物理化学学报 >> 2017, Vol. 33 >> Issue (9): 1905-1914.doi: 10.3866/PKU.WHXB201704274

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ZAβ3和Aβ16-40亲和作用的分子机理解析

刘夫锋1,2,3,4,范玉波1,刘珍1,白姝1,*()   

  1. 1 天津大学化工学院生物工程系,天津300072
    2 工业发酵微生物教育部重点实验室,天津300457
    3 代谢控制发酵技术国家地方联合工程实验室,天津300457
    4 天津科技大学生物工程学院,天津300457
  • 收稿日期:2017-01-26 发布日期:2017-07-05
  • 通讯作者: 白姝 E-mail:sbai@tju.edu.cn
  • 基金资助:
    国家自然科学基金(21576199)

Molecular Mechanism Underlying Affinity Interactions between ZAβ3 and the Aβ16-40 Monomer

Fu-Feng LIU1,2,3,4,Yu-Bo FAN1,Zhen LIU1,Shu BAI1,*()   

  1. 1 Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
    2 Key Laboratory of Industrial Fermentation Microbiology Ministry of Education, Tianjin 300457, P. R. China
    3 National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, P. R. China
    4 College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
  • Received:2017-01-26 Published:2017-07-05
  • Contact: Shu BAI E-mail:sbai@tju.edu.cn
  • Supported by:
    the National Natural Science Foundation of China(21576199)

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摘要：

淀粉样多肽（amyloid-β peptide，Aβ）聚集是引起阿尔兹海默症（Alzheimer's disease，AD）的主要原因。开发Aβ聚集抑制剂是治疗AD的最有效手段之一。利用噬菌体展示技术筛选出来的ZAβ3蛋白质能够有效抑制Aβ聚集，但ZAβ3和Aβ之间的作用区域和关键氨基酸残基尚不清楚。针对此问题，本研究利用分子动力学模拟、MM-PBSA自由能计算和分解方法研究了ZAβ3-Aβ16-40复合物之间的相互作用机制。结果表明，ZAβ3的β-股和Aβ16-40之间的亲和作用占主导，而ZAβ3的α-螺旋贡献很小。利用分子力学-帕松波尔茨曼溶剂可及化表面积方法（MM-PBSA）自由能分解发现ZAβ3的热点残基为E15、I16、V17、Y18、L19、P20、N21和L22，而Aβ16-40的热点残基为F19、F20、A21、E22、D23、K28、I31、I32、G33、L34、M35、V36、G38和V40。ZAβ3通过将发夹型Aβ单体包埋在α-螺旋围成的疏水性腔体内来阻碍Aβ聚集。这种结合模式为设计高效的Aβ蛋白质类抑制剂提供了三个基本要素：高亲和性的结合片段（β-股）、附属结构（α-螺旋）和通过二硫键形成的稳定构象。高亲和性结合片段能竞争性地与Aβ单体结合，附属结构α-螺旋可以阻碍其它Aβ单体靠近，而稳定的构象是上述两种要素发挥作用的基础，三者协同作用可以有效地抑制Aβ聚集。

关键词: 蛋白质抑制剂, 淀粉质蛋白质, 分子动力学模拟, 自由能分解, 亲和机理

Abstract:

Alzheimer's disease (AD) is mainly caused by the aggregation of amyloid-β (Aβ) protein. Development of inhibitors to prevent Aβ aggregation is the most efficient method to devise a cure for AD. Aβ aggregation has been found to be inhibited by the affibody protein ZAβ3, selected via phage display. However, the molecular basis of affinity interactions between Aβ and ZAβ3, the interaction region, and important residues of Aβ and ZAβ3 remain unclear. Herein, molecular dynamics simulations and free energy calculation and decomposition using the molecular mechanics-Poisson-Boltzmann surface area method (MM-PBSA) were coupled to investigate the molecular mechanism underlying interactions between Aβ and ZAβ3. Interactions between the β-strand of ZAβ3 and Aβ16-40 were found to contribute greatly to their binding free energy, while that between the α-helix of ZAβ3 and ZAβ3 has a smaller contribution. Based on the free energy decomposition, hotspot residues of ZAβ3 are E15, I16, V17, Y18, L19, P20, N21, and L22 and those of Aβ16-40 include F19, F20, A21, E22, D23, K28, I31, I32, G33, L34, M35, V36, G38, and V40. ZAβ3 stabilizes the β-sheet by burying the two mostly nonpolar faces of the Aβ hairpin within a large hydrophobic tunnel-like cavity formed by the α-helix. The identified binding motif can be used as a starting point for rational design of protein inhibitors with high affinity for Aβ to prevent Aβ aggregation. The three key characteristics of efficient protein inhibitors are the presence of a high-affinity site (β-strand), a large accessory structure (α-helix), and a stable conformation owing to disulfide bonds. The high-affinity site can competitively bind to the Aβ monomer, and the large accessory structure can block other Aβ monomers; both these elements require a stable conformation via disulfide bonds. These three characteristics of a protein inhibitor can be employed together to suppress Aβ aggregation.

Key words: Protein inhibitor, Amyloid-β protein, Molecular dynamics simulation, Free energy decomposition, Molecular mechanism