While the conformational ensembles of disordered peptides and peptidomimetics are complex and challenging to characterize, they are a critical component in the paradigm connecting macromolecule sequence, structure, and function. In molecules that do not adopt a single predominant conformation, the conformational ensemble contains rich structural information that, if accessible, can provide a fundamental understanding related to desirable functions such as cell penetration of a therapeutic or the generation of tunable enzyme-mimetic architecture. To address the fundamental challenge of describing broad conformational ensembles, we developed a model system of peptidomimetics comprised of polar glycine and hydrophobic N-butylglycine to characterize using a suite of analytical techniques. Using replica exchange molecular dynamics atomistic simulations and liquid chromatography coupled to ion mobility spectrometry, we were able to distinguish the conformations of compositionally identical model sequences. However, differences between these model sequences were more challenging to resolve with characterization tools developed for intrinsically disordered proteins and polymers, including double electron–electron resonance (DEER) spectroscopy and diffusion ordered spectroscopy (DOSY) NMR. Finally, we introduce a facile colorimetric assay using immobilized sequences that leverages a solvatochromic probe, Reichardt's dye, to visually reveal conformational trends consistent with the experimental and computational analysis. This rapid colorimetric technique provides a complementary method to characterize the disorder of macromolecules and examine conformational ensembles as an isolated or multiplexed technique.

中文翻译：

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深入了解组成相同的无序肽模拟物的构象整体


虽然无序肽和肽模拟物的构象整体非常复杂且难以表征，但它们是连接大分子序列、结构和功能的范例中的关键组成部分。在不采用单一主要构象的分子中，构象集合包含丰富的结构信息，如果可以获取，可以提供与所需功能相关的基本理解，例如治疗剂的细胞渗透或可调节的酶模拟结构的生成。为了解决描述广泛构象整体的基本挑战，我们开发了一种由极性甘氨酸和疏水性 N-丁基甘氨酸组成的肽模拟物模型系统，以使用一套分析技术进行表征。使用复制品交换分子动力学原子模拟和液相色谱与离子迁移谱测定相结合，我们能够区分组成相同的模型序列的构象。然而，使用针对本质无序蛋白质和聚合物开发的表征工具（包括双电子-电子共振（DEER）光谱和扩散有序光谱（DOSY）NMR）来解决这些模型序列之间的差异更具挑战性。最后，我们介绍了一种使用固定序列的简便比色测定，该测定利用溶剂化显色探针（Reichardt 染料）来直观地揭示与实验和计算分析一致的构象趋势。这种快速比色技术提供了一种补充方法来表征大分子的无序性并作为分离或多重技术检查构象整体。