Bioinformatics of Voltage-Gated Ion Channels

University Of Illinois At Urbana-Champaign, Urbana IL

Investigators

Abstract

This proposal will study a particular class of proteins, ion channels, by the tools of bioinformatics. The subclass of ion channels to be studied are potassium channels, that selectively permit the passage of passage of potassium ions. Traditionally, the detailed function of ion channels has been studied by biophysical means. This proposal will study the functioning of potassium channels with a different set of tools, the tools of sequence bioinformatics. Essentially, this project will correlate sequence data with knowledge about the structure and function of some members of the potassium channel family, and use that to extrapolate to a prediction of functional details for the very large number of potassium channel genes for which we have no direct structural and functional data. This is very important in expanding our knowledge because it is now much quicker and cheaper to get sequence data than functional and structural data. Any advance that we can make in inferring function from sequence will therefore lead to big advances in functional knowledge. This research clearly can have a large ultimate beneficial pay-off for biomedicine and biotechnology. In addition to disseminating results by the usual route of publishing and presentation at meetings, we will also develop for the general community use profiles and motifs that are specific for particular subclasses of potassium channels, and build them in the formats that are standard for motif/profile databases such as BLOCKS, PROSITE, PFAM, and PRINTS. The findings from this research will be able to be seamlessly and easily used by other researchers with existing analysis software.