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Activated T cells secrete interferon-γ, which triggers intracellular tryptophan shortage by upregulating the indoleamine 2,3-dioxygenase 1 (IDO1) enzyme 1-4 . Here we show that despite tryptophan depletion, in-frame protein synthesis continues across tryptophan codons. We identified tryptophan-to-phenylalanine codon reassignment (W>F) as the major event facilitating this process, and pinpointed tryptophanyl-tRNA synthetase (WARS1) as its source. We call these W>F peptides 'substitutants' to distinguish them from genetically encoded mutants. Using large-scale proteomics analyses, we demonstrate W>F substitutants to be highly abundant in multiple cancer types. W>F substitutants were enriched in tumours relative to matching adjacent normal tissues, and were associated with increased IDO1 expression, oncogenic signalling and the tumour-immune microenvironment. Functionally, W>F substitutants can impair protein activity, but also expand the landscape of antigens presented at the cell surface to activate T cell responses. Thus, substitutants are generated by an alternative decoding mechanism with potential effects on gene function and tumour immunoreactivity., (© 2022. The Author(s).)

Accurate prediction of electrostatic effects on catalytic activity is an essential component of protein design. Site-directed mutagenesis of charged groups in subtilisin of Bacillus amyloliquefaciens has provided experimental measurements of electrostatic interactions which may be used to test such theoretical methods. The pKa of the histidine of the active site has been perturbed by +0.08 to -1.0 units by modifying one or two residues. Electrostatic effects in proteins can be modelled by the algorithm of Warwicker and Watson, which uses classical electrostatics and considers both the charge position and the shape of the molecule. Here we report that the algorithm can model several pKa shifts in subtilisin to fair accuracy.

In principle, it is possible to predict theoretically the three-dimensional structure of a protein from its amino acid sequence. Recently substantial progress towards this goal has been made by the use of simple models to represent protein conformation and interatomic interactions, together with the knowledge gained form analyses of know protein structures.

Analysis of beta-sheet sandwiches (for example immunoglobulin domains) suggests an algorithm that successfully predicts the tertiary fold of these proteins from their sequence and secondary structure. We propose tertiary structures for beta 2-microglobulin and an HLA-B7 antigen fragment. Topological rules are presented that markedly reduce the number of folds for proteins in which a-helices pack against a parallel beta-sheet.