Predicting Function from Structure Using the Poisson−Nernst−Planck Equations: Sodium Current in the Gramicidin A Channel

We predict the sodium current through an ion channel of known structure gramicidin A (gA) using an electrostatic model of the ion channel and an electrodiffusion model of ion movement. We use three-dimensional (3D) spectral elements to represent the channel and macroscopic surrounding baths in a 3D Poisson−Nernst−Planck (PNP) calculation that uses fine resolution only where needed in the channel pore region. Diffusion coefficient and dielectric constants are estimated from a 1D PNP representation of the experimental data. The 3D atomic structure and standard empirical partial charges of gA are used, along with the diffusion coefficients estimated from 1D PNP. No adjustable parameters were used in the 3D PNP calculation. No attempts were made to improve fit by adjusting parameters. Our results show that 3D PNP is an accurate description of charge transport in this channel system and thus a good place to start investigation of other channels. We predict unreported experiments as a further test of the theory.