How COVID-19 wreaks havoc on human lungs
DOE/Brookhaven National Laboratory
The model
showing how the two proteins interact, just published in the journal Nature
Communications, helps explain how the virus could cause extensive lung
damage and escape the lungs to infect other organs in especially vulnerable
COVID-19 patients. The findings may speed the search for drugs to block the
most severe effects of the disease.
"By obtaining atomic-level details of the protein interactions we can explain why the damage occurs, and search for inhibitors that can specifically block these interactions," said study lead author Qun Liu, a structural biologist at Brookhaven Lab.
"If
we can find inhibitors, then the virus won't cause nearly as much damage. That
may give people with compromised health a much better chance for their immune
systems to fight the virus successfully."
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| New structure shows how the COVID-19 virus envelope protein (E, magenta sticks) interacts with a human cell-junction protein (PALS1, surfaces colored in blue, green, and orange). Understanding this complex structure, which was solved using a cryo-electron microscope at Brookhaven National Laboratory, could lead to the discovery of drugs that block the interaction and, potentially, the most severe effects of COVID-19. View animation |
Scientists discovered the details and developed the molecular model using one of the new cryo-electron microscopes at Brookhaven Lab's Laboratory for BioMolecular Structure (LBMS), a new research facility built with funding from New York State adjacent to Brookhaven's National Synchrotron Light Source II (NSLS-II).
"LBMS opened last summer ahead
of schedule because of its importance in the battle against COVID-19,"
said Sean McSweeney, director of LBMS and a coauthor on the paper. "LBMS
and NSLS-II offer complementary protein-imaging techniques and both are playing
important roles in deciphering the details of proteins involved in COVID-19.
This is the first paper published based on results from the new facility."
Liguo Wang, scientific operations
director of LBMS and another coauthor on the paper, explained that
"cryo-electron microscopy (cryo-EM) is particularly useful for studying
membrane proteins and dynamic protein complexes, which can be difficult to
crystallize for protein crystallography, another common technique for studying
protein structures. With this technique we created a 3-D map from which we
could see how the individual protein components fit together."
"Without cryo-EM, we couldn't
have gotten a structure to capture the dynamic interactions between these
proteins," Liu said.
Triggering lung disruption
The SARS-CoV-2 envelope protein (E), which is found on the virus's outer membrane alongside the now-infamous coronavirus spike protein, helps to assemble new virus particles inside infected cells.
Studies published early in the COVID-19 pandemic showed that it
also plays a crucial role in hijacking human proteins to facilitate virus
release and transmission. Scientists hypothesize that it does this by binding
to human cell-junction proteins, pulling them away from their usual job of
keeping the junctions between lung cells tightly sealed.
"That interaction can be good
for the virus, and very bad for humans -- especially elderly COVID-19 patients
and those with pre-existing medical conditions," Liu said.
When lung cell junctions are
disrupted, immune cells come in to try to fix the damage, releasing small
proteins called cytokines. This immune response can make matters worse by
triggering massive inflammation, causing a so-called "cytokine storm"
and subsequent acute respiratory distress syndrome.
Also, because the damage weakens the
cell-cell connections, it might make it easier for the viruses to escape from
the lungs and travel through the bloodstream to infect other organs, including
the liver, kidneys, and blood vessels.
"In this scenario, most damage
would occur in patients with more viruses and more E proteins being
produced," Liu said. And this could become a vicious cycle: More viruses
making more E proteins and more cell-junction proteins being pulled out,
causing more damage, more transmission, and more viruses again. Plus, any
existing damage, such as lung-cell scarring, would likely make it harder for
COVID patients to recover from the damage.
"That's why we wanted to study
this interaction -- to understand the atomic-level details of how E interacts
with one of these human proteins to learn how to interrupt the interactions and
reduce or block these severe effects," Liu said.
From specks to blobs to map to model
The scientists obtained atomic-level details of the interaction between E and a human lung-cell-junction protein called PALS1 by mixing the two proteins together, freezing the sample rapidly, and then studying the frozen sample with the cryo-EM.
The electron microscopes
use high-energy electrons to interact with the sample in much the same way that
regular light microscopes use beams of light. But electrons allow scientists to
see things at a much smaller scale due to their extremely short wavelength (100,000
times shorter than that of visible light).
The first images didn't look like
much more than specks. But image-processing techniques allowed the team to
select specks that were actual complexes of the two proteins.
"We used two-dimensional averaging and started to see some structural features that are shared among these particles. Our images showed the complex from different orientations but at fairly low resolution," Liu said.
"Then we use computational tools
and computation infrastructure at Brookhaven's Computational Science Initiative
to perform three-dimensional reconstructions. These give us a 3-D model -- an
experimental map of the structure."
With an overall resolution of 3.65
Angstroms (the size of just a few atoms), the map had enough information about
the unique characteristics of the individual amino acids that make up the two
proteins for the scientists to fit the known structures of those amino acids
into the map.
"We can see how the chain of
amino acids that makes up the PALS1 protein folds to form three structural
components, or domains, and how the much smaller chain of amino acids that
makes up the E protein fits in a hydrophobic pocket between two of those
domains," Liu said.
The model provides both the
structural details and an understanding of the intermolecular forces that allow
E proteins deep within an infected cell to wrench PALS1 from its place at the
cell's outer boundary.
"Now we can explain how the
interactions pull PALS1 from the human lung-cell junction and contribute to the
damage," Liu said.
Implications for drugs and evolution
"This structure provides the foundation for our computational science colleagues to run docking studies and molecular dynamics simulations to search for drugs or drug-like molecules that might block the interaction," said John Shanklin, chair of Brookhaven Lab's Biology Department and a coauthor on the paper.
"And if they
identify promising leads, we have the analytical capabilities to rapidly screen
through such candidate drugs to identify ones that might be key to preventing
severe consequences of COVID-19."
Understanding the dynamics of this
protein interaction will also help scientists track how viruses like SARS-CoV-2
evolve.
"When the virus protein pulls
PALS1 out of the cell junction, it could help the virus spread more easily.
That would provide a selective advantage for the virus. Any traits that
increase the survival, spread, or release of the virus are likely to be
retained," Liu said.
The longer the virus continues to
circulate, the more chances there are for new evolutionary advantages to arise.
"This is one more reason it is
so essential for us to identify and implement promising therapeutics," Liu
said. "In addition to preventing the most severe infections, drugs that
effectively treat COVID-19 will keep us ahead of these mutations."
This research was funded by
Brookhaven National Laboratory's COVID-19 Laboratory Directed Research and
Development (LDRD) fund. LBMS is supported by the DOE Office of Science (BER),
NSLS-II is a DOE Office of Science user facility, supported by the Office of
Science (BES).