Previously Hidden Dynamics at the TCR-pMHC Interface Revealed

A structural characterization of the interaction between αβT cell receptors (TCR) and cognate peptide-MHC (pMHC) is central to understanding adaptive T cell mediated immunity. X-ray crystallography, although the source of much structural data, traditionally provides only a static snapshot of the protein. Given the emerging evidence for the important role of conformational dynamics in protein function, we interrogated 309 crystallographic structures of pMHC complexes using ensemble refinement, a technique that can extract dynamic information from the X-ray data. We found that a large number of systems contain significant conformational plasticity that confounds, and in some cases overturns, previous functional interpretations that were based on a single static structure. Notable examples include the interpretation of differences in the disease association of HLA subtypes, the relationship between peptide prominence and TCR recognition, the role of conformational flexibility in vaccine design, and discriminating between induced fit and conformational selection models of TCR binding. We show that the currently widespread practise of analyzing pMHC interactions via the study of a single crystallographic structure fails to properly distinguish real results from noise, and argue that biological observations should be explained through the properties of ensembles rather than isolated structures, as these are less prone to observer bias. This new analysis therefore not only raises significant questions regarding the interpretation of decades of structural data, but also provides previously missing information concerning the dynamics of existing characterized TCR-pMHC interactions.