HIV must use a HIV encoded enzyme called protease in order to cleave a large Gag-Pol polyprotein (p120), a Gag polyprotein (p55), and an Env polyprotein (gp160) into functional proteins essential to the structure of HIV and to its RNA packaging. The active site of the HIV protease binds to the polyproteins and cleaves them into the functional proteins needed for viral replication and maturation.

• The Gag polyproteins (p55) will eventually be cleaved by HIV proteases to become HIV matrix proteins (MA; p17), capsid proteins (CA; p24), nucleocapsid proteins (NC, p7), and protein p6.
• The Gag-Pol polyproteins (p160) will eventually be cleaved to become HIV matrix proteins (MA; p17), capsid proteins (CA; p24), proteinase molecules (protease or PR; p10), reverse transcriptase molecules (RT; p66/p51), and integrase molecules (IN; p32).
• The Env polyproteins (gp160) will eventually be cleaved to become HIV envelope glycoproteins gp120 and gp41.