A study of Brownian dynamics simulation for ion transport through a transmembrane pore with a molecular adapter

This paper uses the coarse-grained Brownian dynamics simulation to study ion transport through a protein channel, α-Hemolysin, with a covalently-bonded molecular adapter, β-Cyclodextrin. The goal is to understand the behavior of mobile ions in the pore region and develop a space-dependent model for the diffusion coefficients based only on structural information yielding currents in good agreement with experimental results. In addition, we develop a simple equivalent circuit model for channel conduction that uses a diode and a current source for each ion current component. This equivalent circuit introduces a new way to quantify ion selectivity based on the ratio of the characteristic conductance for cations and anions. The model provides a simple description of ion transport through a-Hemolysin with covalently bonded β-Cyclodextrin which is suitable for possible applications in sensor design.