Conformational Dynamics of Asparagine at Coiled-Coil Interfaces.
Conformational Dynamics of Asparagine at Coiled-Coil Interfaces.
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DOI：
10.1021/acs.biochem.7b00848
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发表时间：
2017-12-19
期刊：
影响因子：
2.9
通讯作者：
Woolfson DN
中科院分区：
文献类型：
--
作者：
Thomas F;Niitsu A;Oregioni A;Bartlett GJ;Woolfson DN
卷曲线圈（CCs）是最容易理解的蛋白质折叠之一。尽管如此，我们对CCs的了解仍存在空白。值得注意的是，CCs在结构上可能比通常认为的更具活力。在这里，我们在一类丰富的CCs，平行二聚体中探索了这一点，重点关注疏水界面中的极性天冬酰胺（Asn）残基。有充分的证据表明，这种包含物可以区分不同的CC低聚物，这已经在Asn是否可以制造侧链氢键方面得到了合理的解释。对蛋白质数据库中平行CC二聚体的分析揭示了Asn侧链的多种构象，但并非所有这些构象都能形成预期的侧链间氢键。我们利用多维核磁共振波谱技术，包括无模型动力学分析和弛豫色散实验，研究了一种全新设计的卷绕式同型二聚体CC-Di的结构和动力学。我们发现Asn构象之间在毫秒时间尺度上的动态交换，侧链指向核心内外。我们进行了与此一致的分子动力学模拟，揭示了侧链是高度动态的，在皮秒到纳秒之间在氢键对构象之间交换。综合起来，我们的数据为Asn at CC接口提供了一个更动态的视图。虽然侧链间的氢键态是最丰富的，但Asn并不总是隐藏或参与这种相互作用。因为界面Asn残基是调节CC稳定性和识别的关键设计特征，这些关于它们如何在CC结构中被容纳的进一步见解将有助于它们的预测建模、工程和设计。
Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a de novo-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation–dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design.
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