This image was made using VMD in the Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign.
Have you ever wondered what the inside of HIV looks like? Well thanks to Juan Perilla of the University of Illinois, we don’t have to wonder any further.
As reported by Cosmos magazine, it took two years and two supercomputers to stimulate 1.2 milliseconds in the life of an HIV capsid from the atoms up. The genetic material of the virus itself has multiple structures that allow it to hide from one’s immune system.
The capsid (in blue) is what protects the virus once it enters a T cell. From there it helps in the transport to the T cell's nucleus, finalizing the process of infection. The capsid is beneath the virus's lipid bilayer membrane barrier, which has glycoproteins sprinkled about its surface.
Thanks to the Titan supercomputer at Oak Ridge National Laboratory in Tennessee, Perilla and physics professor Klaus Schulten were able to take the 64-million-atom simulation and analyze it by a second computer, Blue Waters, at the National Center for Supercomputing Applications in Illinois.
After inspecting the capsid at a closer range (like the one in the picture) the team found certain properties that enhance the capsid’s adeptness at finding a way to nucleus of targeted T cells.
They also found weaknesses and vulnerabilities within the virus itself that might one day lead to its demise.
Check out some of their other findings below, as published in the journal Nature:
(a) The HIV-1 capsid is made of a single capsid protein (CA), containing 11 α-helices and a 310 helix. (b) CA arranges into a fullerenic cone, consisting of pentamers (green) and hexamers (tan). The fully solvated HIV-1 capsid model without genome, including neutralizing ions and 150 mM NaCl, contains a total of 64,423,983 atoms5.
The electrostatic calculation includes all capsid atoms and all solvent molecules for a total of 64,423,983 atoms. The bar scale indicates the magnitude of the electrostatic potential in Volt, ranging from −1.3 V (red) to 6.0 V (blue). (a) Exterior view of the HIV-1 electrostatic potential. The red line indicates the location of the cross-section shown in b. (b) Cross-section of the electrostatic potential of the HIV-1 capsid. The bulk in the interior and exterior of the capsid assume the same electrostatic potential values, namely −1.3 V. (c) Electrostatics of the N-terminal domain of CA. The cypA binding loop and α-helix 4 (Fig. 1a) show a significant potential difference to the inner core of the capsid in d.