Using 3-D weapons of science to fight infectious diseases

After a decade of work, the Center for Structural Genomics of Infectious Diseases (CSGID) -- a consortium of 10 scientific institutions in the U.S., Europe, and Canada -- announced that it has determined the 3-D atomic structures of more than 1,000 proteins.

Determining these structures is an important step in identifying and understanding where a pathogen might be vulnerable to assault by drugs or vaccines. Such vulnerabilities are frequently found at the points where molecules bind to one another, said Dr. Zbyszek Otwinowski, Professor of Biophysics and Biochemistry, who leads the UT Southwestern group participating in the project. Dr. Dominika Borek, Assistant Professor of Biophysics and Biochemistry, who works in Dr. Otwinowski's laboratory, contributed crucial expertise for the successful completion of these studies.

To make a 3-D structure, a protein must be cloned, expressed, and crystallized, and then X-ray diffraction data are collected at the Advanced Photon Source at Argonne National Laboratory. These data define the location of each of the hundreds or even thousands of atoms to generate 3-D models of the structures that can be analyzed with graphics software. Each institution in the Center has an area of expertise it contributes to the project, working in parallel on many requests at once.

The UT Southwestern team manages the salvage pathway, meaning scientists design custom methods for determining structures of molecules that resist standard approaches and for which the high potential for drug or vaccine development justifies applying advanced efforts.

Structures solved with help from the UT Southwestern team include proteins involved in the replication of the Ebola virus -- a pathogen notorious for its ability to evade the body's immune system. Their X-ray crystallography work formed the basis for preclinical studies currently underway in university and industry laboratories.

"When other scientists run into trouble determining crystal structures, Drs. Otwinowski and Borek are among the top people in the world who can develop these advanced approaches because they understand the theory so deeply and they have created such powerful methods to deal with difficult problems," said Dr. Michael Rosen, Chair of Biophysics at UT Southwestern and a Howard Hughes Medical Institute Investigator. Dr. Rosen has secondary appointments as a Professor of Biochemistry and in the Cecil H. and Ida Green Comprehensive Center for Molecular, Computational, and Systems Biology. Dr. Rosen also holds the Mar Nell and F. Andrew Bell Distinguished Chair in Biochemistry.

UT Southwestern's contribution to the Ebola project began when a scientist at the Washington University School of Medicine requested the consortium's help in structural studies of the Ebola protein VP35. UTSW researchers conducted detailed structural studies of a VP35 protein fragment that interacts with the Ebola nuclear protein (NP) to form a complex that protects Ebola's genetic material from digestion by the host's enzymes.

The structure revealing the interactions between the VP35 fragment and the NP protein provided the first glimpse into the protein complex's role in viral replication. That work, part of a multicenter study to better understand the complex's function, was reported as a Cell Reports cover story in 2015.

This 3-D structure is among the 1,000 now deposited by the consortium into the World-Wide Protein Data Bank, an archive supported by the National Institutes of Health that is freely available to the scientific community. The CSGID's breakthrough research is funded by two five-year contracts from the National Institute of Allergy and Infectious Diseases, with a total budget of $57.7 million.

The CSGID, based at the Northwestern University Feinberg School of Medicine, includes UT Southwestern and the University of Chicago, University of Virginia, University of Calgary, University of Toronto, Washington University School of Medicine, J. Craig Venter Institute, Sanford Burnham Prebys Medical Discovery Institute, and University College London.