Ion channels: structural bioinformatics and modelling

Abstract

Ion channels are membrane proteins of key physiological and pharmacological importance. As is the case for many integral membrane proteins, X-ray structures are known for a few bacterial channels, yet structures of human homologues are required for analysis of channel-associated diseases and for drug design. Homology modelling can be used to help remedy this deficit. In combination with molecular dynamics simulations and associated calculations, modelling provides a powerful approach to understanding structure/function relationships in human ion channels. Modelling techniques have been applied to two classes of potassium channels: voltage-gated (Kv) and inward rectifier (Kir) channels. Kir channel models, based on the structure of the bacterial channel KcsA, have been used as a starting point for detailed simulation studies that have increased our understanding of ion permeation and selectivity mechanisms. The transmembrane domain of GluR0, a bacterial homologue of mammalian glutamate receptors, also may be modelled using the KcsA structure as a template. Models of the nicotinic acetylcholine receptor may be constructed in a modular fashion. The snail acetylcholine-binding protein provides a template for the extracellular ligand-binding domain. The transmembrane pore region can be modelled on the basis of NMR structures of the pore-lining M2 helix.