Virtual Viruses

Graphical rendering of the simulation work of the influenza A virus in close apposition with a host cell membrane. Credit: H. Koldsø/Oxford

Just few days ago I mentioned the complexity of studying the folding of molecules (in that post I was referring to RNA). It is so complex that supercomputers are used to calculate the way a protein can fold. And yet, understating the possibile folding is crucial because the folding creates the shape of the other surface of the protein and it is all about shape, like a Lego construction set. If two proteins have surfaces that match they stick, otherwise they don't. In the virus world if the surface of a virus matches the surface of a cell that virus stick to the cell membrane and its DNA/RNA can penetrate the cell and multiply. At a macro level that means that you get infected!

More than that. If you want to create a drug to fight that virus you need to create a surface that will match the virus surface so that the two stick together and the drug can affect the virus.

So far researchers in the pharmaceutical field have progressed through "blind" attempt, hoping to hit on something that works. But now, and this is what the work of the researchers at Oxford is doing, one may sit at a computer and "look" at the surface of a virus (a virtual one) and see it!

The technology used is called "coarse-grained molecular dynamics" a name that indicates the interest in understanding how molecules change at a macro scale (which actually is really a micro scale). What matters is not the fine positioning of atoms in a molecule but the shape resulting from the atoms position.

The researchers have started by creating a tiny ball made of lipid molecules (that are the ones forming the membrane of cells and of viruses) of about 73 nm: This is actually a "simulated" ball, not a real one. Than they have subject the tiny ball to a variety of interactions at different temperatures and studied how its shape changes. They found that it actually shrinks to some 59nm in just 0.3µs. The shrinking makes inner proteins of the virus to stick out on its surface and they stick out in various configurations. These are the "key" to access a host cell membrane.

This is another example how ICT is changing the rules of the game. Scientists can now see viruses as Lego Blocks and understand by looking at their surface rendering how they manage to attack a cell. That same understanding provides the ammunitions needed to develop drugs that can be effective, and all by sitting at a desk and looking at a computer screen.

Author - Roberto Saracco

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