Conserved Biophysical Compatibility Among the Highly Variable Germline-Encoded Regions Shapes TCR-MHC Interactions

Abstract

T cells are critically important components of the adaptive immune system primarily responsible for identifying and responding to pathogenic challenges. This antigen recognition is based on the interaction between membrane-bound T cell receptors (TCRs) and peptides presented on major histocompatibility complex (MHC) molecules. The formation of the TCR-peptide-MHC complex (TCR-pMHC) can be broken into two types of interactions, one between the hypervariable TCR CDR3α/β loops and the presented peptide and the second between germline encoded regions of the TCR and MHC. Experimental investigation of the latter interaction, mediated by the CDR1 and CDR2 loops of αβ TCRs, has been historically difficult. To address this prominent gap in our knowledge, we analyzed every possible germline-encoded TCR-MHC contact in humans, thereby generating the first comprehensive characterization of these antigen independent interactions. Our analysis shows that germline-encoded TCR-MHC interactions that are conserved at the sequence level are rare due to the exceptional diversity of the TCR CDR1 and CDR2 loops. Instead, binding properties such as the docking orientation are defined by regions of biophysical compatibility between these loops and the MHC surface. We further find that TCR genes which encode CDR loops with low potential to interact with MHC are over-represented in autoimmune contexts.

An Integrated Approach to the Characterization of Immune Repertoires Using AIMS: An Automated Immune Molecule Separator

“…The exact encoding scheme adopted varies across the available analysis modes for each molecular species. Among TCR-peptide-MHC complexes, the interaction interface is strikingly similar, with crystal structures consistently finding nearly identical docking angles between the two [37, 40–44]. TCRs contact the peptide and the MHC α -helices via their six complementarity determining region (CDR) loops, which are in turn connected via stem regions to their well conserved framework regions.…”

“…AIMS was developed specifically as an interpretable tool for immune repertoire analysis, capable of utilizing the information provided by conserved structural features of immune molecules for unique analytical approaches while reducing the potential for errors arising from insufficient resolution offered by structural predictions. The generality of the AIMS analysis pipeline allows for the simultaneous characterization of all adaptive immune molecules, including peptides, conserved viral structures, antibodies [36], MHC molecules [37], T cell receptors, and broadly any protein subset with structurally conserved features and localized diversity [38]. Currently the standard AIMS pipeline analyzes each of these molecular subsets individually, and subsequently allows users to compare and contrast biophysical features of paired TCR-pMHC or antibody-antigen interactions.…”

“…Importantly, this bulge alignment can also be applied to TCR and antibody sequences, putting more focus on their conserved stem regions. AIMS is capable of analyzing other molecules with conserved structural features and localized interfacial heterogeneity, including antibodies [36], MHC and MHC-like molecules [37], and, more generally, any molecular subset that can be successfully aligned using existing multisequence alignment software [38]. Antibody sequences can be treated in the same manner as TCRs due to their structural similarity, adopting as a default a central alignment scheme (Fig.…”

“…AIMS is capable of analyzing other molecules with conserved structural features and localized interfacial heterogeneity, including antibodies [36], MHC and MHC-like molecules [37], and, more generally, any molecular subset that can be successfully aligned using existing multi-sequence alignment software [38] (Fig. S2).…”

An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator

“…While the initial input and encoding of sequences into AIMS is different for each of the distinct molecular classes of immune repertoires, the downstream analysis is identical and allows for cross-receptor comparisons and the identification of patterns in the corresponding trends of interacting molecules. The application of AIMS for targeted investigations of specific biological systems has been previously described [36][37][38]. Here, we outline applications of the software to each immune repertoire class with a specific focus on the software's integrated analytical capabilities for cross-repertoire analyses.…”