Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry,ACS Environmental Au

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Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry
ACS Environmental Au ( IF 6.7 ) Pub Date : 2022-06-10 , DOI: 10.1021/jasms.2c00083
Sarah N. Sipe ₁ , Kevin Jeanne Dit Fouque ₂ , Alyssa Garabedian ₂ , Fenfei Leng _{2,

3} , Francisco Fernandez-Lima _{2,

3} , Jennifer S. Brodbelt ₁

Affiliation

Although it is widely accepted that protein function is largely dependent on its structure, intrinsically disordered proteins (IDPs) lack defined structure but are essential in proper cellular processes. Mammalian high mobility group proteins (HMGA) are one such example of IDPs that perform a number of crucial nuclear activities and have been highly studied due to their involvement in the proliferation of a variety of disease and cancers. Traditional structural characterization methods have had limited success in understanding HMGA proteins and their ability to coordinate to DNA. Ion mobility spectrometry and mass spectrometry provide insights into the diversity and heterogeneity of structures adopted by IDPs and are employed here to interrogate HMGA2 in its unbound states and bound to two DNA hairpins. The broad distribution of collision cross sections observed for the apo-protein are restricted when HMGA2 is bound to DNA, suggesting that increased protein organization is promoted in the holo-form. Ultraviolet photodissociation was utilized to probe the changes in structures for the compact and elongated structures of HMGA2 by analyzing backbone cleavage propensities and solvent accessibility based on charge-site analysis, which revealed a spectrum of conformational possibilities. Namely, preferential binding of the DNA hairpins with the second of three AT-hooks of HMGA2 is suggested based on the suppression of backbone fragmentation and distribution of DNA-containing protein fragments.

中文翻译：

使用离子淌度光谱法和 193 nm 紫外光解离质谱法探索 HMGA2·DNA 配合物的构象和结合位置

尽管人们普遍认为蛋白质功能在很大程度上取决于其结构，但内在无序蛋白质 (IDP) 缺乏明确的结构，但在适当的细胞过程中是必不可少的。哺乳动物高迁移率基团蛋白 (HMGA) 是 IDP 的一个此类例子，它执行许多关键的核活动，并且由于它们参与多种疾病和癌症的增殖而受到高度研究。传统的结构表征方法在理解 HMGA 蛋白及其与 DNA 协调的能力方面取得的成功有限。离子迁移光谱法和质谱法提供了对 IDP 采用的结构的多样性和异质性的见解，并在此处用于询问 HMGA2 的未结合状态并与两个 DNA 发夹结合。当 HMGA2 与 DNA 结合时，观察到的载脂蛋白碰撞截面的广泛分布受到限制，这表明在全息形式中促进了增加的蛋白质组织。通过基于电荷位点分析分析主链裂解倾向和溶剂可及性，利用紫外光解来探测 HMGA2 紧凑和细长结构的结构变化，揭示了一系列构象可能性。即，DNA 发夹与 HMGA2 的三个 AT 钩中的第二个优先结合是基于抑制骨架片段化和含 DNA 的蛋白质片段的分布而提出的。通过基于电荷位点分析分析主链裂解倾向和溶剂可及性，利用紫外光解来探测 HMGA2 紧凑和细长结构的结构变化，揭示了一系列构象可能性。即，DNA 发夹与 HMGA2 的三个 AT 钩中的第二个优先结合是基于抑制骨架片段化和含 DNA 的蛋白质片段的分布而提出的。通过基于电荷位点分析分析主链裂解倾向和溶剂可及性，利用紫外光解来探测 HMGA2 紧凑和细长结构的结构变化，揭示了一系列构象可能性。即，DNA 发夹与 HMGA2 的三个 AT 钩中的第二个优先结合是基于抑制骨架片段化和含 DNA 的蛋白质片段的分布而提出的。

更新日期：2022-06-10

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