December 13, 2013

Titan Expands on Molecular Dynamics Discovery

Tiffany Trader

Thanks to the power of supercomputing, scientists at Oak Ridge National Laboratory (ORNL) and the University of Tennessee (UT)–ORNL Joint Institute for Computational Sciences (JICS) have discovered a molecular “switch” in a receptor that controls cell behavior. To allow for an even more detailed simulation and a better understanding of the primary molecular switch that controls cell behavior, scientists have commandeered Titan, the 27-petaflop supercomputer installed at Oak Ridge Leadership Computing Facility.

Details of the study were published today in the journal Nature Communications. Being able to manipulate cellular behavior holds the promise of better disease treatments, according to featured coverage on the OLCF website. Once cellular functions such as movement and development can be controlled, the next step is disarming the cells that are causing disease or engineering cells to attack specific pathogens.

The initial finding relied on the highly specialized, massively parallel Anton supercomputer, designed and built by D.E. Shaw Research to perform high-speed molecular dynamics simulations. In order to identify the molecular switch, team members initially simulated the 140,000 atoms that make up the signaling part of the Tsr chemoreceptor dimer, a complex consisting of two identical receptor molecules, which controls motility in E. coli. As with other receptors, Tsr spans the cell membrane and communicates to proteins inside the cell in response to threats or opportunities in the environment. Exactly how the receptors send these signals is one of molecular cell biology’s most intriguing unanswered questions.

“When we say proteins transmit signals, in most cases we don’t really know what this means in terms of their conformational changes,” said Igor Zhulin, distinguished R&D staff member in the ORNL Computer Sciences and Mathematics Division and joint faculty professor in the UT Department of Microbiology. “For decades, proteins have been viewed as static molecules, and almost everything we know about them comes from static images, such as those produced with X-ray crystallography. But signaling is a dynamic process, which is difficult to fully understand using only snapshots.”

Using the special-purpose Anton supercomputer, the team “determined that the seemingly erratic flipping conformations of a single pair of phenylalanine amino acids called Phe396 at the tip of the chemoreceptor were in fact acting as a receptor switch, impacting the shape of the entire chemoreceptor.”

“To our knowledge, this is the first time this switch has been described,” said lead author Davi Ortega.

The team had made a major breakthrough, but did not yet have a complete picture because the dimer does not act independently. Dimers are naturally grouped in threes. Simulating three interacting dimers at once – a dimer trimer – would require modeling about 400,000 atoms for longer time periods. This would only be possible with a massively-parallel petaflop supercomputer, so researchers turned to Titan, the most powerful supercomputer in the nation, backed by 18,000+ NVIDIA GPU accelerators. With Titan researchers can simulate this large molecular system long enough to pinpoint the amino acids responsible for protein signaling.

“Resources available on Titan are needed to simulate our system at the level of complexity that actually takes place in the cell,” notes one of the authors and team leaders, Jerome Baudry, assistant professor in the UT Department of Biochemistry and Cellular and Molecular Biology and the UT–ORNL Center for Molecular Biophysics. “In addition to its fundamental interest, this work exemplifies the growing importance of numerical experiments in biology.”

Proving the axiom that science never stands still nor rests on its laurels – as the team ramps up its simulations on Titan, it is simultaneously exploring what level of computing power will be required to simulate receptor complexes larger than a single trimer.