Spagnolli Giovanni, Rigoli Marta, Novi Inverardi Giovanni, Codeseira Yaiza B, Biasini Emiliano, Requena Jesús R
Department of Cellular, Computational and Integrative Biology, Centre for Integrative Biology, University of Trento, Trento, Italy.
Dulbecco Telethon Institute, University of Trento, Trento, Italy.
Front Bioeng Biotechnol. 2020 Oct 6;8:590501. doi: 10.3389/fbioe.2020.590501. eCollection 2020.
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 infectious conformer, PrP through deformed templating. The process can take many rounds of replication (if taking place ) or even several passages of the evolving PrP conformers through successive brains if , 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 PrP 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 PrP 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 PrP 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 PrP. 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.
畸形模板化是指具有特定交叉β折叠模式的自我复制蛋白质构象能够引发形成具有不同交叉β折叠模式的另一种自我复制状态的过程。具体而言，无感染性但具有传播性的朊蛋白淀粉样蛋白可以通过畸形模板化转化为感染性构象体PrP。如果通过实验性传播，这个过程可能需要多轮复制（如果发生的话），甚至需要进化的PrP构象体在连续的大脑中经过多次传代。在所有情况下，畸形模板化都涉及一种强制转化，其中模板与底物和/或模板化环境之间存在不匹配，通常是重组朊蛋白淀粉样蛋白，它在变性条件下（例如，存在离液剂）能够转化重组朊蛋白，而在生理转化条件下遇到糖基化的、糖基磷脂酰肌醇锚定的朊蛋白底物。畸形模板化的特征是出现中间构象体，其表现出的生化特征介于初始朊蛋白淀粉样蛋白和最终朊蛋白构象体之间。在此，我们利用了最近通过冷冻电镜对朊蛋白淀粉样蛋白结构的阐明以及我们最近提出的一个物理上合理的朊蛋白原子模型。使用建模和分子动力学（MD）方法，我们构建了一个完整的畸形模板化分子模型，包括一个糖基化中间构象体的原子模型和一个改进的朊蛋白模型。在其他意外结果中我们的结果表明，完全糖基化的朊蛋白可以对齐堆叠，以及4梯级β-螺线管（4RβS）朊蛋白结构如何能与平行对齐的分子间片层（PIRIBS）朊蛋白淀粉样蛋白共享关键结构基序。我们的结果揭示了朊病毒复制的机制。
