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.朊蛋白（PrP）是少数可针对其序列突变体及不同物种解析出大量核磁共振（NMR）结构集合的蛋白质之一。本研究针对球状朊蛋白的三级结构开展全面主成分分析（PCA），旨在识别出会响应点突变及进化枝特异性序列突变趋势而发生构象变化的朊蛋白亚结构域。据我们所知，这是首次针对蛋白质结构多组NMR集合开展的大规模此类分析，同时也是针对朊蛋白的同类首项研究。本研究对人类（n=11）、小鼠（n=14）及野生型（n=21）球状朊蛋白结构集合进行PCA分析，从中鉴定出朊蛋白内部5个构象可变的亚结构域。主成分分析结果显示，不同致病突变体对应着各异的可变亚结构域非局部模式与排序规则。因此，这些亚结构域可能是疾病进程中启动朊蛋白转化的关键区域。此外，本研究还观察到不同传染性海绵状脑病（TSE）非易感物种对的构象聚类现象；这类非系统发育聚类表明，赋予TSE抗性的结构解决方案未必与进化分化相契合。本研究讨论了本方法的创新性，以及朊蛋白亚结构域在疾病进程中结构转化的重要性。