Practically everything the human body does is the work of proteins. And since the function of a protein is intrinsically tied to its structure, structural changes can have dramatic effects on human health and disease.
Associate Professor of Biology Rebecca Page and Associate Professor of Medical Science Wolfgang Peti have successfully developed a new process to determine the detailed structure of proteins, looking specifically at a protein complex called p38alpha-HePTP. Their findings, published Nov. 6 in the online journal Nature Chemical Biology, could have significant applications in the development of new pharmaceuticals.
The team's research focused on p38, a member of the kinase family of enzymes. These proteins are part of the signaling pathway that initiates cellular response mechanisms, such as inflammation, cell death, growth and differentiation. When the kinase malfunctions, it can cause Alzheimer's disease, rheumatoid arthritis and cancer, Page said.
Their new method for determining protein structure integrates small-angle X-ray scattering and nuclear magnetic resonance spectroscopy, allowing a greater level of detail and representing "a new wavefront of biology," said Dorothy Koveal GS, co-author of the study.
A greater-resolution molecular structure tells pharmaceutical developers which region a new drug should target to prevent disease-related kinase functions. "This is an entirely novel pathway for drug development," Page said. It is relatively easy to find a drug that shuts off the kinase completely, but since kinases carry out a number of other essential cell functions, this is not an ideal course of action, she added.
Page and Peti aimed to figure out how the protein HePTP interacts with the kinase p38. They used nuclear magnetic resonance spectroscopy, which allows researchers to determine a protein's chemical composition, giving a hint of the complex's structure.
Looking at the differences in chemical composition of p38 compared to that of the p38alpha-HePTP complex, the team knew which chemical subunits of p38 were affected by HePTP binding. Therefore, they knew which regions of the kinase were directly involved in its interaction with HePTP.
Small-angle X-ray scattering then allowed researchers to determine the protein's three-dimensional shape.
The research team is now looking to use their innovative technique to examine the structures of similar protein complexes, Page said.
The research was "quite labor-intensive," said Dana Francis GS, lead author of the paper.
For the SAXS data collection, the team would sometimes work 12-hour nights, from 7 p.m. to 7 a.m., at the Brookhaven National Laboratory facility on Long Island. "We would be up all night collecting data … and kind of going a little crazy," Francis said.
The research also required very careful preparation of the samples, Page said. Several times, the team members would have to take shifts to carry out 72 hours of continuous preparation.