Chapter 6: Computer Simulation of Ion Channels

Ion channels provide a pathway for charged and polar solutes to cross cell membranes, thereby regulating the electrical excitability of cells and helping to initiate cellular responses. Computer simulations have been an important tool in understanding how this family of proteins work. In this chapter, we describe how simulations have been used to address issues such as how ions move through ion channels, how channels distinguish between ion types, how channels open and close in response to stimuli and how channels can be modulated by drugs and toxins. In doing so, we hope to demonstrate how different simulation approaches can be used to gain a mechanistic understanding of the function of this important protein family.