Inside Ebola

As the 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 functions.

 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 members.

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.

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 virus replication.

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.

She 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.

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 new treatments?

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