The primary goals of this project remain to develop structural models of membrane channel proteins and to work with experimentalist to test and improve these models. We use a long term iterative approach in which models are continuously made more precise. The projects for which this approach has enjoyed the most success are those involving homologous voltage-gated potassium (K), sodium (Na), and calcium (Ca) channels. Almost all our initial predictions about their transmembrane topology and about which segments form ligand binding sites, ion selective regions, and gating mechanisms have now been confirmed experimentally. Now many laboratories have begun to use mutagenesis and other methods to analyze the structure-function properties of these proteins. Based on this wealth of new data, we have developed a new generation of more precise models of the pore portions of several of these channels. Our models of K channels may now be sufficiently precise to be useful in drug design and, in fact, Pfizer is currently using them to develop immunosuppressants. In order to obtain more direct structural data, we have begun a collaboration with Hans Robert Kalbitzer's laboratory at Max-Planck Institut in Heidelberg, Germany, to design water soluble peptides that should fold in the same way as the ion selective portions of K channels. They will determine the structures of these peptides with NMR. We have also started a number of other new modeling projects and are collaborating with several laboratories to test them. These collaborations include John Adelman's laboratory at the Vollum Institute to develop models of a different superfamily of K channels, called minK channel; Bernard Rossier's laboratory in Lausanne, Switzerland, to develop and test models of epithelial Na channels which are unrelated to the voltage-gated Na channels we have modeled previously, and with Ching Kung's laboratory at the University of Wisconsin, to develop models of stretch-activated channels from bacteria. Other projects include using molecular dynamics computer simulations to understand the mechanistic basis of solvation thermodynamics. The goal of this work is to better understand the forces involved in biomacromolecular folding, association, drug binding, and ion permeation through channels.
