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白内障致病突变对 αA-晶体蛋白的影响:一种计算方法。

Influence of Cataract Causing Mutations on αA-Crystallin: A Computational Approach.

机构信息

Department of Bioinformatics, Pondicherry University, Pondicherry, 605014, India.

出版信息

Protein J. 2024 Dec;43(6):1045-1069. doi: 10.1007/s10930-024-10239-4. Epub 2024 Nov 1.

DOI:10.1007/s10930-024-10239-4
PMID:39485632
Abstract

The αA-crystallin protein plays a vital role in maintaining the refractive index and transparency of the eye lens. Significant clinical studies have emerged as the αA-crystallin is prone to aggregation, resulting in the formation of cataracts with varied etiologies due to mutations. This work aims to comprehend the structural and functional role of cataract-causing mutations in αA-crystallin, particularly at N-Terminal and α-Crystallin Domains, using in-silico approaches including molecular dynamics simulation. About 19 mutants of αA-crystallin along with native structure were simulated for 100 ns and the post-simulations analyses reveal pronounced dynamics of αA-crystallin due to the enhanced structure flexibility as its native compactness was lost and is witnessed mainly by the mutants R12L, R21L, R21Q, R54L, R65Q, R116C and R116H. It is observed that αA-crystallin discloses the NTD motions as the dominant one and the same was endorsed by the linear variation between Rg and the center-of-mass of αA-crystallin. Interestingly, such enhanced dynamics of αA-crystallin mutants associated with the structure flexibility is internally modulated by the dynamic exchange of secondary structure elements β-sheets and coils (R = 0.619) during simulation. Besides, the observed pronounced dynamics of dimer interface region (β3-L6-β4 segment) of ACD along with CTD dynamics also gains importance. Particularly, the highly dynamic mutants are also characterized by enhanced non-covalent and hydrophobic interactions which renders detrimental effects towards its stability, and favours possible protein unfolding mechanisms. Overall, this study highlights the mutation-mediated structural distortions in αA-crystallin and demands the need for further potential development of inhibitors against cataract formation.

摘要

αA-晶体蛋白在维持眼睛晶状体的折射率和透明度方面起着至关重要的作用。由于突变,αA-晶体蛋白容易聚集,导致各种病因的白内障形成,因此出现了大量重要的临床研究。这项工作旨在通过包括分子动力学模拟在内的计算方法,理解导致白内障的αA-晶体蛋白突变的结构和功能作用,特别是在 N 端和α-晶体蛋白结构域。对 19 种αA-晶体蛋白突变体及其天然结构进行了 100ns 的模拟,模拟后的分析表明,由于增强了结构的灵活性,αA-晶体蛋白的动力学明显增强,其天然的紧凑性丧失,这主要是由于突变体 R12L、R21L、R21Q、R54L、R65Q、R116C 和 R116H 引起的。观察到αA-晶体蛋白揭示了 NTD 运动是主要的运动,这同样得到了 Rg 和αA-晶体蛋白质心之间的线性变化的支持。有趣的是,这种与结构灵活性相关的αA-晶体蛋白突变体的增强动力学是由β-片层和卷曲(R=0.619)的二级结构元件在模拟过程中的动态交换内部调节的。此外,还观察到 ACD 二聚体界面区域(β3-L6-β4 段)和 CTD 动力学的显著动力学。特别是,高度动态的突变体也表现出增强的非共价和疏水相互作用,这对其稳定性产生不利影响,并有利于可能的蛋白质展开机制。总的来说,这项研究强调了突变介导的αA-晶体蛋白结构扭曲,并需要进一步开发针对白内障形成的抑制剂。

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本文引用的文献

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RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles.RING 3.0:从结构集合中快速生成概率残基相互作用网络。
Nucleic Acids Res. 2022 Jul 5;50(W1):W651-W656. doi: 10.1093/nar/gkac365.
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Current Trends in the Pharmacotherapy of Cataracts.白内障药物治疗的当前趋势
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The structure and oxidation of the eye lens chaperone αA-crystallin.眼晶状体伴侣蛋白 αA-晶体蛋白的结构与氧化。
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Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.根据潜在构象集合验证分子动力学模拟与实验观测结果的一致性。
J Phys Chem B. 2018 Jul 5;122(26):6673-6689. doi: 10.1021/acs.jpcb.8b02144. Epub 2018 Jun 21.
6
The cataract-causing mutation G75V promotes γS-crystallin aggregation by modifying and destabilizing the native structure.导致白内障的突变 G75V 通过修饰和破坏天然结构促进 γS-晶体蛋白聚集。
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Characterization of an N-terminal mutant of αA-crystallin αA-R21Q associated with congenital cataract.αA-晶体蛋白 N 端突变体 αA-R21Q 的特性与先天性白内障相关。
Exp Eye Res. 2018 Sep;174:185-195. doi: 10.1016/j.exer.2018.05.016. Epub 2018 May 19.
8
A molecular dynamics approach to explore the structural characterization of cataract causing mutation R58H on human γD crystallin.采用分子动力学方法探索人γD 晶体蛋白致白内障突变 R58H 的结构特征。
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Novel Mutations in the Crystallin Gene in Age-Related Cataract Patients from a North Indian Population.来自北印度人群的年龄相关性白内障患者晶状体蛋白基因的新突变
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An Integrated Computational Framework to Assess the Mutational Landscape of α-L-Iduronidase IDUA Gene.一种综合计算框架,用于评估α-L-艾杜糖醛酸酶 IDUA 基因的突变景观。
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