Study examines how N protein binds to viral RNA, manipulates host-cell machinery to enhance infection
While the infamous SARS-CoV-2 spike protein grabs headlines and makes for dramatic TV graphics, another SARS protein has gone largely unnoticed.
It’s called the nucleocapsid protein, or N protein, and exactly how it binds to the viral RNA genome – and then wreaks havoc inside healthy human cells – is of intense interest to Elan Eisenmesser, PhD, associate professor of Biochemistry and Molecular Genetics in the University of Colorado School of Medicine.
Eisenmesser and colleagues in the Biochemistry and Molecular Genetics and Immunology and Microbiology departments were among the first on campus to return to their labs after last spring’s initial COVID-19 shutdown.
Thomas “Tem” Morrison, PhD, associate professor in the Department of Immunology & Microbiology, and other CU Anschutz researchers immediately began working to build a “homegrown” COVID-19 antibody test. The serology group needed the coronavirus nucleocapsid protein for its work, so Morrison turned to Eisenmesser, who couldn’t wait to start making N proteins.
RNA binding proteins
“My interest is everything nucleocapsid – how does it work? I ask that question because all of these RNA binding proteins are pretty sloppy – they’ll bind to anything … they are promiscuous,” Eisenmesser said.
On his current study, Eisenmesser’s collaborators include his partner and research associate, Jasmina Redzic, PhD, and fellow Biochemistry department faculty Kirk Hansen, PhD, Angelo D’Alessandro, PhD, and Beat Vogeli, PhD.
‘You had a cohort here at the University of Colorado School
of Medicine that really banded together to tackle
COVID-19. It’s been really fun.’
– Elan Eisenmesser
The study’s two main goals are somewhat akin to a UPS distribution center. One focus is on packaging: How does the N protein specifically bind to viral RNA – both structurally and dynamically – as it guards its genetic material? The dynamism is of particular interest. He’s found parts of the N protein “keep moving, and this is a general trait of proteins until they do something else, such as enzyme active sites that undergo movements that allow for catalysis.”
Then there is the unpacking process: What happens when the N protein gets inside a cell and begins to interact with the host? “The 30,000-foot view is once this virus gets into your cell, and different kinds of cells (eyes, lungs, liver, etc.), how does it manipulate your whole cell’s machinery for itself – for its infection?”
Using nuclear magnetic resonance
Eisenmesser uses nuclear magnetic resonance (NMR) instruments to answer both questions. Because the nucleocapsids are “pretty big proteins,” they can be chopped into pieces and looked at – using NMR – individually. It allows researchers to minutely examine different regions of the N protein and how they’re binding, or not binding, to RNA and host proteins.
When Eisenmesser began studying SARS-CoV-2’s cousin, SARS-CoV-1, about 15 years ago, he looked at how its N protein manipulates host cells to prevent their ability to mount an immune response. “The bottom line is this was my first interest: Understanding how pathogens in general kill you.”
Researchers know the N protein binds to many different proteins, but they don’t know how. “A lot of times we don’t know why either,” he said. “In most cases, it seems that it’s trying to down-regulate your innate immune response.”
Research may lead to therapeutics, treatments
His findings may lead to a menu of targeted therapeutics and treatments. One of those might specifically target the N protein. Others may go after the various SARS strains. Each N protein is made up of about 400 amino acid residues, which form several structural elements like “beads on a string.”
“The N protein has a higher sequence similarity within different coronaviruses than the spike protein,” Eisenmesser said. “Meaning, if you made a vaccine based on this nucleocapsid protein, you’re likely to block more coronaviruses (SARS-CoV-2, SARS-CoV-1, MERS, etc.), much less the different strains of each. There are seven strains of COVID-19 now circulating. There’s a higher likelihood that the (N) protein is more similar between those strains than the S protein, although it is also more highly expressed.”
And that, he said, could lead to something else.
“Maybe we can develop a drug to block coronaviral infection after the fact, or at least slow the viral manipulation of the host,” he said.
Despite the stress of the lockdowns, Eisenmesser and his colleagues keep working on solutions to the virus.
“I’m a biochemist. I can do a lot during a pandemic,” he said. “You had a cohort here at the University of Colorado School of Medicine that really banded together to tackle COVID-19. It’s been really fun.”
Photo at top: Elan Eisenmesser and his partner, Jasmina Redzic, in the Eisenmesser Lab at CU Anschutz.