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PLoS Comput Biol. 2012;8(8):e1002646. doi: 10.1371/journal.pcbi.1002646. Epub 2012 Aug 9.

The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles.

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1
Department of Biology, McGill University, Montreal, Quebec, Canada.

Abstract

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.

PMID:
22912570
PMCID:
PMC3415401
DOI:
10.1371/journal.pcbi.1002646
[Indexed for MEDLINE]
Free PMC Article
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