Covarrubias, M. A. L. | Search bioRxiv

bioRxiv2022

InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires

B and T cell receptor repertoire data has the potential to fundamentally change the way we diagnose and treat a wide range of diseases. However, there are few resources for storing or analyzing repertoire data. InterClone provides tools for storing, searching, and clustering repertoire datasets. Efficiency is achieved by encoding the complementarity-determining regions of sequences as mmseqs2 databases. Single chain search or cluster results can be merged into paired (alpha-beta or heavy-light) results for analysis of single-cell sequencing data. We illustrate the use of InterClone with two recently reported examples: 1) searching for SARS-CoV-2 infection-enhancing antibodies in bulk COVID-19 and healthy donor repertoires; 2) identification of SARS-CoV-2 specific TCRs by clustering paired and bulk sequences from COVID-19, BNT162b2 vaccinated and healthy unvaccinated donors. The core functions of InterClone have been implemented as a web server and integrated database (https://sysimm.org/interclone). All source code is available upon request.

bioinformatics↗

bioRxiv2022

TCR binding to a peptide-MHC complex raises a drawbridge for CD3 cross-membrane signaling

In this study, we present an allosteric mechanism for T cell receptor (TCR) triggering upon binding a peptide-MHC complex (pMHC), in which a conformational change in the TCR upon pMHC binding controls the mobility of the CD3 proteins. We found that the TCR{beta} FG loop serves as a gatekeeper, preventing accidental triggering, while the connecting peptide acts as a hinge for essential conformational changes in the TCR. Atomistic simulations and cell-based experiments with genetically modified connecting peptides demonstrate that rigidified hinge residues result in excessive CD3 dynamics and hypersensitivity to pMHC binding. Our model thus provides a clear connection between extracellular TCR-pMHC binding and changes in CD3 dynamic that propagate from outside to inside the cell.

molecular biology↗