Issue 29, 2024

Insights into conformational ensembles of compositionally identical disordered peptidomimetics

Abstract

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.

Graphical abstract: Insights into conformational ensembles of compositionally identical disordered peptidomimetics

Supplementary files

Article information

Article type
Paper
Submitted
28 Mar 2024
Accepted
19 Jun 2024
First published
04 Jul 2024

Polym. Chem., 2024,15, 2970-2980

Insights into conformational ensembles of compositionally identical disordered peptidomimetics

E. C. Day, K. C. Cunha, R. J. Zhao, A. J. DeStefano, J. N. Dodds, M. A. Yu, J. R. Bemis, S. Han, E. S. Baker, J. Shea, R. B. Berlow and A. S. Knight, Polym. Chem., 2024, 15, 2970 DOI: 10.1039/D4PY00341A

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