Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition.

Christopher Szeto,Demetra S M Chatzileontiadou,Hannah Sloane,Ashley M Buckle,Emma J Grant,Joseph I Bloom,Stephanie Gras,Dhilshan Jayasinghe,James Fodor,Christian A Lobos

doi:10.3390/ijms21197081

Abstract

The interaction between T cell receptor (TCR) and peptide (p)-Human Leukocyte Antigen (HLA) complexes is the critical first step in determining T cell responses. X-ray crystallographic studies of pHLA in TCR-bound and free states provide a structural perspective that can help understand T cell activation. These structures represent a static “snapshot”, yet the nature of pHLAs and their interactions with TCRs are highly dynamic. This has been demonstrated for HLA class I molecules with in silico techniques showing that some interactions, thought to stabilise pHLA-I, are only transient and prone to high flexibility. Here, we investigated the dynamics of HLA class II molecules by focusing on three allomorphs (HLA-DR1, -DR11 and -DR15) that are able to present the same epitope and activate CD4+ T cells. A single TCR (F24) has been shown to recognise all three HLA-DR molecules, albeit with different affinities. Using molecular dynamics and crystallographic ensemble refinement, we investigate the molecular basis of these different affinities and uncover hidden roles for HLA polymorphic residues. These polymorphisms were responsible for the widening of the antigen binding cleft and disruption of pHLA-TCR interactions, underpinning the hierarchy of F24 TCR binding affinity, and ultimately T cell activation. We expanded this approach to all available pHLA-DR structures and discovered that all HLA-DR molecules were inherently rigid. Together with in vitro protein stability and peptide affinity measurements, our results suggest that HLA-DR1 possesses inherently high protein stability, and low HLA-DM susceptibility.

Highlights

T cell-mediated immunity is dependent on the activation of CD4+ and CD8+ T cells, which are responsible for cytokine secretion and induction of apoptosis within infected cells [1]
We have used crystallographic ensemble refinement to investigate the structural flexibility of Human Leukocyte Antigen (HLA)-II molecules that could impact peptide presentation, stability of the pHLA-II complex as well as T cell recognition
We firstly focused on three HLA-DR molecules binding the same peptide, and expanded our analysis to 41 pHLA-DR complexes, for which structures were available

Summary

Introduction

T cell-mediated immunity is dependent on the activation of CD4+ and CD8+ T cells, which are responsible for cytokine secretion and induction of apoptosis within infected cells [1]. HLAs can present a vast range of peptides from both foreign and self-proteins recognised by T cells. This ensures that the immune system efficiently recognises a large range of infectious pathogens. The protein subunits that make up HLA class I (HLA-I, heavy α-chain and β2-microglobulin) and HLA class II molecules (HLA-II, αand β-chains) are different, they share similar secondary structures. Their main differences occur at the ends of the binding clefts, where both ends of the cleft are closed-off in HLA-I but open-ended in HLA-II. Other differences include the α1-helix of HLA-I molecules being continuous and spanning the length of the presented peptide [5], whereas, the α-helix of the HLA-II α-chain (residues 45–79) is discontinuous and possesses an N-terminal kink (residues 52–55), forming a short intermittent unstructured loop, which can stabilize protruding N-terminal residues (P-2 and P-1) [4]

Methods

Results

Conclusion