T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.

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Published in PLOS Computational Biology, v. 10, issue. 2, e1003478.

© 2014 Pierce et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Figure_S1.pdf (731 kB)
Structural variability of nonameric (AAG; cyan) and decameric (ELA; magenta) MART-1 peptides bound to wild-type DMF5 (from wild-type complex structures, PDB IDs 3QDJ and 3QDG). MHC and TCR colors are as in Figure 4; DMF5 residue αG28 is shown as spheres for reference.

Figure_S2.pdf (502 kB)
The high affinity DMF5 variants show no recognition of the Tax11–19 or gp100209(2M)-217 peptide/HLA-A2 complexes. a) Injections over a wild-type DMF5 surface. The main response shows injections of MART-126(27L)-35/HLA-A2, with the binding response indicated. The inset shows injections of gp100/HLA-A2 and Tax/HLA-A2 over the same surface, with no response at concentrations as high as 400 mM. b) Injections over a high affinity YW DMF5 surface. Injected pMHC is as in panel a. c) Injections over a high affinity WW DMF5 surface. Injected pMHC is as in panel a.

Figure_S3.pdf (577 kB)
Electron density for βW98 (gold) and αY26 (purple) in the YW-ELA/HLA-A2 crystal structure contoured at 1σ calculated from an unbiased, iterative-build OMIT map. The density shows the clear, unambiguous positioning of the two mutated residues.

Figure_S4.pdf (393 kB)
Predictions from ZAFFI 1.1 compared with measured ΔΔGs for DMF5 point mutants binding to ELA/HLA-A2 (solid circles) and AAG/HLA-A2 (empty triangles). Best fit line and correlation are given; the four true negative outlier points omitted from Figure 3 are omitted here as well.

Figure_S5.pdf (616 kB)
Comparison of mutant TCR αD26Y residue in the YW-ELA/HLA-A2 complex with the corresponding mutant position (αD27F) in the α24β17-ELA/HLA-A2 complex. Complexes were superposed by fitting pMHC backbone atoms. The mutant αD27F is shown in orange sticks, ELA peptide from α24β17-ELA/HLA-A2 in pink sticks, and all other colors are as in Figure 4.

Table_S1.pdf (11 kB)
DMF5 mutant predictive performance for additional tested packing protocols.

Table_S2.pdf (48 kB)
X-ray data collection and refinement statistics for the crystal structure of the DMF5 αD26Y/βL98W - ELA/HLA-A2 complex.

Table_S3.pdf (25 kB)
Contacts between mutant DMF5 residues and ELA/HLA-A2.

Table_S4.pdf (40 kB)
Correlations with measured values and corresponding p-values for HB36 and HB80 mutants.