Fortifying a New Nobel

By J. William Bell

Early this month, the University of Illinois celebrated two 2003 Nobel Prize wins. Faculty members were awarded prizes in medicine and physics. NCSA, meanwhile, reveled in a third Nobel connection.

Roderick MacKinnon, of New York's Rockefeller University, won the chemistry prize for his work with ion channels, which regulate the travel of charged particles through cell membranes and allow the transmission of nervous-system commands and cell signals. His X-ray crystallographic images of potassium ion channels surprised colleagues with their detail in 1998 and 2001. Many considered them next to impossible to capture—until MacKinnon's team did it.

As MacKinnon's team released its results, longtime NCSA users Benoit Roux and Simon Berneche showed the world incredibly precise computational models of the same structures in action. Their molecular dynamics simulations included a potassium ion channel, cell membrane molecules, and potassium ions. Crystallographic images like those captured by MacKinnon are snapshots, static renderings of biology in motion. Though MacKinnon's team caught the ion traversing the channel at several stages, the computational simulations by Roux and Berneche helped confirm that the activity was what it seemed.

Both teams published their work in a November 2001 issue of Nature. Roux and Berneche, along with their team at Cornell University's Weill Medical College, completed these studies on NCSA's SGI Origin2000. Today, their efforts continue on the Alliance's IBM p690 at Boston University, and the team plans to use NCSA's 17.7-teraflop Tungsten cluster once it enters production in the coming months.

The simulations "fortify" the Nobel-winning experimental work, according to Christopher Miller, a biochemistry professor at Brandeis University who oversaw MacKinnon's postdoctoral work in the late 1980s. "Together the results provide a deep understanding of how ions diffuse through this pore so rapidly," he said in an essay that accompanied the Nature articles. Roux and Berneche's "successful prediction [is] a rarity in computational biochemistry."

But such predictions become more commonplace everyday. "This is an exemplar of the powerful connections between measurement and computational simulation," says Dan Reed, NCSA's director. "The intellectual leverage from combining these two methods is vast, it applies to many disciplines, and it serves as further proof that computational simulation has emerged as a peer to experiment and theory."

Access first covered Roux, Berneche, and MacKinnon in 2002. See the story "Rush Hour" for details on their work.

Access Online | Posted 10-23-2003