Using Domain Based Discovery Methods to Identify Prokaryotic Counterparts to Eukaryotic Protein Ion Channels

Abstract

Our lab, in collaboration with the laboratory of I. Aravind, used domain based methods to discover the prokaryotic counterparts of Ach receptor channels (Tasneem et al), after whole-protein approaches such as BLAST had failed. Our identification was verified by functional studies and by x-ray crystallization of targets we identified. We have subsequently streamlined and formalized the domain search methods and applied them to a variety of ion channels and other membrane proteins. It has become clear that domain based methods are more powerful than whole-protein approaches, provided one has good domain definitions to start the search. The use of domain-based methods depends on a somewhat different model of evolution from BLAST. In BLAST, the operational model is the substitution of one amino acid for another, with gaps being treated as a particular type of substitution. Domain-based methods deal readily and directly with the phenomenon of large scale reorganization of domains, which is now recognized as an essential process for innovation in evolution. In this presentation we will provide an update on prokaryotic Ach receptor channels, a survey of prokaryotic glutamate receptor channels and their relationship to their eukaryotic counterparts, the discovery of a prokaryotic counterpart to HCN and CNG channels which appears likely to be closely related to their common ancestor, and searches on other families that are under way at the time of preparation of this abstract. We gratefully acknowledge support from NSF grants 0835718 and 0235792, from NIH grants 5PN2EY016570-06 and 5R01NS063405-02 from the Beckman Institute for Advanced Science and Technology, the National Center for Supercomputing Applications, and the Renaissance Computing Institute.