Automated science speeds solution of Human Genome data

Aug 6 2004

Scientists in Argonne's Biosciences Division are automating and accelerating the complex processes that coax a protein to reveal its structure so they can learn the role Nature assigned it.

Argonne is a leader in the world-wide scientific race to convert data from the Human Genome Project into three-dimensional images that reveal how proteins function. Because proteins control everything from breathing to digestion and sweating, this information can help prevent or cure diseases in humans. Understanding other proteins may help solve environmental problems.

The Biosciences Division plays many roles in piecing together the meaning of the Human Genome data.

The division designed and operates the Structural Biology Center (SBC) at the Advanced Photon Source, the Western Hemisphere's most brilliant source of research X-rays. The SBC beamline is the world's most productive and efficient for solving protein structures because it delivers the greatest detail to scientists.

For example, Argonne biophysicist and crystallographer Youngchang Kim revealed a knot in an archaebacterium – the first ever observed in this most ancient type of single cell organism and only the second knot ever seen in a protein. Protein folding theory previously held that a knot was not possible in a structure. Argonne 's brilliant X-rays proved otherwise.

Argonne biologists managing the Midwest Center for Structural Genomics (MCSG) determined and deposited in the Protein Data Bank 157 structures – as of Aug. 1, 2004 – in less than four years of operation.

“When you consider it took seven years to determine the first 25 structures, you see how amazing the new processes are,” said Structural Biology Center Director Andrzej Joachimiak. Joachimiak also leads the Midwest Center fro Structural Genomics.

That number – 157 and growing fast -- is more than any of the other nine structural genomic pilot centers funded by the National Institute of General Medical Science's pilot centers. This National Institutes of Health organization leads the country's effort to determine the structures and functions of the human genome.

The MCSG is composed of researchers from Argonne, Northwestern University , Washington University School of Medicine, University College of London, University of Toronto , University of Virginia and the University of Texas Southwestern Medical Center at Dallas.

Argonne biologists and their colleagues use automation to dramatically reduce the time and cost of cloning, expressing, purifying and determining a protein's structure.

In the process, they are changing protein crystallography from a one-lab, one-structure process into a highly automated production line.

Since beginning research in 2000, MCSG biologists have used robotics and computers to slash the cost of determining a structure from $300,000 to $100,000 – they are planning to reduce it further – and the time from years and months to days and hours.

Protein crystallography poses difficult challenges because proteins are unstable, soft molecules and require perfect conditions – temperature, pH, salts and various additives – to crystallize. Hundreds of crystals are created with the help of a robot in the hope of finding one, perfect crystal that will reveal its structure. Converting a protein into a crystal and then using X-rays to reveal its structure requires at least 10 carefully controlled steps.

The Biosciences Division's old wet labs have been converted to new labs with strict temperature and humidity controls that house robots – many of which Argonne has designed with manufacturers.

Now Argonne researchers are cloning more than 1,000 genes a year – up from 100 four years ago -- a 1,000 percent improvement.

Biologists developed a robotic purification system with the manufacturer, Amersham Biosciences, and other labs are now buying the system worldwide.

Researchers have even automated the process of loading the crystal into the beamline for the X-ray study.

MCSG colleagues at the University of Virginia and the University of Texas ' Southwestern Medical Center developed software to speed data manipulation. The software automates the many computer steps that convert the X-ray diffraction image of the protein crystal to reveal its three-dimensional structure. This program has cut the solution time from 8 hours to 2.5.

Center researchers based at the University of London and Argonne's Mathematics and Computer Science Division are taking bioinformatics – the combination of biology and computation -- to the next level by creating structural bioinformatics. The London researchers are developing computer analysis programs to identify potential targets for comparative analysis. Researchers can save valuable research time – and bypass X-ray crystallography -- by predicting unknown protein functions from structures already solved. London researchers are supplying templates of the active site of solved proteins for comparison that will be available to other researchers by the end of the summer.

The Biosciences Division's work for NIH has not gone unnoticed: The U.S. Department of Energy is funding additional bioscience automation research, and Argonne 's Biosciences Division is planning to build the Advanced Protein Crystallization Facility to serve as a regional, state-of-the-art resource for academic and industrial biotechnology and biomedical researchers. The facility is planned to have dedicated beamlines at the APS.

This facility may enhance Argonne 's opportunity to become home to a $200 million Protein Production and Characterization Facility recently announced as one of DOE's highest priority biotechnology projects.

“Argonne is the world's most productive center for protein crystallizations and structure determination,” said Biosciences Division Director Lee Makowski . “We would love to build the Protein Production and Characterization Facility here, because we developed and continue to improve the automation process that is accelerating protein structure determination.”

And the Advanced Photon Source is an incredible draw. While the Structural Biology Center based at the APS is the world's best in speed, resolution and quality, the APS also have 12 macromolecular beamlines and several more are planned.

“With other facilities being planned at Argonne, such as the Center for Nanoscale Materials and the University of Chicago's Howard T. Ricketts Regional Biocontainment Laboratory to study the molecular mechanisms of infectious disease,” Makowski said, “we will also have a strong microbiology facility, and we will be able to make significant contributions to a wide range of biological and medical problems, including new drug design ”