Researchers ran a supercomputer for two years to simulate a mere 1.2 microseconds in the life of the HIV capsid, the protein cage that ferries the virus into the nucleus of a cell it infects and hides it from that cell’s defense mechanisms. Findings about the capsid gleaned from this simulation may help scientists develop new ways of targeting the virus.

Publishing their findings in Nature Communications, researchers used one supercomputer to simulate the capsid and a second one to analyze the data.

The simulation revealed various properties of the capsid that facilitate its ability to sense its environment and travel to the cell nucleus. For example, different parts of the protein cage oscillate at different frequencies, helping to transmit information throughout the capsid.

Additionally, ions travel in and out of the pores of the capsid. The outside surface of the capsid is negatively charged, leading negatively charged ions to accumulate there; conversely, the inside surface of the capsid has a positive charge, causing ions with a negative charge to accumulate there.

The study authors theorize that breaking the electrostatic balance the capsid seeks to maintain could cause it to burst.

The investigators also believe that the positive charge of the capsid’s interior could also help draw in through the pores the negatively charged nucleotide molecules that HIV needs as building blocks to convert its RNA into DNA.

To read a press release about the study, click here.

To read the study abstract, click here.