Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets
Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets
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DOI：
10.1002/pro.4611
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发表时间：
2023-04-01
期刊：
影响因子：
8
通讯作者：
Amacher，Jeanine F.
中科院分区：
文献类型：
--
作者：
Tahti，Elise F.;Blount，Jadon M.;Amacher，Jeanine F.
涉及短肽识别的蛋白质-蛋白质相互作用在细胞过程中至关重要。蛋白质-肽相互作用表面积相对较小且较浅，并且肽结合结构域家族中通常存在重叠的特异性。因此，剖析选择性决定因素可能具有挑战性。PDZ结构域是位于几种细胞内信号传导和运输途径中的肽结合结构域家族。这些结构域也直接被病原体靶向，许多致癌病毒蛋白的标志是PDZ结合基序。然而，在靶向PDZ结构域的序列中，存在相对混杂的宽范围。例如，病毒HPV 16 E6癌蛋白识别细胞中作为囊性纤维化跨膜传导调节因子（CFTR）的含PDZ结构域的蛋白质的数量超过两倍，尽管PDZ靶向序列相似且基序残基相同。在这里，我们使用匹配WT和杂合序列的肽确定已知结合HPV 16 E6单独或CFTR和HPV 16 E6两者的PDZ结构域的结合亲和力。我们还使用能量最小化模型PDZ-肽复合物，并使用序列分析来研究这种差异。我们发现，虽然大多数单突变对整体亲和力有边际效应，但对结合自由能的加性效应准确地描述了观察到的选择性。总之，我们的结果描述了如何复杂和不同的PDZ相互作用可以在细胞中编程。
Protein–protein interactions that involve recognition of short peptides are critical in cellular processes. Protein–peptide interaction surface areas are relatively small and shallow, and there are often overlapping specificities in families of peptide‐binding domains. Therefore, dissecting selectivity determinants can be challenging. PDZ domains are a family of peptide‐binding domains located in several intracellular signaling and trafficking pathways. These domains are also directly targeted by pathogens, and a hallmark of many oncogenic viral proteins is a PDZ‐binding motif. However, amidst sequences that target PDZ domains, there is a wide spectrum in relative promiscuity. For example, the viral HPV16 E6 oncoprotein recognizes over double the number of PDZ domain‐containing proteins as the cystic fibrosis transmembrane conductance regulator (CFTR) in the cell, despite similar PDZ targeting‐sequences and identical motif residues. Here, we determine binding affinities for PDZ domains known to bind either HPV16 E6 alone or both CFTR and HPV16 E6, using peptides matching WT and hybrid sequences. We also use energy minimization to model PDZ–peptide complexes and use sequence analyses to investigate this difference. We find that while the majority of single mutations had marginal effects on overall affinity, the additive effect on the free energy of binding accurately describes the selectivity observed. Taken together, our results describe how complex and differing PDZ interactomes can be programmed in the cell.