Kumar Naresh, Khatua Prabir, Sinha Sudipta Kumar
Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University) Bengaluru 562163 India.
Chem Sci. 2024 Mar 19;15(16):6095-6105. doi: 10.1039/d4sc00103f. eCollection 2024 Apr 24.
The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to offer a strategy to combat Alzheimer's disease. We investigate local heating and crowding effects on Aβ disintegration by selectively heating key Aβ segments and varying the concentration of sodium dodecyl sulphate (SDS), respectively. Despite initiation of disruption, Aβ aggregates resist complete disintegration during local heating due to rapid thermal energy distribution to the surrounding water. Conversely, although SDS molecules effectively inhibit Aβ aggregation at higher concentration through micelle formation, they fail to completely disintegrate the aggregate due to the exceedingly high energy barrier. To address the sampling challenge posed by the formidable energy barrier, we have performed well-tempered metadynamics simulations. Simulations reveal a multi-step disintegration mechanism for the Aβ octamer, suggesting a probable sequence: octamer → pentamer/hexamer ⇌ tetramer → monomer, with a rate-determining step constituting 45 kJ mol barrier during the octamer to pentamer/hexamer transition. Additionally, we have proposed a novel two-state mean-field model based on Ising spins that offers an insight into the kinetics of the Aβ growth process and external perturbation effects on disintegration. Thus, the current simulation study, coupled with the newly introduced mean-field model, offers an insight into the detailed mechanisms underlying the Aβ aggregation process, guiding potential strategies for effective disintegration of Aβ aggregates.
本研究采用分子动力学模拟和理论模型相结合的方法,探索成熟的Aβ八聚体的潜在解体机制,旨在提供一种对抗阿尔茨海默病的策略。我们分别通过选择性加热关键Aβ片段和改变十二烷基硫酸钠(SDS)浓度,研究局部加热和拥挤效应对Aβ解体的影响。尽管引发了破坏,但由于热能迅速分布到周围的水中,Aβ聚集体在局部加热过程中抵抗完全解体。相反,尽管SDS分子在较高浓度下通过形成胶束有效地抑制Aβ聚集,但由于极高的能垒,它们未能完全分解聚集体。为了解决由巨大能垒带来的采样挑战,我们进行了加权元动力学模拟。模拟揭示了Aβ八聚体的多步解体机制,表明可能的顺序为:八聚体→五聚体/六聚体⇌四聚体→单体,在八聚体向五聚体/六聚体转变过程中,速率决定步骤构成45 kJ mol的能垒。此外,我们基于伊辛自旋提出了一种新颖的两态平均场模型,该模型深入了解了Aβ生长过程的动力学以及外部扰动对解体的影响。因此,当前的模拟研究与新引入的平均场模型相结合,深入了解了Aβ聚集过程背后的详细机制,为有效分解Aβ聚集体的潜在策略提供了指导。