Figure 1.

(A) Organization of the Gag and Gag-Pol polyproteins of HIV-1. Nomenclature of domains in Gag:² MA, matrix; CA, capsid; SP1, spacer peptide 1, NC, nucleocapsid; SP2, spacer peptide 2. In Gag-Pol: TFR, transframe region; PR, protease; RT, reverse transcriptase; RN, Rnase H; IN, integrase. FS designates the location of the - 1 frame shift during translation that results in production of Gag-Pol. Numbers shown above (red) and below (blue) the schematic lines designate the order in which sequential cleavages occur in Gag and in Gag-Pol respectively.^2,9 (B) Sequence alignment of PR20 with wild type HIV-1 protease (PR^wt) and its optimized mutant (termed PR). Residues in PR and PR20 shown in blue were introduced to limit autoproteolysis and to preclude cysteine-thiol oxidation. Residues shown in red are natural mutations in the clinical isolate from which PR20 is derived.¹⁹ The gold and white backgrounds indicate highly conserved regions in the protease domain in drug treated patients,⁴¹ and areas of greatest variability among isolates, respectively. The blue background designates regions where major DRMs (as defined in http:/hivdb.stanford.edu/cgi-bin/PIResiNote.cgi) occur. (C) Ribbon representation (in blue) of PR20 in complex with DRV (pdb accession code 3UCB¹³) superimposed on PR (in white, pdb accession code 2IEN³⁰). Locations of the mutations in PR20 are shown as red circles with residue numbers in white. The DRV inhibitor is shown as a stick and surface representation in the active site cavity. Major sites of autoproteolysis are indicated in B and C with red arrows. Molecular representations were prepared using Chimera.⁴²