User:David Canner/Sandbox HIV

HIV is a notoriously lethal virus that is known to cause AIDS. It is a homodimeric protein made by the HIV virus that is crucial to the virus's infectious capacity. The virus makes certain proteins that need to be cleaved, in order to transform into mature, fully-functional proteins that can allow the virus to infect new cells. HIV-1 protease is responsible for cleaving these nascent proteins into their mature form.

Structure of HIV-1 Protease

Looking at the structure of HIV-1 protease, we see that the protein is composed of two symmetrically related subunits, each consisting of identical 99 amino acid chains. The subunits come together in such as way as to form a tunnel where they meet. This tunnel is of critical importance as it is the location where nascent proteins are bound before cleavage. In the middle of the tunnel is the active site of the protease: two Asp-Thr-Gly catalytic triads (residue numbers 25, 26, and 27 on one chain and 125, 126, and 127 on the second). The two Asp's act as the main catalytic residues in the active site and use a water molecule to help break the protein chain that binds in the tunnel.

There currently is no cure or vaccine. But, scientists have discovered treatments that can slow progression of the HIV virus, thanks in large part to our understanding of the structure of HIV-1 protease. seen here on the right in complex with a potent drug used for slowing the progression of HIV, (PDB entry 2nmz).

Saquinavir was the the first protease inhibitor approved by the FDA for the treatment of HIV. It inhibits HIV-1 protease by , thus preventing the protease from cleaving any protein chains. You may be wondering how a protein to be cleaved makes its way into the active-site tunnel to begin with -- after all, the tunnel does not seem so accessible. The key is the two flexible flaps on the top of the tunnel that can (large scene, takes a while to load) to allow proteins to enter the tunnel. A is also illuminating, as the change in the accessibility of the tunnel becomes more obvious. This movement of the flexible flaps is simulated by morphing between two crystal structures, the first being the native HIV-1 protease structure with no inhibitor bound (PDB entry 1hhp) and the second being the HIV-1 protease complexed with Saquinavir.

Other drugs used to treat patients infected with the HIV virus include Indinavir (PDB entry 1hsg), Ritonavir (PDB entry 1hxw), and Nelfinavir (PDB entry 1ohr).