Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6

Abstract

The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.

FIG. 1.

(A) Amino acid sequence alignment of the CRF01_AE protease with the clade B protease. Positions where sequences differ are indicated in red. (B) CRF01_AE protease in complex with p1-p6 (green). Amino acid changes in monomer A (cyan) are indicated in red, and changes in monomer B (magenta) are indicated in blue.

FIG. 2.

(A) Ribbon diagram superposition of the CRF01_AE (blue) and the clade B (gray) p1-p6 structures. The flap hinge region is indicated by the red box. (B) Double-difference plot comparing the CRF01_AE and clade B p1-p6 structures. Contours in the plot represent the degrees of distance between the residues of the structures being compared. Black indicates a distance of <0.6 Å; red indicates −0.59 Å and −0.3 Å; blue indicates 0.3 Å and 0.59 Å; and yellow indicates >0.6 Å. (C) Stereoview of the rearrangement of the flap hinge region of the CRF01_AE structure (blue) compared to that of the clade B structure (gray). The Asn37 side chain in the CRF01_AE structure is disordered and has been modeled as alanine. (D) p1-p6 substrate conformation (blue, CRF01_AE; gray, clade B).