Antagonist HIV-1 Gag peptides induce structural changes in HLA B8

Abstract

In the cellular immune response, recognition by CTL-TCRs of viral antigens presented as peptides by HLA class I molecules, triggers destruction of the virally infected cell (Townsend, A.R.M., J. Rothbard, F.M. Gotch, G. Bahadur, D. Wraith, and A.J. McMichael. 1986. Cell. 44:959-968). Altered peptide ligands (APLs) which antagonise CTL recognition of infected cells have been reported (Jameson, S.C., F.R. Carbone, and M.J. Bevan. 1993. J. Exp. Med. 177:1541-1550). In one example, lysis of antigen presenting cells by CTLs in response to recognition of an HLA B8-restricted HIV-1 P17 (aa 24-31) epitope can be inhibited by naturally occurring variants of this peptide, which act as TCR antagonists (Klenerman, P., S. Rowland Jones, S. McAdam, J. Edwards, S. Daenke, D. Lalloo, B. Koppe, W. Rosenberg, D. Boyd, A. Edwards, P. Giangrande, R.E. Phillips, and A. McMichael. 1994. Nature (Lond.). 369:403-407). We have characterised two CTL clones and a CTL line whose interactions with these variants of P17 (aa 24-31) exhibit a variety of responses. We have examined the high resolution crystal structures of four of these APLs in complex with HLA B8 to determine alterations in the shape, chemistry, and local flexibility of the TCR binding surface. The variant peptides cause changes in the recognition surface by three mechanisms: changes contributed directly by the peptide, effects transmitted to the exposed peptide surface, and induced effects on the exposed framework of the peptide binding groove. While the first two mechanisms frequently lead to antagonism, the third has more profound effects on TCR recognition.

Figure 1

CTL recognition and antagonism by naturally occurring p17 variants. Recognition of variant peptides by two donor 008 clones (18 and 20) (a and b) at an ET of 8:1. (c) Inhibition of killing by clone 20, at an ET of 8:1, by the 3R and 5R variants shown to be encoded for by this provirus (5). Gag p24 (residues 261–269, GEIYKRWII) was used as a control HLA-B8 restricted peptide. (d ) Inhibition of killing by line 84, at an ET of 4:1, by 7R and 7Q. Influenza nuclear protein (residues 380–388, ELRSRYWAI) was used as a HLA B8 restricted control peptide.

Figure 1

CTL recognition and antagonism by naturally occurring p17 variants. Recognition of variant peptides by two donor 008 clones (18 and 20) (a and b) at an ET of 8:1. (c) Inhibition of killing by clone 20, at an ET of 8:1, by the 3R and 5R variants shown to be encoded for by this provirus (5). Gag p24 (residues 261–269, GEIYKRWII) was used as a control HLA-B8 restricted peptide. (d ) Inhibition of killing by line 84, at an ET of 4:1, by 7R and 7Q. Influenza nuclear protein (residues 380–388, ELRSRYWAI) was used as a HLA B8 restricted control peptide.

Figure 1

CTL recognition and antagonism by naturally occurring p17 variants. Recognition of variant peptides by two donor 008 clones (18 and 20) (a and b) at an ET of 8:1. (c) Inhibition of killing by clone 20, at an ET of 8:1, by the 3R and 5R variants shown to be encoded for by this provirus (5). Gag p24 (residues 261–269, GEIYKRWII) was used as a control HLA-B8 restricted peptide. (d ) Inhibition of killing by line 84, at an ET of 4:1, by 7R and 7Q. Influenza nuclear protein (residues 380–388, ELRSRYWAI) was used as a HLA B8 restricted control peptide.

Figure 1

CTL recognition and antagonism by naturally occurring p17 variants. Recognition of variant peptides by two donor 008 clones (18 and 20) (a and b) at an ET of 8:1. (c) Inhibition of killing by clone 20, at an ET of 8:1, by the 3R and 5R variants shown to be encoded for by this provirus (5). Gag p24 (residues 261–269, GEIYKRWII) was used as a control HLA-B8 restricted peptide. (d ) Inhibition of killing by line 84, at an ET of 4:1, by 7R and 7Q. Influenza nuclear protein (residues 380–388, ELRSRYWAI) was used as a HLA B8 restricted control peptide.

Figure 2

Crystal structures of the HLA B8–index and variant peptide complexes. The index peptide (P1–P8; GGKKKYKL) in the HLA B8 binding groove (top right) is viewed through the α2 helix with surface delineating the peptide volume in blue and the HLA B8 in green. The basic features of peptide binding are comparable to those observed in other MHC class I–peptide complexes (–, –33). From top left to bottom right, three close up views depict details of the differences between the index versus 3R, index versus 5R and index versus 7R plus 7Q complexes, respectively. The mainchain of the HLA B8 index complex is shown schematically in green, the peptide and representative HLA B8 sidechains in cyan, and the equivalent residues of the variant complexes are colored red in the 3R and 5R panels, red for 7R, and gold for 7Q in the joint P7 variants panel. Hydrogen bonds are depicted by appropriately colored dashed lines. In the 3R variant panel, the P5 sidechain is omitted for clarity. The most significant, concerted differences in HLA B8 mainchain positions are observed for the 3R variant (Fig. 3). The yellow arrow indicates the lateral shift in the position of the peptide backbone and consequent repositioning of a portion of the α1 helix spanning residues 61–66 (for this view, the shift is primarily into the plane of the paper). This region of the α1 helix has previously been observed to flex to accommodate different peptide binding requirements (17, 29). Direct expansion of the D pocket by movement of the α2 helix may be limited by the disulphide bond between residues 164 on the α2 helix and 101 on the floor of the binding groove. The figure was produced using programs SYBYL (Tripos Assoc., St. Louis, MO), MOLSCRIPT (34) (with modifications by R. Esnouf), and RASTER3D (35).

Figure 3

Mainchain structural differences between index and variant complexes. Ribbon representations of the index complex are coloured according to differences in pairwise Cα superpositions of index and variant complex HLA B8 α1 and α2 domains plus peptide (188 structurally equivalent residues). Regions colored green show the least variation in Cα position (⩽0.2 Å) while those in red correspond to changes of ⩾0.5 Å. (a) The 3R variant complex (overall RMS deviation 0.23 Å). (b) The 5R variant complex (overall RMS deviation 0.26 Å). (c) The 7R variant complex (overall RMS deviation 0.1 Å). (d) The 7Q variant complex (overall RMS deviation 0.1 Å). From these comparisons we estimate that the likely positional errors on main atom coordinates in all of these structures is less than 0.2 Å. The peptide mainchain position is significantly altered for the 3R variant over residues P1–P4 (0.4–1.1 Å) and residues P3–P5 for the 5R variant (0.4–0.8 Å). For the HLA B8 residues, significant concerted shifts (0.4-0.5 Å) are observed for residues 61–66 of the α1 helix in the 3R variant complex. Changes also occur at residues 159, 162, and 163 of the α2 helix (0.5 Å). For 5R, changes occur at residues 154, 155, and 163 of the α2 helix (0.4–0.5 Å). Figures were produced using programs MOLSCRIPT (34) (with modifications by R. Esnouf ) and RASTER3D (35). Structural superpositions were made using the program SHP (36).