12] Relationships of human immunodeficiency virus protease with eukaryotic aspartic proteases

Abstract

Publisher Summary This chapter describes the methods used in the comparative studies of the evolutionary relationships and catalytic mechanism of HIV-1 protease and representative eukaryotic aspartic proteases. The evidence for the evolutionary relationship of eukaryotic and retroviral aspartic proteases originates from the observation that the single-chain eukaryotic aspartic proteases contain internal twofold similarity in secondary and tertiary structures that was postulated to be derived from gene duplication and fusion in the evolution of this group of enzymes. Mature HIV-1 protease is a homodimer with a monomer size of 99 amino acids. Its three-dimensional structure retains the important core-β structure of eukaryotic aspartic proteases, while the conformation of the active site, including the aspartic acids, is virtually identical to those of the eukaryotic enzymes. In both HIV and eukaryotic enzymes, a water molecule is found to be hydrogen bonded between the two active site aspartic carboxyls. Like the eukaryotic enzyme, HIV protease has a substrate-binding cleft that contains at least eight substrate side chain-binding pockets. These similarities suggest that HIV protease and the eukaryotic aspartic proteases are related in evolution and are similar in their catalytic mechanisms. Therefore, comparative studies of these enzymes may provide insights into their structure–function relationships.