OAK RIDGE, Tenn., Dec. 17, 2013 If scientists can control cellular functions such as movement and development, they can cripple cells and pathogens that are causing disease in the body.
Supported by National Institutes of Health grants, researchers at Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and the UTORNL Joint Institute for Computational Sciences (JICS) discovered a molecular "switch" in a receptor that controls cell behavior using detailed molecular dynamics simulations on a computer called Anton built by D. E. Shaw Research in New York City. To study an even larger signaling complex surrounding the switch, the team is expanding these simulations on the 27-petaflop, CPUGPU machine Titanthe nation's most powerful supercomputer, managed by the Oak Ridge Leadership Computing Facility at ORNL.
Researchers identified the molecular switch on Anton (which was designed to perform speedy molecular dynamics simulations) by simulating 140,000 atoms that make up the signaling part of the Tsr chemoreceptor that controls motility in E. coli. Like other receptors, Tsr spans the cell membrane, communicating to proteins inside the cell in order to respond to threats or opportunities in the environment.
The results, published in Nature Communications, stand apart from previous research because of the computational power applied to the problem.
"This work exemplifies the growing importance of numerical experiments in biology," said Jerome Baudry, assistant professor in the UT Biochemistry and Cellular and Molecular Biology Department and the UTORNL Center for Molecular Biophysics.
The team led by Baudry and Igor Zhulin, distinguished research and development staff member in the ORNL Computer Science and Mathematics Division, joint professor in the UT Department of Microbiology, and JICS joint faculty member determined that a single pair of phenylalanine amino acids called Phe396 locate
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DOE/Oak Ridge National Laboratory