Battling Infectious Diseases with 3-D Protein Structures

A representation of the structure of a protein from the bacterium Listeria monocytogenes, which causes foodborne illness, with an inhibitor molecule bound. (Image by Lizbeth Hedstrom (Brandeis University)/University of Chicago/Argonne National Laboratory.)

An international team of scientists led by Northwestern University Feinberg School of Medicine has determined the 3-D atomic structures of more than 1,000 proteins that are potential targets for drugs and vaccines to combat some of the world’s most dangerous emerging and re-emerging infectious diseases.

These experimentally determined structures have been deposited into the World-Wide Protein Data Bank, an international archive freely available to the scientific community. The 3-D structures help expedite drug and vaccine research and advance the understanding of pathogens and organisms causing infectious disease.

“Almost 50 percent of the structures that we have deposited in the Protein Data Bank are proteins that were requested by scientific investigators from around the world,” said Feinberg’s Wayne Anderson, who is director of the project. “The NIH has also requested us to work on proteins for potential drug targets or vaccine candidates for many diseases, such as the Ebola virus, the Zika virus and antibiotic-resistant bacteria. We have determined several key structures from these priority organisms and published the results in high-impact journals such as Nature and Cell.”

This milestone effort, funded by two five-year contracts from the National Institute of Allergy and Infectious Diseases (NIAID), totaling a budget of $57.7 million, represents a decade of work by the Center for Structural Genomics of Infectious Diseases (CSGID) at Feinberg. CSGID is led by Anderson in partnership with the University of Chicago, the University of Virginia School of Medicine, the University of Calgary, the University of Toronto, the Washington University School of Medicine in St. Louis, the UT Southwestern Medical Center, the J. Craig Venter Institute, the Sanford Burnham Prebys Medical Discovery Institute and University College London.

How the 3-D structures are made
Before work begins on a targeted protein, a board appointed by the NIH examines each request. Once approved, the protein must be cloned, expressed and crystallized, and then X-ray diffraction data is collected at the U.S. Department of Energy’s (DOE) Advanced Photon Source, a DOE Office of Science User Facility at Argonne National Laboratory. This data defines the location of each of the hundreds or even thousands of atoms to generate 3-D models of the proteins’ 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 University of Chicago team focuses on antibiotic resistance factors such as metallo β-lactamases, essential enzymes that are potential drug candidates, as well as transcription factors responsible for virulence from pathogenic bacteria.

Argonne Distinguished Scientist Andrzej Joachimiak, the co-principal investigator of CSGID, said the initiative was a highly collaborative effort. The team works closely with microbiologists and chemists from the biology community to identify chemicals that will inhibit protein activity; then they produce and crystallize proteins with those inhibitors bound to determine their structures using X-ray crystallography.

The University of Chicago team has recently characterized protein crystal structures with novel inhibitors from two important agents that cause human disease: Mycobacterium tuberculosis and Cryptosporidium parvium, responsible for tuberculosis and the parasitical infection cryptosporidiosis, respectively.

In their research, the team uses community resources in the Advanced Protein Characterization Facility and data collection facilities at the Advanced Photon Source.

Until recently, the process of determining the 3-D structure of a protein took many months or even years – but advances in technology, such as crystallization methods, the powerful X-rays from the Advanced Photon Source, upgrades to computational hardware and software, and automation of many of the steps have dramatically accelerated the process.

The Seattle Structural Genomics Center for Infectious Disease, a similar center funded by NIAID, is also on track to complete 1,000 3-D protein structures soon. Interested readers can browse all of the structures deposited by the CSGID; anyone in the scientific community interested in requesting the determination of structures of proteins from pathogens in the NIAID Category A-C priority lists, or organisms causing emerging and re-emerging infectious diseases, can submit requests to the Center’s web portal. As part of the services offered to the scientific community, the CSGID can also provide expression clones and purified proteins, free of charge.

This project has been supported by federal funds from the NIAID and NIH of the U.S. Department of Health and Human Services.

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