Examining ion channel properties using free-energy methods

Recent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels.