Many cell signaling pathways are orchestrated by the weak, transient, and reversible protein-protein interactions that are mediated by the binding of a short peptide segment in one protein (parent protein) to a globular domain in another (partner protein), known as peptide-mediated interactions (PMIs). Previous studies normally had an implicit hypothesis that a PMI is functionally equivalent or analogous to the protein-peptide interaction (PTI) involved in the PMI system, while ignoring parent context contribution to the peptide binding. Here, we perform a systematic investigation on the reasonability and applicability of the hypothesis at structural, energetic and dynamic levels. It is revealed that the context impacts PMIs primarily through conformational constraint of the peptide segments, which can (i) reduce the peptide flexibility and disorder in an unbound state, (ii) help the peptide conformational selection to fit the active pocket of partner proteins, and (iii) enhance the peptide packing tightness against the partners. Long, unstructured and/or middle-located peptide segments seem to be more vulnerable to their context than short, structured and/or terminal ones. The context is found to moderately or considerably improve both the binding affinity and specificity of PMIs as compared to their PTI counterparts; with the context support a peptide segment can contribute to ∼30-60% total binding energy of the whole PMI system, whereas the contribution is reduced to ∼5-50% when the context constraint is released. In addition, we also observe that peptide selectivity is largely impaired or even reversed upon stripping of their parent context (global selectivity decreases from 34.2 to 1.7-fold), by examining the crystal structures of full-length Src family kinases in an autoinhibitory state. Instead of the direct interaction and desolvation that are primarily concerned in traditional studies, peptide flexibility and the entropy penalty should also play a crucial role in the context effect on PMIs. Overall, we suggest that the context factor should not be ignored in most cases, particularly those with peptide segments that are long, highly disordered, and/or located at the middle region of their parent proteins.

中文翻译：

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蛋白质环境对肽介导的相互作用负责吗？

许多细胞的信号传导途径是由蛋白质之间的弱，瞬时和可逆的蛋白质相互作用而编排的，蛋白质之间的相互作用是由一种蛋白质（母体蛋白质）中的短肽段与另一种蛋白质（伙伴蛋白质）中的球状结构域的结合所介导的。介导的互动（PMI）。先前的研究通常有一个隐含的假设，即PMI在功能上与PMI系统中涉及的蛋白质-肽相互作用（PTI）等效或相似，而忽略了母体对肽结合的贡献。在这里，我们对假说的合理性和适用性在结构，能量和动态水平上进行了系统的研究。揭示了上下文主要通过肽段的构象约束影响PMI，这可以（i）减少处于未结合状态的肽的柔韧性和紊乱，（ii）帮助肽的构象选择以适应伴侣蛋白的活性口袋，以及（iii）增强针对伴侣的肽包装紧密性。长的，非结构化的和/或中间位置的肽段似乎比短的，结构化的和/或末端的肽段更容易受到上下文的影响。与PTI对应物相比，发现该背景适度或显着改善了PMI的结合亲和力和特异性。在上下文支持下，肽段可占整个PMI系统的约30-60％的总结合能，而当上下文约束被释放时，该贡献降低到约5-50％。此外，我们还观察到，通过检查处于自抑制状态的全长Src家族激酶的晶体结构，在去除其亲本环境后，肽的选择性会大大受损，甚至发生逆转（全局选择性从34.2降低至1.7倍）。除了在传统研究中主要关注的直接相互作用和去溶剂化作用之外，肽的柔韧性和熵损失也应在对PMI的背景影响中起关键作用。总体而言，我们建议在大多数情况下，尤其是那些肽段长，高度无序和/或位于其亲本蛋白质中间区域的肽段，不应忽略上下文因素。除了在传统研究中主要关注的直接相互作用和去溶剂化作用之外，肽的柔韧性和熵损失也应在对PMI的背景影响中起关键作用。总体而言，我们建议在大多数情况下，尤其是那些肽段长，高度无序和/或位于其亲本蛋白质中间区域的肽段，不应忽略上下文因素。除了在传统研究中主要关注的直接相互作用和去溶剂化作用之外，肽的柔韧性和熵损失也应在对PMI的背景影响中起关键作用。总体而言，我们建议在大多数情况下，尤其是那些肽段长，高度无序和/或位于其亲本蛋白质中间区域的肽段，不应忽略上下文因素。