Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Bioinformatics, Modeling, and Computation
61
Towards a Physics and Systems Understanding of Ion Transport in Prokaryotes
Shreedhar Natarajan1, Asba Tasneem*1, Sameer Varma1, Lakshminarayan Iyer2, L. Aravind2, and Eric Jakobsson*2 (jake@ncsa.uiuc.edu)
1University of Illinois, Urbana, IL and 2National Institutes of Health, Bethesda, MD
Ion transport mechanisms play three fundamental roles in biological systems: 1) generation and sensing of electrochemical signals, 2) generation of osmotic force for regulating water flow, and 3) energy transduction. It is useful to study these functions in an integrated manner because: 1) Ion transporters as they perform all three functions pose similar issues in understanding the physical bases of those functions, and 2) it is common for the same transporter to be critical for more than one function. Indeed, it is universally true that transporters which are critical for one function will affect the functioning of networks of transporters critical to other functions, because every transporter in a membrane affects osmotic, chemical, and electrical driving forces for every other transporter in the same membrane.
In this paper we report on our efforts along three lines: 1) By bioinformatics means we have discovered homologues of chemo-sensitive postsynaptic ion channels in prokaryotes, including in Synechococcus, which is the organism whose GTL project we are associated with. This discovery may point to a previously unknown molecular mechanism for electrochemical signaling between prokaryotes, and may also facilitate determination of structures for the ligand-gated channel family of gene proteins. 2) We have developed improved methods for assigning protonation states of electrically interacting titratable residues in the lumen of bacterial porins. This is critical in order to make realistic models for ion permeation through these channels. 3) We are adapting phylogenetic profiling methods to infer transport and regulatory networks that govern ion and water homeostasis in prokaryotes.
Supported by grant # 0235792 from the National Science Foundation, the U.S. Department of Energy’s Genomics:GTL program (genomicsgtl.energy.gov) under project, “Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,” (www.genomes-to-life.org), and the intramural program of the National Center for Biotechnology Information.
* Presenting author
