Scientists Catch Shape-Shifting Coronavirus Protein Complex in the Act

Coronavirus Papain-Like Protease

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ORNL scientists discovered the papain-like protease (in orange) can bind to the human interferon-stimulated gene 15 protein (in blue) in numerous methods and shapes. Credit: ORNL/Jill Hemman

While all infections have some methods of combating the body’s body immune system, researchers have actually been studying how the SARS-CoV-2 coronavirus—the reason for the COVID-19 worldwide pandemic—can avert the body immune system in people.

Now researchers operating at the United States Department of Energy’s (DOE’s) Oak Ridge National Laboratory (ORNL) have actually exposed the molecular information of how an essential protein (the papain-like protease, or “PLpro”) from the infection link to form a paired-structure, or “complex,” with a human protein called interferon-stimulated gene 15 (ISG15). PLpro strips ISG15 from other human cellular proteins to assist SARS-CoV-2 in averting the immune action. Understanding how the 2 proteins engage might assist in establishing healing drug treatments that avoid its development and permit an individual’s body immune system to much better combat the attacking infection.

The research study results, entitled “Conformational Dynamics in the Interaction of SARS-CoV-2 Papain Like Protease with Human Interferon-Stimulated Gene 15 Protein,” were released in the Journal of Physical Chemistry Letters.

“In human cells that the virus has infected, the PLpro from the SARS-CoV-2 virus tends to seek out and bind with the ISG15 protein, a key component of the cells’ immune response,” stated Hugh O’Neill, leader of ORNL’s Bio-Facilities group and director of the laboratory’s Center for Structural Molecular Biology. “When PLpro binds to ISG15, it causes the ISG15 to change shape. The key finding is that the ISG15 can assume multiple shapes when it binds to PLpro.”

Using small-angle neutron scattering (SANS) at ORNL’s High Flux Isotope Reactor (HFIR), the scientists had the ability to study the modifications in the complex while they happened.

“We enhanced the contrast between the PLpro and ISG15 by preparing PLpro in which many of the hydrogen atoms were replaced with deuterium atoms,” stated Kevin Weiss, a specialist in bio-deuteration. “Neutrons engage in a different way with deuterium atoms, so this assisted us much better distinguish in between the 2 proteins.

“We used neutrons to analyze the complex in solution, which better simulates the actual physiological environment of the human body,” stated Leighton Coates, instrument systems science and innovation supervisor for ORNL’s Second Target Station. “This allowed us to study the changing shapes of the complex, which other techniques could not have picked up.”

“The information we obtained from our experiments increases our knowledge of how the virus works and will enable us to build more accurate computer models for other scientists to use,” stated Wellington Leite, lead author and ORNL postdoctoral scientist. “Researchers will be able to use the model to quickly search for sites on the ISG15 where the PLpro attaches and then try to block those sites.”

Susan Tsutakawa, a biochemist personnel researcher at Lawrence Berkeley National Laboratory (Berkeley Lab), gotten small-angle x-ray scattering (SAXS) information on the PLpro-ISG15 complex at the Berkeley Lab’s Advanced Light Source Synchrotron. “In the SAXS studies, we could separate out different complexes in the sample by coupling SAXS with size exclusion chromatography and at the same time, get higher resolution data of the complex’s overall configuration, to complement the SANS studies that revealed the conformations of individual components in the complex,” stated Tsutakawa.

The group prepares to carry out extra experiments on this kind of biological complex to take a look at how little particles can obstruct the binding of PLpro to ISG15.

Reference: “Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein” by Wellington C. Leite, Kevin L. Weiss, Gwyndalyn Phillips, Qiu Zhang, Shuo Qian, Susan E. Tsutakawa, Leighton Coates and Hugh O’Neill, 10 June 2021, Journal of Physical Chemistry Letters.
DOI: 10.1021/acs.jpclett.1c00831

This research study was supported by the DOE National Virtual Biotechnology Laboratory, a consortium of DOE nationwide labs with financing offered by the Coronavirus CARES Act. Additional assistance was offered by the DOE Office of Science, the Molecular Biophysics and Integrated Bioimaging Division at Berkeley Lab, and the Center for Structural Molecular Biology at ORNL.

HFIR is a DOE Office of Science user center. UT-Battelle LLC handles ORNL for the DOE Office of Science. The Office of Science is the single biggest advocate of standard research study in the physical sciences in the United States and is working to deal with a few of the most important difficulties of our time.

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