The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles

Prion Proteins (PrP) are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species. Here, we perform a comprehensive principle components analysis (PCA) on the tertiary structures of PrP globular proteins to discern PrP subdomains that exhibit conformational change in response to point mutations and clade-specific evolutionary sequence mutation trends. This is to our knowledge the first such large-scale analysis of multiple NMR ensembles of protein structures, and the first study of its kind for PrPs. We conducted PCA on human (n = 11), mouse (n = 14), and wildtype (n = 21) sets of PrP globular structures, from which we identified five conformationally variable subdomains within PrP. PCA shows that different non-local patterns and rankings of variable subdomains arise for different pathogenic mutants. These subdomains may thus be key areas for initiating PrP conversion during disease. Furthermore, we have observed the conformational clustering of divergent TSE-non-susceptible species pairs; these non-phylogenetic clusterings indicate structural solutions towards TSE resistance that do not necessarily coincide with evolutionary divergence. We discuss the novelty of our approach and the importance of PrP subdomains in structural conversion during disease. Author Summary: Prion Proteins (PrP) cause a variety of incurable TSE diseases, and are among a small number of proteins for which large numbers of NMR ensembles have been resolved for sequence mutants and diverse species. Here, we perform a comprehensive PCA study to assess conformational variation and discern the landscape of the PrP structural response to sequence mutation. This is to our knowledge the first large-scale analysis of multiple NMR ensembles for a specific protein, and the first study to perform a multivariate PCA on the native globular structures of PrP. We conducted exhaustive PCA on three PrP subsets: human and mouse subsets that include structures of sequence mutants, and the set of wild-type PrP (16 PrP species). PCA shows that different non-local patterns of variable subdomains arise for different pathogenic mutants. These subdomains may thus be key areas for initiating PrP conversion during disease. Furthermore, we observed that some evolutionarily divergent species that are non-susceptible to TSEs have surprising structural similarities in their PrPs. We discuss the novelty of our approach with respect to prions, and the advantage of this analysis as a fast, reliable starting point to identify interesting domains that may warrant further experimental and computational analysis.