Our large goal is to construct a physical description on the atomic scale of resolution of ion permeation through a particular polypeptide membrane channel; i.e., gramicidin A and variants formed by substitutions in various side chains. Particular specific aims in pursuit of this large goal follow: We are using liquid crystal theory and molecular simulations to understand the mechanisms of gramicidin channel formation and dissociation. We are using Brownian dynamics to study the properties of channels that permit multiple-ion occupancy, and will compare our results to data for gramicidin and potassium channels. We will use Poisson-Boltzmann theory to map electrical potentials outside the channel mouth and then use Brownian dynamics to calculate trajectories through that region in order to evaluate the resistance between the bulk of the solution and the channel mouth. We will also apply Brownian dynamics to analysis of data on blocking times of gramicidin currents by organic cations, to test the hypothesis that the blocking times for the alkali metal currents are passage times for the organic cations. We will use Brownian dynamics to compute distributions of passage times and compare them to the experimental distributions of blocking times. We will use a variant of molecular dynamics called the thermodynamic cycle-perturbation method to calculate the effect of side chain substitution on the free energy profile for ion translocation in gramicidin. We will also use time correlation therory to calculate in diffusion coefficients in the channel from these simulations. The above calculations can probably be done with only the channel, the permeant ion, and the channel waters to get the free energy difference associated with side chain substitution. We intend to proceed from there to do more elaborate molecular dynamics on a more complete system to calculate mobilities and full free energies for the ion entry, translocation, and exit processes. The methods we are developing will be applicable to understanding in detail the functioning of membrane channels of wide biological importance. This understanding, in conjunction with modern genetic techniques, may facilitate the treatment of disease involving these molecules. A second potential application lies in guiding the manufacture of synthetic ionophores, which may have transport properties tailored to effect desirable changes in the functional properties of living membranes.
