Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions

Abstract

The crystal structures of the 2C/H-2K(bm3)-dEV8 allogeneic complex at 2.4 A and H-2K(bm3)-dEV8 at 2.15 A, when compared with their syngeneic counterparts, elucidate structural changes that induce an alloresponse. The Asp77Ser mutation that imbues H-2K(bm3)-dEV8 with its alloreactive properties is located beneath the peptide and does not directly contact the T cell receptor (TCR). However, the buried mutation induces local rearrangement of the peptide itself to preserve hydrogen bonding interactions between the peptide and the alpha(1) 77 residue. The COOH terminus of the peptide main chain is tugged toward the alpha(1)-helix such that its presentation to the TCR is altered. These changes increase the stability of the allogeneic peptide-major histocompatibility complex (pMHC) complex and increase complementarity in the TCR-pMHC interface, placing greater emphasis on recognition of the pMHC by the TCR beta-chain, evinced by an increase in shape complementarity, buried surface area, and number of TCR-pMHC contacting residues. A nearly fourfold increase in the number of beta-chain-pMHC contacts is accompanied by a concomitant 64% increase in beta-chain-pMHC shape complementarity. Thus, the allogeneic mutation causes the same peptide to be presented differently, temporally and spatially, by the allogeneic and syngeneic MHCs.

Figure 1.

Superposition of dEV8 peptides from the free and TCR-bound forms of pMHCs. (A) Comparison of the unbound H-2K^b–dEV8 (magenta) and unbound H-2K^bm3–dEV8 (green) complexes. (B) Comparison of the TCR-bound H-2K^b–dEV8 (PDB code 2CKB) (cyan) and TCR-bound H-2K^bm3–dEV8 (orange). (C) Comparison of the unbound H-2K^b–dEV8 (magenta) and TCR-bound H-2K^b–dEV8 (cyan) (PDB code 2CKB). (D) Comparison of the unbound H-2K^bm3–dEV8 (green) and TCR-bound H-2K^bm3–dEV8 (orange).

Figure 2.

Effect of the alloreactive mutation on peptide-MHC and peptide-MHC–TCR interactions. Hydrogen bonding networks to the peptide proximal to Asp77Ser mutation are reorganized. Hydrogen bonding around the Asp77Ser mutation is shown between the peptide and MHC (A and B) and between peptide, MHC, and TCR (C and D). (A) H-2K^b–dEV8, (B) H-2K^bm3–dEV8, (C) 2C/H-2K^b–dEV8 (PDB code 2CKB), and (D) 2C/H-2K^bm3–dEV8. Peptide in yellow, MHC in cyan, TCR in green, water molecules in red.

Figure 3.

Comparison of syngeneic and allogeneic 2C TCR–pMHC complexes. The syngeneic 2C/H-2K^b–dEV8 complex is in gray; the allogeneic 2C/H-2K^bm3–dEV8 complex is colored, V_α CDRs (–4) in cyan, V_β CDRs (–4) in yellow, H-2K^bm3 α₁ and α₂ helices in green, dEV8 (P1-P8) in red, and waters directly mediating TCR–pMHC contact in purple.

Figure 4.

A comparison of shape complementarity at the TCR–pMHC interface between the allogeneic (2C/H-2K^bm3–dEV8) and syngeneic complexes (2C/H-2K^b–dEV8). Shape complementarity is markedly increased at the TCR β-chain interface in the allogeneic complex. Shape complementarity at the TCR–pMHC interfaces was calculated using SC as implemented in CCP4 (CCP4, 1994) and mapped onto the corresponding surfaces in GRASP (reference 52). (A) 2C/H-2K^b–dEV8 (PDB code 2CKB). 2C at top and H-2K^b–dEV8 at bottom. (B) 2C/H-2K^bm3–dEV8. 2C at top and H-2K^bm3–dEV8 at bottom. The intensity of the cyan surface correlates with the magnitude of the Sc coefficient on the projected surface. Shape complementarity increases in 2C/H-2K^bm3–dEV8 at the surface projected by β-chain (area within the enclosed ovals).

Figure 5.

Bar graphs depicting changes in contacts, shape complementarity, and buried surface area in 2C/H-2K^bm3–dEV8 relative to 2C/H-2K^b–dEV8. Recognition by the β-chain is emphasized in the allogeneic (orange bar) vs. syngeneic (blue bar) complex. Bars at left compare pMHC interactions with the entire TCR (α, β), middle bars compare pMHC interactions with the α-chain, and bars at right compare pMHC interactions with the β-chain. (A) Number of overall contacts between TCR and pMHC and number of pMHC contacts for individual chains. (B) Sc coefficients for 2C bound to H-2K^b–dEV8 and H-2K^bm3–dEV8 and Sc coefficients for individual chains. (C) Buried pMHC surface area for 2C bound to H-2K^b–dEV8 and H-2K^bm3–dEV8, and pMHC surface area buried by individual α and β chains.