Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent ‘snapshots’ and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6–9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into ‘scanning’ mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.未结合肽段与结合肽段的肽-MHC复合物（peptide-MHC, pMHC）的晶体结构，为T细胞受体（T cell receptor, TCR）的识别提供了结构基础，但这些结构仅为静态快照，难以全面揭示可能对相互作用及T细胞活化至关重要的动态过程。人类白细胞抗原（Human Leukocyte Antigen, HLA）-B*3501与HLA-B*3508均可结合13聚体病毒肽段LPEP，但仅HLA-B*3508-LPEP复合物可诱导以优势TCR克隆型SB27为特征的细胞毒性T淋巴细胞（cytotoxic T lymphocyte, CTL）应答。HLA-B*3508-LPEP与SB27可形成紧密且稳定持久的复合物，而HLA-B*3501-LPEP与SB27的相对较弱相互作用则无法触发免疫应答。HLA-B*3501与HLA-B*3508仅在α2螺旋上存在一个氨基酸残基差异（L/R156），但该差异并未改变MHC分子或肽段的结构，且该多态性残基亦不与肽段或SB27发生相互作用。由于无法通过晶体结构对TCR识别的差异给出结构层面的合理解释，我们对两种pMHC复合物以及与SB27结合的HLA-B*3508-LPEP开展了分子动力学（Molecular Dynamics, MD）研究。研究结果显示，相较于HLA-B*3508，HLA-B*3501中肽段的柔性显著更高——这一特征仅通过晶体结构无法观测到——其在SB27识别过程中可能发挥了未被充分重视的作用。T细胞受体在肽段残基6-9的上方发生枢转运动，并形成超出晶体结构中观测到的接触范围的短暂MHC分子相互作用。因此，分子动力学研究揭示了SB27的扫描机制，该机制拓展了种系编码的互补决定区2α（Complementarity Determining Region 2α, CDR2α）与互补决定区2β（Complementarity Determining Region 2β, CDR2β）环的功能。本研究数据与pMHC-LPEP-SB27相互作用的大量实验观测结果一致，并提供了晶体学方法无法获取的额外认知。