Comparison of gramicidin A and gramicidin M channel conductance dispersities

Analysis of Ion Transport through a Single Channel of Gramicidin A in Bilayer Lipid Membranes

Ion transport through a single channel of gramicidin A (GA) within the bilayer lipid membrane (BLM) between two aqueous phases (W1 and W2) has been analyzed based on the electroneutrality principle. The single-channel current increases in proportion to the magnitude of the applied membrane potential and is also dependent on the permeability coefficients of electrolyte ions (K(+) and Cl(-)). By varying the ratio of the concentration of KCl in W1 to that in W2, the ratio of the diffusion coefficient of K(+) in the BLM to that of Cl(-) in the BLM can be evaluated.

Molecular dynamics simulations of Trp side-chain conformational flexibility in the gramicidin A channel

Gramicidin A (gA) is prototypical peptide antibiotic and a model ion channel former. Configured in the solid-state NMR beta(6.5)-helix channel conformation, gA was subjected to 1-ns molecular dynamics (MD) gas phase simulations using the all-atom charmm22 force field to ascertain the conformational stability of the Trp side chains as governed by backbone and neighboring side-chain contacts. Three microcanonical trajectories were computed using different initial atomic velocities for each of twenty different initial structures. For each set, one of the four Trp side chains in each monomer was initially positioned in one of the five non-native conformations (A. E. Dorigo et al., Biophysical Journal, 1999, Vol. 76, 1897-1908), the other Trps being positioned in the native state, o1. In three additional control simulations, all Trps were initiated in the native conformation. After equilibration, constraints were removed and subsequent conformational changes of the initially constrained Trp were measured. The chi(1) was more flexible than chi(2.1). The energetically optimal orientation, o1 (Dorigo et al., 1999), was the most stable in all four Trp positions (9, 11, 13, 15) and remained unchanged for the entire 1 ns simulation in 19 of 24 trials. Changes in chi(1) from each of the 5 suboptimal states occur readily. Two of the non-native conformations reverted readily to o1, whereas the other three converted to an intermediate state, i2. There were frequent interconversions between i2 and o1. We speculate that experimentally observed Trp stability is caused by interactions with the lipid-water interface, and that stabilization of one of the suboptimal conformations in gA, such as i2, by lipid headgroups could produce a secondary, metastable conformational state. This could explain recent experimental studies of differences in the channel conductance dispersity between gA and a Trp-to-Phe gA analog, gramicidin M (gM, J. C. Markham et al., Biochimica et Biophysica Acta, 2001, Vol. 1513, 185-192).

The role of Trp side chains in tuning single proton conduction through gramicidin channels

We present an extensive set of measurements of proton conduction through gramicidin A (gA), B (gB), and M (gM) homodimer channels which have 4, 3, or 0 Trp residues at each end of the channel, respectively. In gA we find a shoulder separating two domains of conductance increasing with concentration, confirming the results of Eisenman, G., B. Enos, J. Hagglund, and J. Sandblom. 1980. Ann. NY. Acad. Sci. 339:8-20. In gB, the shoulder is shifted by approximately 1/2 pH unit to higher H(+) concentrations and is very sharply defined. No shoulder appears in the gM data, but an associated transition from sublinear to superlinear I-V values occurs at a 100-fold higher [H(+)] in gM than in gA. The data in the low concentration domain are analyzed using a configuration space model of single-proton conduction, assuming that the difference in the proton potential of mean force (PMF) between gA and its analogs is constant, similar to the results of Anderson, D., R. B. Shirts, T. A. Cross, and D. D. Busath. 2001. Biophys. J. 81:1255-1264. Our results suggest that the average amplitudes of the calculated proton PMFs are nearly correct, but that the water reorientation barrier calculated for gA by molecular dynamics using the PM6 water model (Pomès, R., and B. Roux. 1997. Biophys. J. 72:246a) must be reduced in amplitude by 1.5 kcal/mol or more, and is not rate-limiting for gA.

Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125-A internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and extended simple point charge water. Channel and bath currents were computed from 10 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration dependent and superlinear at high concentrations.