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

doi:10.12211/2096-8280.2023-005

合成生物学 ›› 2023, Vol. 4 ›› Issue (3): 590-610.DOI: 10.12211/2096-8280.2023-005

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

唐一鸣, 姚逸飞, 杨中元, 周运, 王子超, 韦广红

复旦大学物理学系，表面物理国家重点实验室，计算物质科学教育部重点实验室，上海 200438

收稿日期:2023-01-12 修回日期:2023-03-28 出版日期:2023-06-30 发布日期:2023-07-05
通讯作者: 韦广红
作者简介:唐一鸣（1994—），男，博士后。研究方向为神经退行性疾病相关蛋白液液相分离的分子动力学模拟。 E-mail：ymtang@fudan.edu.cn
韦广红（1969—），女，教授，博士生导师。研究方向为短肽纳米结构自组装，神经退行性疾病相关蛋白的构象分布、聚集和相分离微观机理的计算模拟。 E-mail：ghwei@fudan.edu.cn
基金资助:
国家自然科学基金(12074079)

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

Yiming TANG, Yifei YAO, Zhongyuan YANG, Yun ZHOU, Zichao WANG, Guanghong WEI

Department of Physics，State Key Laboratory of Surface Physics，and Key Laboratory of Computational Physical Sciences （Ministry of Education），Fudan University，Shanghai 200438，China

Received:2023-01-12 Revised:2023-03-28 Online:2023-06-30 Published:2023-07-05
Contact: Guanghong WEI

摘要/Abstract

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

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

中图分类号:

Q816

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.

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

图/表 7

表1 代表性神经退行性疾病相关蛋白的聚集和相分离能力

Table 1 Aggregation and phase separation of proteins associated with neurodegenerative diseases

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]

表2 研究蛋白质病理性聚集的主要实验方法

Table 2 Major experimental methods for studying protein pathological aggregation

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]

图1 神经退行性疾病相关的五种蛋白的氨基酸组成和代表性纤维结构

Fig. 1 Amino acid composition and fibril structures of neurodegenerative disease-related proteins

图2 神经退行性疾病相关的四种蛋白的单体、淀粉样纤维和共聚集形成的异质凝聚体［84-87］

Fig. 2 Monomer conformations, amyloid fibrils of proteins related to neurodegenerative diseases and their heterogeneous aggregates[84-87]

图3 通过计算模拟研究蛋白质相互作用及病理性聚集的流程图

Fig. 3 Flow sheet for studying protein interactions and pathological aggregation by computational simulation

图4 无膜细胞器与蛋白质通过液液相分离形成的小液滴［4-6，9，106，110-115］

Fig. 4 Membrane-free organelles and liquid droplets formed by liquid-liquid phase separation of proteins[4-6,9,106,110-115]

图5 研究蛋白质液液相分离的相关计算模拟方法［155，157，159，171，175-176］

Fig. 5 Computational methods for studying protein liquid-liquid phase separation[155,157,159,171,175-176]

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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

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

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