Upload new images. The image library for this site will open in a new window.
Upload new documents. The document library for this site will open in a new window.
Show web part zones on the page. Web parts can be added to display dynamic content such as calendars or photo galleries.
Choose between different arrangements of page sections. Page layouts can be changed even after content has been added.
Move this whole section down, swapping places with the section below it.
Check for and fix problems in the body text. Text pasted in from other sources may contain malformed HTML which the code cleaner will remove.
Accordion feature turned off, click to turn on.
Accordion featurd turned on, click to turn off.
Change the way the image is cropped for this page layout.
Cycle through size options for this image or video.
Align the media panel to the right/left in this section.
Open the image pane in this body section. Click in the image pane to select an image from the image library.
Open the video pane in this body section. Click in the video pane to embed a video. Click ? for step-by-step instructions.
Remove the image from the media panel. This does not delete the image from the library.
Remove the video from the media panel.
A coiling protein shell, called a nucleocapsid,
surrounds Ebolas genetic material, which consists of single-strand RNA.
world grapples with the coronavirus (COVID-19) pandemic, another virus
has been raging again in the Democratic Republic of the Congo in recent
months: Ebola. Since the first terrifying outbreak in 2013, the Ebola
virus has periodically emerged in Africa, causing horrific bleeding in
its victims and, in many cases, death.
How can we battle these infectious
agents that reproduce by hijacking cells and reprogramming them into
virus-replicating machines? Science at the molecular level is critical
to gaining the upper hand research youll find underway in the
laboratory of Professor Juan Perilla at the University of Delaware.
Perilla and his team of graduate and undergraduate students in UDs Department of Chemistry and Biochemistry
are using supercomputers to simulate the inner workings of Ebola,
observing the way molecules move, atom by atom, to carry out their
Move this whole section up, swapping places with the section above it.
Juan Perilla and his team are studying Ebola.
In the teams latest work, they reveal structural features of
the viruss coiled protein shell, or nucleocapsid, that may be
promising therapeutic targets, more easily destabilized and knocked out
by an antiviral treatment.
The research is highlighted in the Tuesday, Oct. 20 issue of the Journal of Chemical Physics,
which is published by the American Institute of Physics, a federation
of societies in the physical sciences representing more than 120,000
The Ebola nucleocapsid looks like a
Slinky walking spring, whose neighboring rings are connected, Perilla
said. We tried to find what factors control the stability of this
spring in our computer simulations.
The life cycle of Ebola is highly dependent on this coiled
nucleocapsid, which surrounds the viruss genetic material consisting of
a single strand of ribonucleic acid (ssRNA). Nucleoproteins protect
this RNA from being recognized by cellular defense mechanisms. Through
interactions with different viral proteins, such as VP24 and VP30, these
nucleoproteins form a minimal functional unit a copy machine for
viral transcription and replication.
While nucleoproteins are important to the nucleocapsids stability,
the teams most surprising finding, Perilla said, is that in the absence
of single-stranded RNA, the nucleocapsid quickly becomes disordered.
Graduate research assistant Chaoyi Xu
But RNA alone is not sufficient to stabilize it. The team also observed
charged ions binding to the nucleocapsid, which may reveal where other
important cellular factors bind and stabilize the structure during the
viruss life cycle.
Perilla compared the teams work to
a search for molecular knobs that control the nucleocapsids
stability like volume control knobs that can be turned up to hinder
The UD team built two molecular dynamics systems of the Ebola
nucleocapsid for their study. One included single-stranded RNA; the
other contained only the nucleoprotein. The systems were then simulated
using the Texas Advanced Computing Centers Frontera supercomputer the
largest academic supercomputer in the world. The simulations took about
two months to complete.
Graduate research assistant Chaoyi Xu ran the molecular simulations,
while the entire team was involved in developing the analytical
framework and conducting the analysis. Writing the manuscript was a
learning experience for Xu and undergraduate research assistant Tanya
Nesterova, who had not been directly involved in this work before.
also received training as a next-generation computational scientist with
support from UDs Undergraduate Research Scholars program and NSFs
XSEDE-EMPOWER program. The latter has allowed her to perform the
highest-level research using the nations top supercomputers.
Undergraduate research assistant Tanya Nesterova
Postdoctoral researcher Nidhi Katyals expertise also was essential to
bringing the project to completion, Perilla said.
While a vaccine exists for Ebola,
it must be kept extremely cold, which is difficult in remote African
regions where outbreaks have occurred. Will the teams work help advance
As basic scientists we are excited to understand the fundamental
principles of Ebola, Perilla said.
The nucleocapsid is the most
abundant protein in the virus and its highly immunogenic able to
produce an immune response. Thus, our new findings may facilitate the
development of new antiviral treatments.
Currently, Perilla and Jodi Hadden-Perilla are using supercomputer simulations to study the novel coronavirus that causes COVID-19.
Although the structures of the nucleocapsid in Ebola and COVID-19 share
some similarities both are rod-like helical protofilaments and both
are involved in the replication, transcription and packing of viral
genomes that is where the similarities end.
We now are refining the methodology we used for Ebola to examine SARS-CoV-2, Perilla said.
Article by Tracey Bryant; photos by Kathy F. Atkinson and courtesy of Juan Perilla Laboratory
Published Oct. 20, 2020