For many but not for all: how the conformational flexibility of the peptide/MHCII complex shapes epitope selection

Abstract

The adaptive immune response starts when CD4+ T cells recognize peptide antigens presented by class II molecules of the Major Histocompatibility Complex (MHCII). Two outstanding features of MHCII molecules are their polymorphism and the ability of each allele to bind a large panoply of peptides. The ability of each MHCII molecule to interact with a limited, though broad, range of amino acid sequences, or "permissive specificity" of binding, is the result of structural flexibility. This flexibility has been identified through biochemical and biophysical studies, and molecular dynamic simulations have modeled the conformational rearrangements that the peptide and the MHCII undergo during interaction. Moreover, there is evidence that the structural flexibility of the peptide/MHCII complex correlates with the activity of the "peptide-editing" molecule DM. In light of the impact that these recent findings have on our ability to predict MHCII epitopes, a review of the structural and thermodynamic determinants of peptide binding to MHCII is proposed.

Figure 1. Cellular trafficking of MHCII proteins within an APC

MHC/Ii complexes are synthesized in the ER, and directed through the trans-Golgi, where the majority is sorted to the endosomal compartment. In the endosome, Ii is cleaved, leaving CLIP bound to the peptide-binding groove. Endocytosed antigens enter the APC and are degraded through the endosomal/lysosomal pathway via the action of proteases. MHCII may bind antigenic peptides in the endosome, but the majority traffics to the lysosome/MIIC where accessory molecules for peptide loading such as DM and DO (not represented) reside. Once bound to the peptide, MHCII can be translocated to the surface of an APC for T cell recognition. In addition to the canonical MIIC pathway, there is also evidence that MHCII/Ii complexes can sort directly from the trans-Golgi to the cell surface. From there they may directly bind antigen at the cell surface, or access endosomal compartments through receptor-mediated internalization.

Figure 2. Overall structure of an MHCII/peptide complex

Presented is the structure of the human MHCII molecule HLA-DR3 in complex with CLIP. The orientation is such that the membrane distal α1 and β1 domains are located at the top, and the membrane proximal α2 and β2 domains are at the bottom. CLIP is presented in full atomic detail with carbon in yellow, nitrogen in blue and oxygen in red. The peptide interacts with the DR3 binding groove mainly through four residues (magenta asterisks). All known class II-associated peptides adopt a similar extended conformation, although peptides bound to I-A alleles tend to dip lower in the center of the binding groove relative to peptides bound to either I-E or HLA-DR alleles. Coordinates are from ref. 26. The model was visualized with PyMol (60).

Figure 3. Structural rearrangement of the MHC binding groove between peptide bound and peptide free states

Diagram of the DR1 binding site bound to HA (top panel) and in empty state (bottom panel). The figure is adapted from the model proposed in ref. 48. The N-terminal region of the binding site is expected to undergo the most significant modifications. In particular, the α50-59 region of DR is expected to fold into the amino-terminal end of the groove, taking the place of the bound peptide in the P1 to P4 region.

Figure 4. Thermodynamic model of peptide/MHCII complex formation and DM activity

Peptide binding can be envisaged as a folding process, quantifiable in terms of Cooperativity . The impact of cooperative effects on peptide affinity has been investigated applying the mutant cycle approach to the DR/HA system. Due tothe disruptive nature of the modifications, the observed Cooperativity can be interpreted as lack of folding. Cooperativity affects complex formation in an exponential fashion, indicating that disrupting interaction after interaction has an amplified effect on the ability of the complex to fold into a stable conformer. At the left side of the curve, an affinity range can be identified, for which null or little cooperativity can be measured (Compensatory Range, CR framed in the plot). The broader is this range, the greater is the ability of the system to compensate any lack of interactions (H-bonds, Hydrophobic or salt bridges) with the residual flexibility (phenomenon of entropy-enthalpy compensation). To the extent that DM interacts and destabilizes complexes featuring greater residual entropy, thus reducing the compensatory range for stable complexion, this approach may also be used to identify the susceptibility to DM of a complex on the basis of its thermodynamic profile.