Oak Ridge National Laboratory

X-rays size up protein structure at the ‘heart’ of COVID-19 virus

25-Jun-2020 2:40 PM EDT, by Oak Ridge National Laboratory

Newswise — A team of researchers at the Department of Energy’s Oak Ridge and Argonne national laboratories has performed the first room-temperature X-ray measurements on the SARS-CoV-2 main protease — the enzyme that enables the virus to reproduce.

The X-ray measurements mark an important first step in the researchers’ ultimate goal of building a comprehensive 3D model of the enzymatic protein. The model will be used to advance supercomputing simulations aimed at finding drug inhibitors to block the virus’s replication mechanism and help end the COVID-19 pandemic. Their research results are publicly available and have been published in the journal Nature Communications.

SARS-CoV-2 is the virus that causes the disease COVID-19. The virus reproduces by expressing long chains of proteins that must be cut into smaller lengths by the protease enzyme.

“The protease is indispensable for the virus life-cycle. The protein is shaped like a valentine’s heart, but it really is the heart of the virus that allows it to replicate and spread. If you inhibit the protease and stop the heart, the virus cannot produce the proteins that are essential for its replication. That’s why the protease is considered such an important drug target,” said ORNL’s Andrey Kovalevsky, corresponding author. While the structure is known from cryogenically preserved crystals, “This is the first time the structure of this enzyme has been measured at room temperature, which is significant because it’s near the physiological temperature where the cells operate.”

Building a complete model of the protein structure requires identifying each element within the structure and how they are arranged. X-rays are ideal for detecting heavy elements such as carbon, nitrogen and oxygen atoms. Because of the intensity of the X-ray beams at most large-scale synchrotron facilities, biological samples typically must be cryogenically frozen to around 100 K, or approximately minus 280 degrees Fahrenheit, to withstand the radiation long enough for data to be collected.   

To extend the lifetime of the crystallized protein samples and measure them at room temperature, ORNL researchers grew crystals larger than required for synchrotron cryo-studies and used an in-house X-ray machine that features a less intense beam.

“Growing protein crystals and collecting data is a tedious and time-consuming process. In the time it typically takes to prepare and ship the sample to a synchrotron, we were able to grow the crystals, take the measurements and begin analyzing the data,” said ORNL’s Daniel Kneller, the study's first author. “And, when there’s a pandemic with many scientists mobilizing to study this problem, there’s not a day to spare.”

The protease enzyme consists of chains of amino acids with a repeating pattern of nitrogen-carbon-carbon atoms that form the backbone of the protein. Side groups of the amino acid building blocks, or “residues”, extend from each of the central backbone carbon atoms. The enzyme is folded into a specific 3D shape, creating special pockets where a drug molecule would attach.

The study revealed significant structural disparities between the orientations of the backbone and some of the residues in the room-temperature and cryogenic samples. The research suggests that freezing the crystals may introduce structural artifacts that could result in a less accurate understanding of the protease structure.

The team’s results are being shared with researchers, led by ORNL-University of Tennessee Governor’s Chair Jeremy Smith, who are conducting drug docking simulations using Summit at ORNL — the nation’s fastest supercomputer.

“What researchers are doing on Summit is taking known drug compounds and trying to computationally bind them to the main protease for drug repurposing, as well as looking for new leads into other potential drug candidates,” said ORNL corresponding author Leighton Coates. “Our room temperature data is being used to build a more accurate model for those simulations and improve drug design activities.”

The researchers’ next step in completing the 3D model of the SARS-CoV-2 main protease is to use neutron scattering at ORNL’s High Flux Isotope Reactor and the Spallation Neutron Source. Neutrons are essential in locating the hydrogen atoms, which play a critical role in many of the catalytic functions and drug design efforts.

The protease plasmid DNA used to make the enzyme was provided by Argonne’s Structural Biology Center at the Advanced Photon Source. Crystallization of the proteins used in the X-ray scattering experiments was performed at ORNL’s Center for Structural and Molecular Biology.

In addition to Kovalevsky, Kneller, and Coates, the paper’s authors are ORNL’s Gwyndalyn Phillips, Hugh M. O'Neill and Paul Langan; and Argonne’s Robert Jedrzejczak, Lucy Stols and Andrzej Joachimiak.

The work was funded by ORNL’s Laboratory Directed Research and Development program, the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, and the National Science Foundation, with facilities support from DOE’s Office of Science.

UT-Battelle LLC manages ORNL for the DOE Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, please visit http://science.energy.gov/.




Filters close

Showing results

110 of 2927
Released: 14-Aug-2020 4:55 PM EDT
Managing your child’s diabetes during COVID-19
University of Texas Health Science Center at Houston

These days it’s hard not to worry about whether a quick outing to the grocery store will result in catching COVID-19. But for parents with children who have preexisting health conditions such as diabetes, it can be especially hard not to worry about whether their child is at a higher risk of becoming severely ill from the virus.

Newswise: 1200x800?cb=1597350935
Released: 14-Aug-2020 3:35 PM EDT
Gaiters do no harm: WVU toxicologists find coverings help contain the spread of exhaled droplets
West Virginia University

Experts with the West Virginia University Center for Inhalation Toxicology found that – assuming it’s a good fit - a gaiter will, despite recent reports, provide a respiratory containment of exhaled droplets comparable to a common over-the-ear cloth mask.

Newswise: AI software enables real-time 3D printing quality assessment
Released: 14-Aug-2020 3:05 PM EDT
AI software enables real-time 3D printing quality assessment
Oak Ridge National Laboratory

Oak Ridge National Laboratory researchers have developed artificial intelligence software for powder bed 3D printers that assesses the quality of parts in real time, without the need for expensive characterization equipment.

Newswise: Is the COVID-19 virus pathogenic because it depletes specific host microRNAs?
Released: 14-Aug-2020 3:05 PM EDT
Is the COVID-19 virus pathogenic because it depletes specific host microRNAs?
University of Alabama at Birmingham

Why is the COVID-19 virus deadly, compared to cold-causing coronaviruses? Analysis current literature and bioinformatic study of seven coronaviruses, suggests that SARS-CoV-2 acts as a microRNA “sponge,” leading to better viral replication and blockage of the host immune response.

Released: 14-Aug-2020 2:30 PM EDT
UW team developing model to help lower COVID-19 infections in Seattle, other major cities
University of Washington

A UW team has received a grant to develop a model that uses local data to generate policy recommendations that could help lower COVID-19 infections in King County, which includes Seattle.

Newswise: Cardiovascular risk factors tied to COVID-19 complications and death
12-Aug-2020 7:05 PM EDT
Cardiovascular risk factors tied to COVID-19 complications and death
PLOS

COVID-19 patients with cardiovascular comorbidities or risk factors are more likely to develop cardiovascular complications while hospitalized, and more likely to die from COVID-19 infection, according to a new study published August 14, 2020 in the open-access journal PLOS ONE by Jolanda Sabatino of Universita degli Studi Magna Graecia di Catanzaro, Italy, and colleagues.

Newswise: Study shows frequently used serology test may not detect antibodies that could confirm protection against reinfection of COVID-19
Released: 14-Aug-2020 1:55 PM EDT
Study shows frequently used serology test may not detect antibodies that could confirm protection against reinfection of COVID-19
University of Texas M. D. Anderson Cancer Center

Two different types of detectable antibody responses in SARS-CoV-2 (COVID-19) tell very different stories and may indicate ways to enhance public health efforts against the disease, according to researchers at The University of Texas MD Anderson Cancer Center. Antibodies to the SARS-CoV-2 spike protein receptor binding domain (S-RBD) are speculated to neutralize virus infection, while the SARS-CoV-2 nucleocapsid protein (N-protein) antibody may often only indicate exposure to the virus, not protections against reinfection.

Released: 14-Aug-2020 1:50 PM EDT
USC scientists identify the order of COVID-19's symptoms
University of Southern California (USC)

USC researchers have found the likely order in which COVID-19 symptoms first appear: fever, cough, muscle pain, and then nausea, and/or vomiting, and diarrhea.

Released: 14-Aug-2020 1:45 PM EDT
Stay the Course with Personal Finances during Pandemic, Johns Hopkins Expert Advises
Johns Hopkins University Carey Business School

Keeping on a careful and steady path is the wisest approach to personal money management during the uncertainties of the COVID-19 crisis, says Associate Professor Yuval Bar-Or of the Johns Hopkins Carey Business School.

access_time Embargo lifts in 2 days
Embargo will expire: 17-Aug-2020 11:00 AM EDT Released to reporters: 14-Aug-2020 1:25 PM EDT

A reporter's PressPass is required to access this story until the embargo expires on 17-Aug-2020 11:00 AM EDT The Newswise PressPass gives verified journalists access to embargoed stories. Please log in to complete a presspass application. If you have not yet registered, please Register. When you fill out the registration form, please identify yourself as a reporter in order to advance to the presspass application form.


Showing results

110 of 2927

close
1.99081