The National Institute of Health awarded UW-Madison a four-year, $17.5 million grant to aid in research of the three dimensional structure of proteins. Further understanding of protein structure will help interpret the genetic code unlocked by the Human Genome Project.

The UW team, led by biochemistry professor John Markley, is one of nine pilot programs across the United States trying to develop a faster and more cost effective way to determine protein structure.

Today, scientists use complicated technological mechanisms like X-ray crystallography and NMR spectroscopy. These intricate procedures first determine atom location and then analyze that information to understand protein structure.

Unfortunately, many scientists say, these techniques are too slow. Scientists now want to speed up the process by using robots to take care of the more repetitive steps and by creating new computer programs to analyze the data.

Currently, it takes one month to a year to solve a single protein structure at an average cost of $100,000. With the new grant, scientists hope to shorten the time and cut the cost to about $20,000 per protein.

“What we’re trying to do is increase the flow,” Markley said. “We have the goal of being able to solve in excess of one hundred structures per year at the end of the four-year period.”

This project is much like the Human Genome Project, which sequenced and cataloged the human genome in a short period of time. But without a better understanding of the structure and function of proteins, the genetic code is not very useful to scientists.

“Basically, [protein] function is very intimately related to their shape and structure,” said Craig Newman, program administrator for the Center for Eukariotic Structural Genomics. “If we can figure out what their shape is, we can have a better idea of what they do and how they do it.”

Scientists at UW will focus their efforts on Arabidopsis thaliana, the first plant to have its entire genome sequenced. Since many basic proteins are shared by most organisms, answering questions about this plant’s protein structure will enable scientists to design better drugs and herbicides. They will also have a better understanding of genetic diseases in humans.

“There are certainly genes in the Arabidopsis genome that are found in the human genome,” Newman said. “They are known to be important in diseases, especially when they’re defective.”

Newman said it is a great honor for UW to be chosen for this project. The university has a strong group of scientists that study Arabidopsis, he said, which provides the support needed for this type of endeavor.

UW already has a strong reputation for determining the three-dimensional structure of proteins through the use of X-ray crystallography and NMR spectroscopy.

At the end of the four-year period, NIH will evaluate the nine centers and determine which are the most successful. The most productive centers will be funded further to begin focusing attention on producing and understanding all protein structures and functions, hopefully getting scientists one step closer to understanding and treating genetic diseases.