N@a and N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces
N@a and N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces
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DOI：
10.1021/acschembio.6b00935
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发表时间：
2017-02-01
影响因子：
4
通讯作者：
Woolfson, Derek N.
中科院分区：
文献类型：
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作者：
Fletcher, Jordan M.;Bartlett, Gail J.;Woolfson, Derek N.
α-螺旋卷曲螺旋是蛋白质相互作用基序中研究得最多的基序之一。因此，序列-结构关系可用于预测天然卷曲螺旋序列和从头设计新的卷曲螺旋序列。然而，卷曲的线圈采用了广泛的低聚状态和拓扑结构，我们对这些规范的理解和它们之间的区别仍然是不完整的。随着螺旋线圈越来越多地用于构建更高复杂性的仿生系统，我们知识中的差距变得更加重要;为此，螺旋线圈组件需要是鲁棒的，正交的，并且可以在上下文之间转移。在这里，我们探讨如何极性侧链天冬酰胺（天冬酰胺，N）是容忍内，否则疏水螺旋螺旋接口的卷曲螺旋。长期以来的观点是，放置在卷曲螺旋序列重复的某些位点的Asn选择一种寡聚体状态而不是其他状态，这是通过侧链形成氢键的能力或与有利状态的卷曲螺旋内部的螯合离子相互作用来合理化的。我们测试这与从头肽序列的实验传统上被认为是指导平行二聚体和三聚体，更广泛地通过生物信息学分析天然卷曲螺旋序列和结构。我们发现，当位于中央，而不是靠近这样的卷曲螺旋序列的末端，天冬酰胺发挥预期的寡聚体指定的影响。然而，在这些界限之外，Asn在天然序列中观察到的频率较低，并且合成肽是超热稳定的并且失去寡聚体状态特异性。这些发现强调了并非所有卷曲螺旋重复序列的区域都是等效的，并且在设计卷曲螺旋接口时需要小心。
The alpha-helical coiled coil is one of the best-studied protein protein interaction motifs. As a result, sequence-to-structure relationships are available for the prediction of natural coiled-coil sequences and the de novo design of new ones. However, coiled coils adopt a wide range of oligomeric states and topologies, and our understanding of the specification of these and the discrimination between them remains incomplete. Gaps in our knowledge assume more importance as coiled coils are used increasingly to construct biomimetic systems of higher complexity; for this, coiled-coil components need to be robust, orthogonal, and transferable between contexts. Here, we explore how the polar side chain asparagine (Asn, N) is tolerated within otherwise hydrophobic helix helix interfaces of coiled coils. The long-held view is that Asn placed at certain sites of the coiled-coil sequence repeat selects one oligomer state over others, which is rationalized by the ability of the side chain to make hydrogen bonds, or interactions with chelated ions within the coiled-coil interior of the favored, state. We test this with experiments on de novo peptide sequences traditionally considered as directing parallel dimers and trimers, and more widely through bioinformatics analysis of natural coiled-coil sequences and structures. We find that when located centrally, rather than near the termini of such coiled-coil sequences, Asn does exert the anticipated oligomer-specifying influence. However, outside of these bounds, Asn is observed less frequently in the natural sequences, and the synthetic peptides are hyperthermostable and lose oligomer-state specificity. These findings highlight that not all regions of coiled-coil repeat sequences are equivalent, and that care is needed when designing coiled-coil interfaces.