Kuyucak, SerdarChung, Shin-Ho2015-12-130092-0606http://hdl.handle.net/1885/71604Recent determination of the molecular structures of potassium and mechanosensitive channels from x-ray crystallography has led to a renewed interest in ion channels. The challenge for permeation models is to understand the functional properties of channels from the available structural information. Here we give a critical review of the three main contenders, namely, continuum theories, Brownian dynamics and molecular dynamics. Continuum theories are shown to be invalid in a narrow channel environment because they ignore the self-energy of ions arising from the induced charges on the dielectric boundary. Brownian and molecular dynamics are thus the only physically valid methods for studying the structure-function relations in ion channels. Applications of these methods to potassium and calcium channels are presented, which illustrate the multi-ion nature of the permeation mechanism in selective biological channels.Keywords: calcium channel; potassium channel; calculation; conference paper; dielectric constant; energy; molecular dynamics; permeability; priority journal; structure activity relation; structure analysis; theory; X ray crystallography Brownian dynamics; Ion channels; Molecular dynamics; Permeation models; Poisson-Nernst-Planck equations200210.1023/A:10199399005682015-12-11