Stapled peptides are a promising class of molecules with potential as highly specific probes of protein–protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.

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剖析钉合肽的几何和疏水性限制

钉合肽是一类很有前途的分子，具有作为蛋白质-蛋白质相互作用的高度特异性探针和治疗药物的潜力。烃装订通过两个因素的相互作用影响肽的特性：增强整体疏水性和限制构象灵活性。通过构建一系列虚拟肽，我们研究了每个因子在调节碳氢化合物肽 PM2 的结构特性中的作用，PM2 已被证明可以进入细胞，与其靶标小鼠双分钟 2 (MDM2) 结合，并激活 p53 。哈密​​顿复制品交换分子动力学 (HREMD) 模拟表明，碳氢化合物通过结合几何约束和增强的肽疏水性，有利于 PM2 的螺旋群。为了进一步了解沿着结合途径钉合的肽的构象景观，我们通过将肽限制在距 MDM2 不同距离处来进行 HREMD 模拟。当肽接近 MDM2 时，结合袋会发生脱水，与线性肽相比，在钉合肽存在的情况下，脱水程度似乎更大。在结合口袋中，由于肽残基以及钉书和结合口袋的微环境之间的有利相互作用，钉书肽的螺旋度增加，从而有助于增强亲和力。将碳氢化合物装订的多方面机制分解为各个因素不仅加深了对肽装订的基本理解，而且为新装订肽的设计提供了指导。