Deformed templating is the process by which self-replicating protein conformations with a given cross-β folding pattern can seed formation of an alternative self-replicating state with different cross-β folding pattern. In particular, uninfectious but propagative PrP amyloid can transform into a bona fide infectious conformer, PrPSc through deformed templating. The process can take many rounds of replication (if taking place in vitro) or even several passages of the evolving PrP conformers through successive brains if in vivo, through experimental transmission. In all cases, deformed templating involves a forced conversion in which there is a mismatch between the template and the substrate and/or the templating environment, typically a recombinant PrP amyloid, adept at converting recombinant PrP under denaturing conditions (e.g., presence of chaotropic agents), encountering a glycosylated, GPI-anchored PrPC substrate under physiological conversion conditions. Deformed templating is characterized by emergence of intermediate conformers that exhibit biochemical characteristics that are intermediate between those of the initial PrP amyloid and the final PrPSc conformers. Here, we took advantage of the recent elucidation of the structure of a PrP amyloid by cryo-EM and the availability of a physically plausible atomistic model of PrPSc that we have recently proposed. Using modeling and Molecular Dynamics (MD) approaches, we built a complete molecular modelization of deformed templating, including an atomistic model of a glycosylated intermediate conformer and a modified model of PrPSc. Among other unanticipated outcomes, our results show that fully glycosylated PrP can be stacked in-register, and how 4-rung β-solenoid (4RβS) PrP architectures can share key structural motifs with parallel-in register intermolecular sheet (PIRIBS) PrP amyloids. Our results shed light on the mechanisms of prion replication.

中文翻译：

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通过变形模板对 PrPSc 生成进行建模

变形模板是具有给定交叉β折叠模式的自我复制蛋白质构象可以种子形成具有不同交叉β折叠模式的替代自我复制状态的过程。特别是，无感染性但可繁殖的 PrP 淀粉样蛋白可以通过变形模板转化为真正具有感染性的构象异构体 PrPSc。该过程可能需要多轮复制（如果发生在体外），甚至在体内，通过实验传输，进化的 PrP 构象异构体可以通过连续的大脑进行多次传递。在所有情况下，变形模板都涉及强制转化，其中模板与底物和/或模板环境之间存在错配，通常是重组 PrP 淀粉样蛋白，擅长在变性条件下转化重组 PrP（例如，离液剂的存在），在生理转化条件下遇到糖基化的、GPI 锚定的 PrPC 底物。变形模板的特征在于中间构象异构体的出现，这些构象呈现出介于初始 PrP 淀粉样蛋白和最终 PrPSc 构象异构体之间的生化特征。在这里，我们利用了最近通过冷冻电镜对 PrP 淀粉样蛋白结构的阐明以及我们最近提出的物理上合理的 PrPSc 原子模型的可用性。使用建模和分子动力学 (MD) 方法，我们构建了变形模板的完整分子模型，包括糖基化中间体构象异构体的原子模型和 PrPSc 的修改模型。在其他意想不到的结果中，我们的结果表明，完全糖基化的 PrP 可以对齐堆叠，以及 4 级 β-螺线管 (4RβS) PrP 架构如何与平行对齐的分子间片 (PIRIBS) PrP 淀粉样蛋白共享关键结构基序。我们的结果阐明了朊病毒复制的机制。