Pathological aggregation and liquid-liquid phase separation of proteins associated with neurodegenerative diseases

doi:10.12211/2096-8280.2023-005

Abstract

Abstract:

Protein misfolding and aggregation are closely related to the development of neurodegenerative diseases. Their main pathological hallmark is protein inclusion bodies, whose major components are amyloid fibrils formed by abnormal protein aggregation. For example, Alzheimer's disease is related to the amyloid plaques formed by β-amyloid proteins and the neurofibrillary tangles formed by tubulin-associated unit (tau) proteins. The pathological feature of Parkinson's disease is Lewy bodies formed by aggregation of α-synuclein. In addition, recent studies have shown that a majority of neurodegenerative disease-related proteins including Tau, α-synuclein, and TDP-43 can undergo liquid-liquid phase separation to form liquid condensates or membrane-free organelles. These condensates are involved in a number of cellular physiological processes, such as regulating signal transduction. Pathological fibrosis and liquid-liquid phase separation are two forms of protein aggregation, and protein liquid-liquid phase separation may be a driving force for misaggregation and fibrosis. Disease-related mutations, post-translational modifications including truncations, acetylations, and phosphorylations, and microenvironments such as pH, ion strength, and temperature can promote or inhibit liquid-solid phase transitions and the formation of pathological fibrils. Uncovering molecular mechanism underlying pathological protein aggregation and liquid-liquid phase separation is crucial to understanding the pathogenic process and developing effective therapeutic drugs as well. This review focuses on recent progress in experimental and computational studies on the pathological aggregation and liquid-liquid phase separation of neurodegenerative disease-related proteins, including β-amyloid, α-synuclein, TDP-43, tau, and FUS proteins. We briefly introduce the application of experimental methods (nuclear magnetic resonance, X-ray diffraction, and cryo-electron microscopy) for studying protein aggregation and determining fibril structure with cutting-edge techniques (differential interference contrast and fluorescence recovering after photobleaching) to explore protein phase separation. Advances in the conformational ensemble of proteins using enhanced sampling methods such as replica-exchange molecular dynamics simulations, and studies of the phase behavior of proteins using field-theoretic simulation and multiscale simulations are summarized. Machine learning in predicting protein phase separation ability is also addressed.

Key words: neurodegenerative diseases, pathological aggregation, fibrillization, liquid-liquid phase separation, protein-protein interactions, molecular mechanism

摘要：

蛋白质的错误折叠和聚集与一系列神经退行性疾病密切相关，比如阿尔茨海默病、帕金森病等，其主要病理特征是以蛋白质异常聚集形成的淀粉样纤维为主要成分的包涵体。近期研究表明疾病相关蛋白大多能够发生液液相分离，形成动态可逆的液态凝聚物（亦称无膜细胞器），并参与细胞生理过程，而突变、翻译后修饰以及微环境等因素则能促进其发生不可逆液固相变形成病理性纤维。本文以几种神经退行性疾病相关蛋白为例，重点介绍蛋白质病理性聚集和液液相分离的实验研究方法和前沿进展，蛋白质相互作用、聚集和相分离微观机理的理论和计算研究，以及预测蛋白相分离能力的机器学习方法。这些研究对深入理解蛋白质病理性聚集、相变和相分离的微观机制，以及相关疾病致病机理具有重要的科学意义，并对治疗药物的设计和开发具有潜在应用价值。

关键词: 神经退行性疾病, 病理性聚集, 纤维化, 液液相分离, 蛋白质相互作用, 微观机理

CLC Number:

Q816

TANG Yiming, YAO Yifei, YANG Zhongyuan, ZHOU Yun, WANG Zichao, WEI Guanghong. Pathological aggregation and liquid-liquid phase separation of proteins associated with neurodegenerative diseases[J]. Synthetic Biology Journal, 2023, 4(3): 590-610.

唐一鸣, 姚逸飞, 杨中元, 周运, 王子超, 韦广红. 神经退行性疾病相关蛋白病理性聚集和液液相分离研究进展[J]. 合成生物学, 2023, 4(3): 590-610.

Figures/Tables 7

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蛋白质	相关疾病	相关文献
蛋白质	相关疾病	纤维化能力	相分离能力
β淀粉样蛋白(β-amyloid)	阿尔茨海默病	[11-12]	暂无报道
微管相关蛋白(Tau)	阿尔茨海默病、额颞叶痴呆、帕金森病	[13-14]	[8,15]
普里昂蛋白(Prion)	疯牛病、家族性致死性失眠症、羊瘙痒症、库鲁病	[16]	[17-18]
α-突触核蛋白(α-synuclein)	帕金森病	[19-20]	[5]
反式激活核酸结合蛋白-43(TDP-43)	肌萎缩侧索硬化症、额颞叶变性运动神经元疾病	[21]	[6]
融合肉瘤蛋白(FUS)	肌萎缩侧索硬化症、额颞叶痴呆	[22]	[23]
亨廷顿蛋白(Huntingtin)	亨廷顿病	[24-25]	[26-27]

蛋白质	相关疾病	相关文献
蛋白质	相关疾病	纤维化能力	相分离能力
β淀粉样蛋白(β-amyloid)	阿尔茨海默病	[11-12]	暂无报道
微管相关蛋白(Tau)	阿尔茨海默病、额颞叶痴呆、帕金森病	[13-14]	[8,15]
普里昂蛋白(Prion)	疯牛病、家族性致死性失眠症、羊瘙痒症、库鲁病	[16]	[17-18]
α-突触核蛋白(α-synuclein)	帕金森病	[19-20]	[5]
反式激活核酸结合蛋白-43(TDP-43)	肌萎缩侧索硬化症、额颞叶变性运动神经元疾病	[21]	[6]
融合肉瘤蛋白(FUS)	肌萎缩侧索硬化症、额颞叶痴呆	[22]	[23]
亨廷顿蛋白(Huntingtin)	亨廷顿病	[24-25]	[26-27]

实验方法	研究内容				参考文献
实验方法	解析空间结构	表征二级结构	表征空间形貌	表征蛋白内/间相互作用	参考文献
圆二色谱(CD spectra)	×	√	×	×	[33]
傅里叶红外光谱(FTIR)	×	√	×	×	[34]
ThT荧光光谱(ThT-FS)	×	√	×	×	[35]
扫描电子显微镜(SEM)	×	×	√	×	[36]
透射电子显微镜(TEM)	x	x	√	×	[37]
原子力显微镜(AFM)	×	×	√	×	[38]
微分干涉差显微镜(DIC)	×	×	√	×	[39]
固体核磁共振(ssNMR)	√	√	×	√	[40-41]
X射线衍射(XRD)	√	√	×	×	[42]
冷冻电镜(Cryo-EM)	√	√	×	×	[43]
化学交联质谱(XL-MS)	×	×	×	√	[44]
荧光共振能量转移(FRET)	×	×	×	√	[45]

实验方法	研究内容				参考文献
实验方法	解析空间结构	表征二级结构	表征空间形貌	表征蛋白内/间相互作用	参考文献
圆二色谱(CD spectra)	×	√	×	×	[33]
傅里叶红外光谱(FTIR)	×	√	×	×	[34]
ThT荧光光谱(ThT-FS)	×	√	×	×	[35]
扫描电子显微镜(SEM)	×	×	√	×	[36]
透射电子显微镜(TEM)	x	x	√	×	[37]
原子力显微镜(AFM)	×	×	√	×	[38]
微分干涉差显微镜(DIC)	×	×	√	×	[39]
固体核磁共振(ssNMR)	√	√	×	√	[40-41]
X射线衍射(XRD)	√	√	×	×	[42]
冷冻电镜(Cryo-EM)	√	√	×	×	[43]
化学交联质谱(XL-MS)	×	×	×	√	[44]
荧光共振能量转移(FRET)	×	×	×	√	[45]