October 15, 2009
A research team led by Andrew Lee, PhD, has demonstrated that a protein’s function can be changed without modifying its structure, creating a new comprehension of how proteins bind to each other and to drugs.
“This is a fundamental change in the way we understand the simple act of binding, which is important not only for biology but for drug development.” says Lee, a professor in the School’s Division of Medicinal Chemistry and Natural Products. “This mechanism has never been seen before in single protein domains whose job it is to simply bind something. It is a nice, clear example of protein dynamics affecting protein function.”
Lee’s team studied the third PDZ domain of protein PSD-95, which is commonly found in neural synapses. PSD-95 is a scaffolding protein, attracting and joining other proteins so that those proteins can communicate with each other. The PDZ domain is the binding site where other proteins join with PSD-95.
“The fundamental function of PDZ domains is to serve as molecular Velcro,” Lee says. “PDZ domain structure and function is well understood at this point. In fact, this third PDZ domain on PSD95 is the archetypal PDZ domain. It was the first one that was solved structurally.”
A protein domain is a section of a protein that can exist separately from the rest of the protein. Many proteins consist of several domains. PDZ domains are found in signaling proteins of many different organisms and are named for the first three proteins that were discovered that shared the domain.
“What we found interesting about this particular PDZ domain is that it has a piece of structure that most PDZ domains don’t have,” Lee says of the third PDZ domain of PSD-95. “We wanted to know why, so we lopped it off and tested PSD-95 for function.”
Lee discovered that by removing the extra bit of structure, called an alpha helix, PSD-95’s affinity for binding to a certain peptide, or protein tail, of the protein CRIPT was reduced twenty-fold. The findings are published October 13, 2009, in the Proceedings of the National Academy of Sciences in an article titled “Hidden Dynamic Allostery in a PDZ Domain.”
“While the helix is in the PDZ domain, it is not part of the actual binding site, so the question is how is it affecting the binding site if the structure isn’t changing at all?” Lee says.
Using nuclear magnetic resonance spectroscopy, the researchers examined the domain in four different states: with and without the alpha helix and with and without the CRIPT peptides. Removing the alpha helix caused the structure of the protein to become more rigid without changing configuration, Lee says.
“To move from a flexible to a rigid state, the protein must pay a cost in energy,” he says. “This mechanism has never been seen before in single protein domains whose job it is to simply bind something.”
Lee says that this finding is significant because this nonstructural mechanism for manipulating binding function by “removing” the alpha helix may actually be used in neurons since the alpha helix may accept a phosphate group. Phosphorylation could essentially remove the helix and reduce binding function. Also, the discovery raises the possibility that other types of protein domains may be affected by this type of mechanism, he says.
Lee is the senior author of the paper. The other authors are Chad M Petit, PhD, and Paul J Sapienza, PhD, postdoctoral fellows in the UNC Eshelman School of Pharmacy; Jun Zhang, a graduate student in the UNC School of Medicine; and Ernesto J. Fuentes, PhD, assistant professor of biochemistry at the University of Iowa. The work was funded by a grant from the National Science Foundation.
Latest News
RASP poster presentations capture student research
Delesha Carpenter promoted to full professor
