多肽协同作用下淀粉样成核的粗粒化模拟
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1.浙江大学工程力学系;2.中国科学院大学物理科学学院

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Cooperative effects of β-propensity of peptides on amyloid nucleation
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    摘要:

    摘要:目的 针对淀粉样多肽系统,探究考虑了协同作用的多肽构象转变能力对多肽成核及相关产物的影响。 方法 基于淀粉样多肽的两态(可溶态和β纤维化态)粗粒化模型,分别考虑协同作用(局域浓度)对多肽构象转变能力的两种影响(抑制和促进构象转变),通过蒙特卡罗模拟,探讨多肽间协同作用对淀粉样成核的调控。 结果 对于协同作用抑制多肽构象转变的情况,淀粉样成核只在一定多肽浓度区间内、具有特定大小的寡聚体内才易发生,且出现“通路寡聚体”和“非通路寡聚体”共存的现象;而对于协同作用促进多肽构象转变的情况,观察到即使在很低的浓度下(~4 μM,这也是体外实验所能观察到的多肽纤维化的最低浓度),体系仍然可以形成原纤维。这是国际上首次在模拟中观察到如此低的浓度下多肽可以纤维化。 结论 引入局域浓度对淀粉样多肽构象转变的影响,使多肽的粗粒化模型更加接近真实情况,观察到一些此前未见报道的新奇现象。本论文有助于人们更好地理解淀粉样多肽的纤维化机制,并有望为面向神经退行性疾病的治疗策略,提供理论借鉴。

    Abstract:

    Objective With the inclusion of cooperative effects, we investigate the β-propensity of amyloidogenic peptides (and proteins) on amyloid nucleation. Methods Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic peptides containing two states, i.e., a soluble state and a β-prone state (denoted by s and β state, respectively), we investigate how β-propensity of peptides affect amyloid nucleation, under the considerations of two classes of cooperative effects – the existence of surrounding peptides “inhibiting” and “promoting”, respectively, the peptide’s s-to-β conformational conversion. Results In the “inhibiting” case, amyloid nucleation occurs only within a certain interval of the peptide concentration, and occurs inside the oligomers with certain sizes. Besides, we observed the coexistence of on-pathway and off-pathway oligomers. In the “promoting” case, we observed, for the first time to our knowledge, amyloid nucleation at a peptide concentration as low as ~4 μM, which is the lowest nucleation concentration found in experiments (in vitro). Conclusions In this study, we develop a more realistic model for amyloidogenic peptides (and proteins) by introducing surrounding-monomer-dependent β-propensity of peptides. Using this model, we observe some intriguing phenomena not reported in previous simulations. Our findings not only improve current understandings of the mechanism of amyloid formation, but also provide useful insights into the therapeutic strategies for curing neurodegenerative diseases.

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  • 收稿日期:2022-10-14
  • 最后修改日期:2022-11-17
  • 录用日期:2022-11-18
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