Physicists simulate how SARS-CoV-2 forms

The assembly and formation of SARS-CoV-2 from its constituent parts. (Courtesy: Zandi Lab, UC Riverside)

The genetic material inside viruses cannot survive for long without a protective coating of proteins. However, the process by which these proteins assemble to encapsulate (and therefore protect) the viral genome is not well understood – especially for coronaviruses, which have very large RNA genomes. A pair of researchers at the University of California in Riverside, US and Songshan Lake Materials Laboratory in China have now identified the interactions at play during the assembly of SARS-CoV-2, the coronavirus that causes COVID-19, and explored how these interactions lead to the genome being packaged into a new virion. The work could aid the design and development of drugs to fight this and other coronaviruses.

SARS-CoV-2 contains four structural proteins: envelope (E); membrane (M); nucleocapsid (N); and spike (S). The M, E and S proteins are vital for assembling and forming the virus’ outermost layer, or envelope, which helps the virus enter host cells as well as protecting it from damage.

Compact ribonucleoprotein complex

In the new work, UC-Riverside physicist Roya Zandi and her former graduate student Siyu Li (who is now a postdoc at Songhan Lake) used computational tools known as coarse-grained models to simulate how SARS-CoV-2 forms from these constituent parts. These models mimic viral components at large length scales and provide precious information on virus assembly processes.

Using these models, the pair calculated that the N proteins condense the viral RNA to form a so-called compact ribonucleoprotein complex, which is an assembly of molecules consisting of both protein and RNA. This assembly then interacts with the M proteins embedded in the lipid membrane. Finally, a process known as the “budding” of the ribonucleoprotein complex takes place, completing the viral formation.

Interaction between N proteins is very important

The researchers based the shape of the N protein in their model on a well-known structure described in the literature. “RNA is a negatively-charged polymer and there are a lot of positive charges in the N proteins,” Zandi explains. “The interaction between the positive charges on N proteins and negative charges on RNA results in the condensation of RNA.”

Zandi tells Physics World that the interactions between N proteins turned out to be very important in RNA condensation. “We didn’t know about this effect before performing our simulations,” she adds.

The pair also modelled the M proteins based on their structure and function as described in the literature. They designed these proteins such that they interact with the N proteins and also bend the membrane. “The coarse-grained model has allowed us to understand the mechanisms of protein oligomerization, RNA condensation by structural proteins and the membrane-protein interactions, predicting the factors that control the virus assembly,” Li explains.

In the past, Zandi notes that understanding the factors that contribute to virus assembly has often led to new therapeutic strategies. In her view, the findings from this research, which is detailed in the journal Viruses, could similarly help provide the means to combat SARS-CoV-2. “The assembly mechanism we have unearthed could inform the design and development of small molecules that target the viral structure proteins, modifying their functions to disrupt the fidelity of the assembly process,” she says.

In the longer term, Zandi thinks the new work could even become a benchmark for experiments and microscopic all-atom simulations. “We are currently collaborating with experimental and computational groups for the next stage of our investigations,” she reveals. “Ultimately, we aim to connect multiscale research to further the continued development of antiviral drugs to arrest coronaviruses in their assembly stage.”

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