National Center for Design of
Biomimetic Nanoconductors

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Eric Jakobsson

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Eric Jakobsson is the Director of the National Center for Design of Biomimetic Nanoconductors and is Professor in the Department of Molecular and Integrative Physiology at the University of Illinois at Urbana-Champaign. He also has appointments at the National Center for Supercomputing Applications (NCSA) and the Beckman Institute for Advanced Science and Technology. His lab works on computational studies of membrane biophysics and organization, ion channel function, and ion channel evolution.

Research

Recent work that is of particular interest to the work of the Center include:

• The group discovered prokaryotic members of the ART-LGIC ligand binding channel family (Tasneem et al, 2005). Potentially this specific result and the methods we used may be important for mining prokaryotic genomes for technologically useful channels and transporters, especially since prokaryotic channel and transporter proteins are notably easier to produce in quantity than are eukaryotic versions. Also, some prokaryotic proteins function well under extreme conditions, such as heat, cold acidity, etc.
• They developed an improved protocol for calculating protonation states in cases where there are multiple electrostatically interacting amino acid side chains, utilizing porin as the specific case. (Varma and Jakobsson, 2004). In a sequel paper, under review at the Biophysical Journal, they showed that their newly assigned protonation states corrected previous problems with drift of molecular dynamics simulations away from the appropriate crystal structure.
• They demonstrated the phenomenon of high-temperature freezing of water by confinement in nanotubes of critical diameter (Mashl et al, 2003). If controlled, they believe confinement-induced phase change may be a useful switching mechanism in nanoscale conductors.

Current collaborations within the Center include work on membrane and channel simulations with Larry Scott, and computer-aided design of nanodevices with Narayan Aluru and Umberto Ravaioli. Also, work on automating multiscale calculations of KscA I-V and I-C curves from first principles will be enhanced in collaboration with the Klimeck/McLennan Network for Computational Nanotechnology team. Jakobsson is also responsible for overall coordination of the activities of the Center.

Related Publications

Tasneem, A., Iyer, L.M., Jakobsson, E., and Aravind, L. (2005), “Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels,” Genome Biology, 6/1.

Varma S. and Jakobsson E. (2004), “Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions Between Residue,” Biophysics Journal, 86/2, pp. 690-704.

Chiu S.W., Vasudevan S., Jakobsson E., Mashl R.J., and Scott H.L. (2003), “Structure of Sphingomyelin Bilayers: A Simulation Study,” Biophysics Journal 85/6, pp. 3624-3635.

Shealy, R.T., Murphy, A.D., Ramarathnam, R., Jakobsson, E., and Subramaniam, S. (2003), “Sequence-function Analysis of the K+-selective Family of Ion Channels Using a Comprehensive Alignment and the KcsA Channel Structure,” Biophysics Journal, 84/5, pp. 2929-2942.

Joseph, S., Mashl, R.J., Jakobsson, E., and Aluru, N.R. (2003), “Electrolytic Transport in Modified Carbon Nanotubes,” Nano Lettters (Communication), 3/10, pp. 1399-1403.

Mashl, R.J., Joseph, S., Aluru, N.R., and Jakobsson, E. (2003), “Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes,” Nano Letters (Communication), 3/5, pp. 589-592.

Related Links

Comprehensive List of Publications

Eric Jakobsson's Beckman Institute Profile

Eric Jakobsson's Molecular and Integrative Physiology Profile

The National Center for Design of Biomimetic Nanoconductors is funded by Grant Number PHS 2 PN2 EY016570B from the National Institutes of Health through the NIH Roadmap for Medical Research and is based at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Partner institutions include Yale University, University of Southern California, University of Chicago, Illinois Institute of Technology, Sandia National Laboratories, Argonne National Laboratory, Oxford University, Wabash College, University of California, Davis, nanoHUB at Purdue University, and the University of New Mexico.