By Matthew Dublin
Researchers at Oak Ridge National Laboratory and North Carolina State University used ORNL's 2.33 petaflop Jaguar supercomputer to study how copper induces misfolding in the protein alpha-synuclein, which is associated with Parkinson's disease. This misfolding leads to the creation of fibrillar plaques that characterize the disease.
"We knew that the copper was interacting with a certain section of the protein, but we didn't have a model for what was happening on the atomic level," says Frisco Rose, a North Carolina State University graduate student in physics. "Think of a huge swing set, with kids all swinging and holding hands — that's the protein. Copper is a kid who wants a swing. There are a number of ways that copper could grab a swing, or bind to the protein, and each of those ways would affect all of the other kids on the swing set differently. We wanted to find the specific binding process that leads to misfolding."
Rose and NC State colleagues Miroslav Hodak, research assistant professor of physics, and Jerzy Bernholc, director of the NCSU Center for High Performance Simulation, developed a series of computer simulations designed to identify the most likely protein binding scenario. The number of calculations was so large that standard deskside computers would not suffice, so the team reworked the code to run on ORNL's Jaguar.
The results of their research appeared in the June 14th edition of Scientific Reports.