Metastability of Protein Solution Structures in the Absence of a Solvent: Rugged Energy Landscape and Glass-like Behavior
Metastability of Protein Solution Structures in the Absence of a Solvent: Rugged Energy Landscape and Glass-like Behavior
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DOI：
10.1021/jacs.3c12892
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发表时间：
2024-04-10
影响因子：
15
通讯作者：
Bleiholder，Christian
中科院分区：
文献类型：
--
作者：
Cropley，Tyler. C.;Liu，Fanny. C.;Bleiholder，Christian
天然离子迁移率/质谱法很好地准备在结构上筛选蛋白质组，但在没有溶剂的情况下表征蛋白质结构。这就提出了关于通过离子迁移率/质谱法鉴定的蛋白质结构的生物学意义的长期悬而未决的问题。使用新开发的计算和实验的离子迁移率/离子迁移率/质谱方法，我们研究的蛋白质泛素在无溶剂环境中的展开。我们的数据表明，折叠的，无溶剂的泛素离子迁移率/质谱观察存在于一个完整的β-抓基序和α-螺旋在很大程度上天然折叠。折叠的，无溶剂的泛素离子的合奏，可以划分成动力学稳定的亚群，似乎对应于在溶液中的泛素的结构异质性。时间分辨离子迁移率/离子迁移率/质谱测量表明，折叠，无溶剂的泛素表现出强烈的拉伸指数时间依赖性，模拟跟踪到一个崎岖的能源景观与动力学陷阱。估计解折叠速率常数比在水存在下小约800至20，000倍，有效地淬灭典型离子迁移率/质谱测量的时间尺度上的解折叠过程。我们提出的无溶剂泛素解折叠途径与溶剂存在下的泛素解折叠途径有很多共同的特征，包括在N-末端β-发夹和α-螺旋中具有显著的天然含量的极化过渡态。我们的实验和计算数据表明：（1）控制折叠的无溶剂蛋白质运动的能量景观与玻璃态系统相似;（2）大规模蛋白质运动至少部分由多肽链的氨基酸序列决定;（3）溶剂促进而不是控制蛋白质运动。
Native ion mobility/mass spectrometry is well-poised to structurally screen proteomes but characterizes protein structures in the absence of a solvent. This raises long-standing unanswered questions about the biological significance of protein structures identified through ion mobility/mass spectrometry. Using newly developed computational and experimental ion mobility/ion mobility/mass spectrometry methods, we investigate the unfolding of the protein ubiquitin in a solvent-free environment. Our data suggest that the folded, solvent-free ubiquitin observed by ion mobility/mass spectrometry exists in a largely native fold with an intact β-grasp motif and α-helix. The ensemble of folded, solvent-free ubiquitin ions can be partitioned into kinetically stable subpopulations that appear to correspond to the structural heterogeneity of ubiquitin in solution. Time-resolved ion mobility/ion mobility/mass spectrometry measurements show that folded, solvent-free ubiquitin exhibits a strongly stretched-exponential time dependence, which simulations trace to a rugged energy landscape with kinetic traps. Unfolding rate constants are estimated to be approximately 800 to 20,000 times smaller than in the presence of water, effectively quenching the unfolding process on the time scale of typical ion mobility/mass spectrometry measurements. Our proposed unfolding pathway of solvent-free ubiquitin shares substantial characteristics with that established for the presence of solvent, including a polarized transition state with significant native content in the N-terminal β-hairpin and α-helix. Our experimental and computational data suggest that (1) the energy landscape governing the motions of folded, solvent-free proteins is rugged in analogy to that of glassy systems; (2) large-scale protein motions may at least partially be determined by the amino acid sequence of a polypeptide chain; and (3) solvent facilitates, rather than controls, protein motions.