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NCSA users publish on nuclear pore selectivity
The first atomic-level investigation into the mechanism of nuclear pore selectivity was reported in the December 2005 issue of Structure. Tim Isgro and Klaus Schulten, both from the University of Illinois at Urbana-Champaign's Theoretical and Computational Biophysics Group, authored the paper based on simulations completed at NCSA.
For large molecules, passage through a eukaryotic cell's nuclear pores is highly selective and controlled. The control involves import and export proteins (transport receptors) that load and release cargo on the proper side of the nucleus upon interaction with signaling proteins. The group's study inspected the interaction between the transport receptor importin-beta and key nuclear pore proteins. The simulations showed that the key sequences of the proteins interact strongly with certain spots on the surface of importin-beta. They confirmed spots that had previously been identified experimentally and found numerous binding spots not yet seen in experiment. One of the predicted binding spots has been confirmed recently. Further experiments and simulations promise an understanding of the selectivity of entry and exit from the nucleus, a key element of the cell's genetic control, according to Schulten and Isgro. The bulk of the simulations was performed on NCSA computers over the course of six months, using TCBG's molecular dynamics program NAMD2.5. Other simulations were run at NCSA's sister sites in Pittsburgh and San Diego. "For a computational scientist, the ideal situation is to work with a powerful computing platform that provides output quickly and with minimal disturbance. In this way, the underlying science is the focus of effort. NCSA provided exactly that," says Isgro. For more information, see: "Binding Dynamics of Isolated Nucleoporin Repeat Regions to Importin-beta." Structure, Vol. 13, 1869–1879, December 2005. This work is supported by the National Institutes of Health.
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