The SARS-CoV-2 virus, as we have never seen it before: this is the most detailed 3D model obtained so far

Although they are invisible, there are a number of cutting-edge techniques that allow us to model viruses in three dimensions. This has become an art in recent years, as this model of the SARS-CoV-2 demonstrates.

These images correspond to the most specific and detailed three-dimensional representation, obtained on an atomic scale, that has been made to date. In order to model the coronavirus, hundreds of genetic data and the consultation of dozens of virologists have been required. But the result will help us better understand how the virus works.

The most detailed model of the coronavirus

The company Visual Science works in 3D modeling oriented to scientific needs. Among the models that generate the most interest in the scientific community are those of complex proteins, especially viruses. Viruses, remember, are not living organisms, but molecules capable of performing amazing tasks.

Coronaviruses (not SARS-CoV-2) had previously been photographed by electron micrograph. With this model, however, we can better understand what is seen under a microscope. What's more, you can see in incredible detail what each part of the virus looks like.

3D model of the SARS-CoV-2 virus at atomic resolution from Visual Science on Vimeo.

Thus, the model shows in proportional size how the capsid, the covering that surrounds the genetic material of the virus, is seized by the pointed glycoproteins. These structures are the protagonists in the infective process, since they are the ones that bind to the human cell and begin the process. Inside you can see the typical RNA of the coronavirus, which contains all the information necessary to form its components, as well as instructions to hijack the cellular machinery and copy itself within the host.

This model is not limited to being aesthetically impressive but is incredibly successful, explain expert virologists in coronaviruses such as Dr. Jason S. McLellan, from the Department of Molecular Biosciences of the U. of Texas; and Dr. Benjamin Neuman, professor and president of the Society for Biological Sciences at Texarkana, scientific advisers to the model. These researchers explain how this design very accurately displays the data known to date.

How to model a particle

What is special about a 3D model? Unlike other models, those made with proteins and particles are not a mere artistic work of interpretation. On the contrary, there are several very specific techniques for making these models. Among them is homology modeling, which is a computing technique that predicts with 99% confidence how an atom is placed with respect to what is around it.

Of course, this is not easy and requires an incredible amount of data and its processing. Specifically, in SARS-CoV-2, the general data on the particles contained in the virus (its capsid, external glycoproteins, RNA ...) were required, in addition to specific data. These are the most complicated to obtain since they are part of the work that is currently underway in many laboratories around the world that are testing the virus against the clock.

In them, simplifying a lot, different parts of the virus are observed by crystallography and other similar techniques. In other laboratories, work is carried out by sequencing the genome and analyzing which proteins the genetic material expresses. With all these data, virologists can make a "robot portrait" of the virus structure, which is confirmed according to mathematical computational models.

The particles around the virus are the specific antibodies against the virus, modeled

Thus, these particle models are among the most accurate and useful, since they allow the prediction of active regions and possible therapeutic targets. Returning to this model, according to the Visual Science team, he has worked with the latest scientific material and consulting with a dozen virologists who are experts in SARS-CoV.

"We use the published scientific information on the virus and the structures of the viral components available in the protein data bank as a starting point," said Yury Stefanov, scientific director of Visual Science. After a thorough and careful analysis of the data, we reconstructed complete models of the viral proteins and their interactions using computational biology software, and then assembled the entire virion model based on these structures, "he confirmed.

Images | Unsplash

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