Supercomputer Creates Atomic Model of HIV

DNA-1The ongoing fight to end HIV has been a long and arduous one, but progress is being made. In addition to potential treatments being created that have shown promise, there are also efforts being mounted to understand how the virus works at an atomic level. This is great news, for as any practitioner of medicine will tell you, understanding a disease and knowing how to strike at the heart of it is the key to stopping it and making sure future generations don’t have to fear it.

In recent years, several major breakthroughs were announced for the treatment of HIV, treatments which many heralded as cures. In January of last year, the Danish Research Council awarded funding to a group of researchers who demonstrated that HIV could be “flushed” from infected cells where it tends to congregate and protect itself. Combined with vaccinations that turbocharge the body’s immune system, this method proved effective at eliminating the HIV virus in infected cells.

HIV-budding-ColorAnother came back in November, when researchers at Caltech were even able to successfully spawn a significant amount of HIV antibodies in lab mice by using a new approach, known as Vectored ImmunoProphylaxis (VIP). An inversion of the traditional vaccination method, this new method produced plenty of HIV-preventing antibodies which they believed could be fashioned into a  vaccine.

And finally, there were the experiments being conducted over at the Washington University School of Medicine, where researchers designed a solution that employed bee venom and a nanoparticle delivery system. Knowing that bee venom is capable of killing HIV, and that the virus is thousands of times smaller than your average cell, the solution proved quite effective at filtering out the virus and killing it while leaving surrounding tissue unharmed. Taken together, these two proposed solutions have left many thinking a cure is just around the corner.

blue-waters-super-computer-at-petascale-020908Nevertheless, in order for this virus to truly be beaten, we need to understand it better. Hence why a group of scientists – using the University of Illinois’ “Blue Waters” supercomputer — have developed a new series of computer models that are finally giving researchers an atomic-level look at the formidable barrier mechanism enclosing the heart of the virus.

For example, its been known for some time that the HIV virus it’s covered in several layers of protective proteins. But beneath that outer shell resides a conical structure called the capsid, which houses the virus’ payload of genetic material. (See diagram below.) When HIV invades a cell, it’s the capsid that opens up to initiate the takeover process, allowing the virus to replicate inside the healthy host cell. Better understanding of how this mysterious delivery system operates could be one of the final steps to finding a cure.

HIVAnd that’s where the modelling software really comes into play. How and when the HIV cell opens to deliver the capsid has long eluded researchers, and as Klaus Schulten, a physicist that was part of the team that modeled the virus, pointed out: “The timing of the opening of the capsid is essential for the degree of virulence of the virus.”

Using the Blue Waters, Schulten and his associates managed to map out the model all 64 million of the capsid’s atoms. Through countless simulations, they also discovered that the capsid’s microscopic outer casing is composed of 216 hexagon-shaped proteins that fit together in a honeycomb formation. These hexagonal structures are what give the capsid it’s tough outer shell and allow it to be such a harmful and insidious killer.

AIDS_memorialThis painstakingly delicate process would have been unthinkable until just a few years ago, and represents the most complete picture of the HIV virus to date. What’s more, knowing what HIV looks like at the atomic level will help scientists to understand the timing of the virus’ delivery system. Since the opening of the virus’ protective layer is when it’s most vulnerable, Schulten and his colleagues hope to determine the precise timing of this event so a treatment can be developed that could attacks the virus at this exact moment.

Think of it as throwing a bomb into the mouth of a terrible war machine, right as it opens up its armored maw to bite you! Better yet, think of it as another step on the road to ending one of the greatest plagues humankind has ever had to deal with. Safety for the future, and justice for the victims!

Sources:,, (2)

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