FLC | PNNL, SSGCID take on COVID-19 one protein at a time

PNNL, SSGCID take on COVID-19 one protein at a time

April 3, 2020

Scientists from the Pacific Northwest National Laboratory (PNNL) and the Seattle Structural Genomics Center for Infectious Disease (SSGCID) are working together to look for any signs of COVID-19 virus vulnerability that could be exploited for treatment or prevention.

The SSGCID is a consortium funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN272201700059C. In the 13 years since its creation, SSGCID has solved the structures of close to 1,300 proteins from more than 70 organisms that cause human death and disease. The group has brought discovery to bear on diseases like tuberculosis, plague, Ebola and the flu.

Now, PNNL and SSGCID collaborators are looking carefully at the coronavirus proteins, creating atomic-level pictures of the proteins' structures. Scientists get a lock on many proteins by using X-ray crystallography, which yields an extraordinary snapshot at the atomic level, but some proteins resist the process. That’s where PNNL scientist Garry Buchko comes in, tackling some of the toughest proteins using nuclear magnetic resonance (NMR) spectroscopy – a cousin to magnetic resonance imaging used widely in medicine.

Buchko does not work directly with the entire coronavirus, known as SARS-CoV-2. Rather, he and his Seattle colleagues use snippets of genetic code to study one protein at a time by growing the individual proteins in bacteria. The individual proteins are harmless.

From there, other scientists at SSGCID solve the bulk of the protein structures using X-ray crystallography, while Buchko turns his focus to the protein subset that resists crystallizing by using NMR. NMR has an added advantage: It allows scientists to watch a protein in action in a way other methods do not.

To do so, Buchko inserts a small glass tube containing the dissolved protein, itself just one ten-thousandth the width of a human hair, into a machine four times the weight of an Asian elephant. He does the protein prep work late at night, when laboratory staffing is minimal and social distancing is easy.

Then he heads home and remotely manipulates the experiments happening inside the NMR located in the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy Office of Science user facility at PNNL. The protein in the spectrometer is surrounded by a very strong magnetic field, thousands of times stronger than the typical MRI, and then pumped with additional radiofrequency energy to watch how individual atomic nuclei respond.

In this way, he can look in incredible detail at not just a single protein but at tiny segments – for instance, specific amino acids in precise locations. Indeed, scientists can monitor the environment of almost every carbon, nitrogen, and hydrogen atom in the protein.

Ultimately, after weeks of data collection, Buchko is left with thousands of pieces of data. He feeds that into a computer program to calculate the position of every single atom, resulting in a complete 3D reconstruction of the protein. That’s crucial information for scientists around the globe who are working on ways to stop the virus, supplying them with a how-to guide to identify viral vulnerabilities.

His findings, like those of his SSGCID counterparts, will be deposited in a bank – the Protein Data Bank, a public database of protein structures that the group shares with the scientific community so that scientists worldwide can exploit the team’s findings to make further discoveries.