A team led by biophysicist Jeremy Smith of UT and Oak Ridge National Laboratory (ORNL) has taken a step toward discovering how proteins fold into unique, three-dimensional shapes.
The team used ORNL's Cray XT4 Jaguar supercomputer as well as computer systems in Italy and Germany to determine that the folding of proteins is affected by how they interact with water.
When we do eventually find out how to calculate protein structure from sequence, then a major revolution will come upon us.Jeremy Smith, UT-ORNL Governor's Chair A protein is a string of amino acids whose shape is determined by the sequence of these amino acids. Proteins carry out a variety of tasks, such as fighting infections, turning food into energy, copying DNA and catalyzing chemical reactions. The shape the protein takes influences what its function will be.
"Understanding the mechanism by which proteins fold up into unique three-dimensional architectures is a holy grail in molecular biology," explained Smith, who holds the first UT-ORNL Governor's Chair and is a member of the Biochemistry and Molecular Biology Department at UT.
The team worked with a smaller chain of amino acids called a peptide. They concluded that hydrophobic areas of the peptide, or areas that shun water, ultimately determined the shape and the behavior of the peptide when these areas were exposed to water.
For longer simulations on larger peptides, the team will need increasingly powerful supercomputers.
"The runs were a couple of microseconds, which was adequate for the peptide that was simulated," Smith explained. "But the team is looking forward to increased computing capacity as it moves forward."
Smith said further findings they make will have a great impact on the field.
"When we do eventually find out how to calculate protein structure from sequence," he said, "then a major revolution will come upon us, as we will have the basis to move forward with understanding much of biology and medicine, and the applications will range from rationally designing drugs to fit clefts in protein structures to engineering protein shapes for useful functions in nanotechnology and bioenergy."
The team's results are being published in this week's edition of the Proceedings of the National Academy of Sciences.