A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids

Abstract

Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. While parameters describing subsets of disordered proteins and synthetic materials have been established, they are often tailored to specific chemical interactions and monomer classes, limiting their broader applicability. To address this gap, we present a high-throughput workflow that implements a versatile colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and pioneers a data-driven sequence parameterization methodology that integrates into a predictive algorithm. Using a model system consisting of two-component peptidomimetics (20mer peptoids) containing polar glycine and hydrophobic N-butylglycine residues in a one-bead one-compound (OBOC) library, we visually identified nine classifications of conformational disorder. From this library, we identified 122 unique sequences across varied compositions and conformations, and we developed an image analysis tool that ultimately characterized an order of magnitude larger fraction of the complete library. Low-throughput techniques, atomistic simulations and ion mobility spectrometry coupled with liquid chromatography and mass spectrometry separations (LC-IMS-MS) of purified peptoids, yielded quantitative descriptors of the conformational ensembles formed by three compositionally identical sequences selected from the library. Finally, a data-driven technique was developed that exploits ‘motifs’ within the 20mer sequences to inform a gradient-boosted tree machine learning algorithm towards conformation prediction. This multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery and development of advanced materials with precise conformational control.