Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States
Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States
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DOI：
10.1016/j.jmb.2009.05.019
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发表时间：
2009-07-17
影响因子：
5.6
通讯作者：
Chen, Jianhan
中科院分区：
文献类型：
--
作者：
Ganguly, Debabani;Chen, Jianhan
顺磁弛豫增强 (PRE) 是研究未折叠和部分折叠蛋白质的瞬时三级组织的强大技术。无序蛋白质状态的异质性和动态性质，以及 PRE 的 r(-6) 依赖性，对 PRE 衍生距离的可靠结构解释提出了重大挑战。在没有可访问构象子状态的额外知识的情况下，基于集成模拟的协议已被用于计算结构集成，该结构集成似乎与通过适当的 r(-6) 权重对集成水平施加的 PRE 距离限制一致。然而，如果不深入了解无序蛋白质状态的真实性质，就很难对此类方案的可靠性进行严格评估。在这里，我们利用从代表小蛋白质的折叠、部分折叠和展开状态的模拟结构系综导出的理论 PRE 距离集来研究基于系综模拟的 PRE 距离结构解释的有效性。结果证实了一个关键限制，即由于 r(-6) 权重，只有一个或几个成员需要满足距离限制，而整体的其余部分基本上不受限制。因此，无论 PRE 距离是从折叠、部分展开还是展开状态导出，计算出的结构系综都会呈现人为的异质性。此外，异质系综的性质很大程度上取决于结构计算中采用的蛋白质模型，并且很少反映潜在无序状态的真实性质。这些发现表明，仅对无序蛋白质状态进行 PRE 测量通常不包含足够的信息来进行可靠的结构解释，而后者将需要可访问的构象亚状态的额外知识。有趣的是，当可以获得大量 PRE 测量结果时，在理想条件下使用中间系综尺寸可能可以实现忠实的结构解释。 (C) 2009 Elsevier Ltd. 保留所有权利。
Paramagnetic relaxation enhancement (PRE) is a powerful technique for studying transient tertiary organizations of unfolded and partially folded proteins. The heterogeneous and dynamic nature of disordered protein states, together with the r(-6) dependence of PRE, presents significant challenges for reliable structural interpretation of PRE-derived distances. Without additional knowledge of accessible conformational substates, ensemble-simulation-based protocols have been used to calculate structure ensembles that appear to be consistent with the PRE distance restraints imposed on the ensemble level with the proper r(-6) weighting. However, rigorous assessment of the reliability of such protocols has been difficult without intimate knowledge of the true nature of disordered protein states. Here we utilize sets of theoretical PRE distances derived from simulated structure ensembles that represent the folded, partially folded and unfolded states of a small protein to investigate the efficacy of ensemble-simulation-based structural interpretation of PRE distances. The results confirm a critical limitation that, due to r(-6) weighting, only one or a few members need to satisfy the distance restraints and the rest of the ensemble are essentially unrestrained. Consequently, calculated structure ensembles will appear artificially heterogeneous no matter whether the PRE distances are derived from the folded, partially unfolded or unfolded state. Furthermore, the nature of the heterogeneous ensembles is largely determined by the protein model employed in structure calculation and reflects little oil the true nature of the underlying disordered state. These findings suggest that PRE measurements on disordered protein states alone generally do not contain enough information for a reliable structural interpretation and that the latter will require additional knowledge of accessible con formational substates. Interestingly, when a very large number of PRE measurements is available, faithful structural interpretation might be possible with intermediate ensemble sizes under ideal conditions. (C) 2009 Elsevier Ltd. All rights reserved.