The AlphaFold protein structure prediction network can be specialized for T cell receptor docking, leading to improved models of ternary complexes and some ability to discriminate correct from incorrect peptide epitopes.
High-throughput sequencing of the memory T cell receptor repertoire and machine learning can predict robust antibody and CD4 T cell response to de novo hepatitis B vaccine.
Adjuvants, MPLA and CpG especially, modulate the peptide repertoires presented on the surface of APCs, preferring the presentation of low-affinity exogenous peptides rather than high-affinity peptides.
Christopher T Boughter, Marta T Borowska ... Erin J Adams
A new software developed for high-throughput antibody, T cell receptor, and MHC repertoire analysis uncovers neutrality of the binding interface and intramolecular crosstalk as distinguishing properties of polyreactive antibodies.
Michael B Winter, Florencia La Greca ... Charles S Craik
Divergence in immunoproteasome substrate specificity and regulation from the constitutive proteasome impacts peptide cleavage quantity and the cellular capacity of the ubiquitin-proteasome system.
HIV vaccine-induced binding and neutralizing antibody epitope specificities were mapped at high resolution directly from polyclonal sera, overcoming shortcomings in traditional serum mapping approaches and enabling highly detailed vaccine design.
Barbara Bravi, Andrea Di Gioacchino ... Rémi Monasson
An interpretable machine learning approach can recapitulate the molecular features associated to immune protein-protein binding and leverage them for the prediction of immune response specificity.
Casey K Hua, Albert T Gacerez ... Chris Bailey-Kellogg
The combination of computational modeling and protein design can reveal key determinants of antibody–antigen binding and optimize small sets of antigen variants for efficient experimental localization of epitopes.
Thuy-Lan V Lite, Robert A Grant ... Michael T Laub
A generalizable approach to understanding the logic of molecular recognition reveals the contributions of individual residues to the specificity of protein-protein interactions.
Helle Rus Povlsen, Amalie Kai Bentzen ... Morten Nielsen
A bioinformatics approach shows how to reduce noise in single-cell TCR-pMHC specificity data while retaining sensitivity toward cross-binding events to facilitate investigation of the rules governing TCR-pMHC binding.
