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An aspartic protease is a protease whose catalytic chemistry depends on aspartic acid side chains. In common examples, their carboxyl groups position and activate a water molecule for peptide bond hydrolysis. Water supplies the attacking nucleophile, unlike a mechanism in which an enzyme side chain itself makes the initial covalent attack.^[ref]

The name concerns catalytic groups, rather than requiring an aspartic-acid residue at every substrate cleavage site. Substrate recognition and catalytic mechanism are distinct properties.

HIV-1 protease provides an experimentally characterized example. In 1989, T. D. Meek and colleagues measured apparent masses of approximately 11,000 under denaturing conditions and 22,000 under nondenaturing conditions; protein cross-linking supplied additional evidence for an active protein dimer. The ratio $22,000/11,000=2$ explains the subunit interpretation.^[ref]

The same study found pH-dependent inactivation consistent with a required unprotonated carboxyl group in the active site. Combining this chemical perturbation with cleavage activity and subunit measurements supported a catalytic classification more specifically than the enzyme's molecular mass alone.^[ref]

T. D. Meek is the first author of a 1989 study characterizing HIV-1 protease produced in Escherichia coli. The purified enzyme processed a viral precursor protein into fragments consistent with the expected mature products. The investigators also compared molecular masses under denaturing and nondenaturing conditions and used protein cross-linking to probe subunit association.^[ref]

The apparent mass changed from about 11,000 to 22,000 between dissociated and associated conditions, consistent with a dimer. Cross-linking supplied a separate line of evidence for association. Pairing such structural measurements with an activity assay was important: a single chain observed under denaturing conditions need not be the functional unit of an active enzyme.^[ref]