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Molecular simulations to understand coronavirus

The rapid characterization of the SARS-CoV-2 virus has allowed researchers at the Soft Matter Theory Group to learn more about how it interacts with surfaces through extremely precise simulations. The results have been published in the scientific journal Biointephases.

Nov 27, 2020
Image: Electron microscopy image of a typical SARS-CoV-2 coronavirus particle, freely distributed by the NIAID’s Rocky Mountain Laboratories (NIAID-RML),1 colored to emphasize the virus structure.

As efforts to face the Covid-19 pandemic continue, researchers from the Soft Matter Theory Group Jordi Faraudo and David Malaspina are applying their experience to help understand how does the virus latch on different surfaces. In the recently published article “Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces”, these ICMAB Researchers have modeled the interaction between two different materials and the SARS-CoV-2 virus’ most external part: the spike-shaped glycoproteins that surround it and give its family of viruses the “Corona” on their name.

Their research modeled the contact of the spike with cellulose and graphite. These two materials are chosen because of their hydrophilic or hydrophobic nature, which has been shown to be an important factor when studying virus-surface interactions, and because both are used in adsorbents and filters. Cellulose is an amphiphilic material, meaning that because of its molecular structure it is both hydrophilic and lipophilic. Both interactions are essential in the process. Graphite has a strongly lipophilic surface and is hydrophobic, which makes it unable to pursue hydrogen bonds and prone to hydrophobic interactions.

Their model shows two different phases of the contact. On an initial stage, both materials show a similar adsorption, both involving three receptor-binding domains (RBDs) and two N-terminal domains (NTDs). After the first few nanoseconds, the two interactions take different routes. The adsorption on cellulose stabilizes through a large number of hydrogen bonds between the materials and the spike’s RBDs. This phenomenon does not occur on the adsorption onto graphite. As a result of the lack of stabilization between the surface and the proteins in the spike, a large number of residues appear and there is a substantial deformation of the spike, as you can see in this video of the simulation:

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Figure: Representative snapshots of SARS-CoV-2 spike glycoprotein during the final adsorption stage onto cellulose (left) and graphite (right) surfaces. In graphite, the spike experiences a deformation, while in cellulose it does not. (Credit: Jordi Faraudo and David Malaspina, ICMAB)

This information could be useful in the design of virucides against COVID-19, with carbon materials presenting a helpful strain on the virus’ spikes, which are what allows it to adhere to surfaces. Understanding how the virus interacts with surfaces helps stop its transition.

The researchers consider this a first step in understanding SARS-CoV-2 molecular interactions, requiring of further research. This study is not exactly the Soft Matter Theory Group’s usual line of work:

“I was not really aware before this pandemic that from the field of material sciences you could contribute to slowing the spread of pandemics,” said Jordi Faraudo in an article for AIP Scilight. “But we have experience modeling the interactions of protein with nanoparticles, which isn’t that different than how the most external thing on the virus – a protein – interacts with materials.”

The article offers possible ways to expand on this research, like using models that consider the virus as a whole, or further research into other carbon based surfaces. Researchers are already planning on continuing their investigation on other materials, like some metals like silver, which has antibacterial properties and could help find an antiviral material to stop a virus transmission.

Watch Jordi Faraudo on the European Researchers' Night

Jordi Faraudo explained this research in this short video for the European Researcher's Night (Nit Europea de la Recerca, in Catalan):, celebrated on 27 November 2020 in multiple cities in Europe:

More information

Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces
David C. malaspina, Jordi Faraudo
Biointerphases 15, 051008 (2020); DOI: 10.1116/6.0000502
This paper is part of the Biointerphases Special Topic Collection on Molecular Scale Modeling of Biological Molecules at Interfaces. The paper was selected as Featured.

Simulations suggest graphite may deform coronaviruses and limit their spread
Mara Johnson-Groh
AIP SciLight, 30 Oct 2020. DOI: 10.1063/10.0002430

Cover Image: Electron microscopy image of a typical SARS-CoV-2 coronavirus particle, freely distributed by the NIAID’s Rocky Mountain Laboratories (NIAID-RML),1 colored to emphasize the virus structure.

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