系统识别结构特异的蛋白质-蛋白质相互作用。

IF 8.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Molecular Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-05-03 DOI:10.1038/s44320-024-00037-6
Aleš Holfeld, Dina Schuster, Fabian Sesterhenn, Alison K Gillingham, Patrick Stalder, Walther Haenseler, Inigo Barrio-Hernandez, Dhiman Ghosh, Jane Vowles, Sally A Cowley, Luise Nagel, Basavraj Khanppnavar, Tetiana Serdiuk, Pedro Beltrao, Volodymyr M Korkhov, Sean Munro, Roland Riek, Natalie de Souza, Paola Picotti
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引用次数: 0

摘要

蛋白质的物理相互作用组在受到干扰时会发生改变,从而调节细胞生理机能并导致疾病。鉴别正常和疾病状态下蛋白质相互作用组的差异有助于了解疾病机制,但目前的方法无法精确定位整个蛋白质组结构特异性的蛋白质相互作用和相互作用界面。我们利用有限蛋白水解质谱法(LiP-MS)筛选结构特异性PPIs,方法是探测细胞提取物中的蛋白质在处理特定结构状态的蛋白质时对蛋白酶敏感性的变化。我们首先证明,LiP-MS 能检测特征明确的 PPI,包括抗体与目标蛋白的相互作用以及与膜蛋白的相互作用,并能精确定位包括表位在内的界面。然后,我们将这种方法用于研究帕金森病标志性蛋白α-突触核蛋白(aSyn)的构象特异性相互作用体。我们确定了 aSyn 单体和淀粉样纤维的已知相互作用物,并提供了新的构象特异性 aSyn 相互作用物资源,供进一步研究验证。我们还在两种 Rab GTP 酶的 GDP 结合型和 GTP 结合型上使用了我们的方法,发现了构象相似蛋白质的不同候选相互作用物。这种方法适用于筛选任何蛋白质的结构特异性相互作用组,包括翻译后修饰和未修饰,或代谢物结合和未结合的蛋白质状态。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Systematic identification of structure-specific protein-protein interactions.

The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.

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来源期刊
Molecular Systems Biology
Molecular Systems Biology 生物-生化与分子生物学
CiteScore
18.50
自引率
1.00%
发文量
62
审稿时长
6-12 weeks
期刊介绍: Systems biology is a field that aims to understand complex biological systems by studying their components and how they interact. It is an integrative discipline that seeks to explain the properties and behavior of these systems. Molecular Systems Biology is a scholarly journal that publishes top-notch research in the areas of systems biology, synthetic biology, and systems medicine. It is an open access journal, meaning that its content is freely available to readers, and it is peer-reviewed to ensure the quality of the published work.
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