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The hepatitis B capsid, a protein shell that encloses the
virus, is described as a spiky ball consisting of dimers, or two-part
molecular structures that assemble to form it.
at the University of Delaware, using supercomputing resources and
collaborating with scientists at Indiana University, have gained new
understanding of the virus that causes hepatitis B and the spiky ball
that encloses the viruss genetic blueprint.
The research, which has been published online, ahead of print, by the
American Chemical Association journal ACS Chemical Biology, provides
insights into how the capsid a protein shell that protects the
blueprint and also drives the delivery of it to infect a host cell
Computer simulations performed by the UD scientists investigated the
effects of a mutation that impairs the assembly process. Together with
collaborators, the researchers revealed that the region of the protein
that contains the mutation, the spike, can communicate with the region
of the protein that links with other subunits to assemble the capsid.
They found evidence that a change in the shape of the capsid protein
switches it into an "on" state for assembly.
Scientists believe that the capsid is an important target in
developing drugs to treat hepatitis B, a life-threatening and incurable
infection that afflicts more than 250 million people worldwide.
The capsid looks like a spiky
ball, with 120 protein dimers that assemble to form it; each dimer
contains a spike, said Jodi A. Hadden-Perilla, assistant professor in
UDs Department of Chemistry and Biochemistry
and a co-author of the new paper. The capsid is key to the virus
infection cycle. If we could disrupt the assembly process, the virus
wouldnt be able to produce infectious copies of itself.
Move this whole section up, swapping places with the section above it.
The Indiana University researchers had been studying the dimers,
which are two-part, T-shaped molecular structures, and investigating
whether a mutation could activate or deactivate a switch to turn on the
capsids assembly mechanism. They worked with Hadden-Perillas group,
which ran computer simulations to explain how changes in the protein
structure induced by the mutation affected the capsids ability to
What we learned is that this mutation disrupts the structure of the
spike at the top of the dimer, Hadden-Perilla said. This mutation
slows down assembly, which actually involves a region of the protein
that is far away from the spike. Its clear that these two regions are
connected. A change in the shape of the protein, particularly at the
spike, may actually activate or deactivate assembly.
Her team did its work using the National Science Foundation-supported
Blue Waters supercomputer at the University of Illinois at
Urbana-Champaign, the largest supercomputer on any university campus in
the world, to perform what are known as all-atom molecular dynamics
Molecular dynamics simulations allow researchers to study the way
molecules move in order to learn how they carry out their functions in
nature. Computer simulations are the only method that can reveal the
motion of molecular systems down to the atomic level and are sometimes
referred to as the computational microscope.
The paper, titled The integrity of the intradimer interface of the
Hepatitis B Virus capsid protein dimer regulates capsid self-assembly,
can be viewed on the journals website.
Carolina Perez Segura
For doctoral student Carolina P??rez Segura, a co-author of the paper,
working with data from the supercomputer simulations was the kind of
research experience that first brought her to the University of Delaware
and then inspired her to stay.
She examined numerous simulations
and vast amounts of data to investigate the effect of the mutation and
made some important discoveries, Hadden-Perilla said. We threw her
into the deep end in my brand-new research group [last summer], and she
did a great job.
P??rez Segura came to UD as a participant in the Universitys Latin
American Summer Research Program. A graduate of the Universidad Nacional
de Colombia (National University of Colombia), the program marked her
first time leaving Colombia and, indeed, her first time traveling by
plane. She planned to conduct research under Hadden-Perillas mentorship
for a couple of months and then return home.
But, she said, the experience was so meaningful to her that she
canceled her plane ticket home and stayed on to work as a visiting
scholar with Hadden-Perilla while applying to UDs doctoral program in
chemistry. She was accepted and began her studies during spring
It was her fascination with computational chemistry that brought her
to Delaware, she said, and the work with supercomputers that made her
decide to continue that research.
While I was an undergraduate, I chose that branch of chemistry as
the kind of career I wanted, said P??rez Segura, who worked with a
research group in the field, on a smaller scale, in Colombia. When I
was introduced to the idea that math and physics can help you understand
biological processes, I knew that was what I wanted to do.
I thought it was really amazing to be able to explain biological
processes with numbers and computers. I wanted to learn more, and here,
theres so much more opportunity to learn it.
Although the social and travel restrictions imposed by the
coronavirus (COVID-19) pandemic have limited her ability to fully
experience American life and culture, she said her experience at UD
remains very positive. Shes eager to be able to go out more, practice
her English and feel a part of American culture, but meanwhile, shes
busy with exciting research, she said.
Shes currently also working on research that Hadden-Perilla is conducting into the virus that causes COVID-19.
Its unusual for a student to be accepted into our graduate program
off-cycle, beginning in spring semester, Hadden-Perilla said. But
Carolina is exceptional.
Article by Ann Manser; illustration by iStock; photos courtesy of Jodi Hadden-Perilla
Published Aug. 11, 2020