be significantly voltage-sensitive and had a value of about 17 +/- 2 kJ . mol-1 at a voltage of -70 mV. The Arrhenius plot of conductance appeared linear between 11 and 20 degrees C at all potentials examined. The data was consistent with a break in the slope of the Arrhenius plot at temperatures between 5 and 11 degrees C at all potentials examined, suggesting a possible phase transition of the membrane lipids. In contrast to the relative permeability, which was not very temperature sensitive, the relative binding constant was significantly affected by temperature. The relative Na/K binding constant sequence was: K5 degrees C greater than K20 degrees C greater than K15 degrees C much greater than K11 degrees C. In addition, the decrease in conductance observed at the most depolarized potentials was accentuated as the temperature was increased, suggesting a rate-limiting access step for ions from the intracellular solution into the channel.

Gramicidin A--phospholipid model systems

Gramicidin A forms ion-conducting channels which can traverse the hydrocarbon core of lipid bilayer membranes. The structures formed by gramicidin A are among the best characterized of all membrane-bound polypeptides or proteins. In this review a brief summary is given of the occurrence, conformation, and synthesis of gramicidin A, and of its use as a model for ion transport and the interaction of proteins and lipids in biological membranes.

Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels

The structure and dynamics of solvated alkali metal cations in transmembrane channels are treated using the molecular dynamics simulation technique. The simulations are based on a modified Fischer-Brickmann model (Fischer, W., and J. Brickmann, 1983, Biophys. Chem., 18:323-337) for gramicidin A-type channels. The trajectories of all particles in the channel as well as two-dimensional pair correlation functions are analyzed. It is found from the analysis of the stationary simulation state that one-dimensional solvation complexes are formed and that the number of water molecules in the channel varies for different alkali metal cations.

Simulation of voltage-driven hydrated cation transport through narrow transmembrane channels

Molecular dynamics studies for the voltage-driven transport of the alkali metal ions lithium, sodium, and potassium through gramicidin A-type channels filled with water molecules are presented. The number of water molecules in the channel is obtained from a previous study (Skerra, A., and J. Brickmann, 1987, Biophys. J., 51:969-976). It is shown that the selectivity of the intrachannel ion diffusion through our model pore conforms to the experimentally observed selectivity of the gramicidin A channel. It is demonstrated that the number of water molecules in the channel plays a key role for the selectivity.

Analysis of the ion transfer through the channel of 9,11,13,15-phenylalanylgramicidin A

The behavior of an analogue of gramicidin A in which all four tryptophanyl residues are substituted by phenylalanyl and which shows a strong voltage effect on the single channel conductance is analyzed on the basis of a 'three-barrier--two-site' model. It is shown that in the gramicidin family the side chains of some amino acids, in spite of their location, which point outside the channel can play a major role in the binding of ions in the channel and thus can significantly modify the energy profile of the channel.

Solvent effects in ionic transport through transmembrane protein channels

Ion transport through a gramicidin A like channel in the presence of solvent molecules with van der Waals parameters of water has been studied by means of the molecular dynamics simulation technique. It was found that the presence of solvent molecules in the channel has a tendency to equalize the effective masses of the ions through "association" thus giving the experimentally found ion selectivity to the gramicidin A channel.

Structure and dynamics of ion transport through gramicidin A

Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed.

Ion-specific diffusion rates through transmembrane protein channels. A molecular dynamics study

The migration of different alkali metal cations through a transmembrane model channel is simulated by means of the molecular dynamics technique. The parameters of the model are chosen in close relation to the gramicidin A channel. Coulomb- and van der Waals-type potentials between the ions and flexible carbonyl groups of the pore-forming molecule are used to describe the ion channel interaction. The diffusion properties of the ions are obtained from three-dimensional trajectory calculations. The diffusion rates for the different ions Li+, Na+, K+ and Rb+ are affected not only by the mass of the particles but also very strongly by their size. The latter effect is more pronounced for rigid channels, i.e., for binding vibrational frequencies of the CO groups with v greater than 400 cm-1. In this range the selectivity sequence for the diffusion rates is the inverse of that expected from normal rate theory but agrees with that found in experiments for gramicidin A.