Data-Driven Engineering of Thermostable Collagen-Mimetic Peptoid Triple Helices

Collagen-mimetic peptides (CMPs) are engineered molecules designed to replicate the triple-helical structure of natural collagen. A repeating x-y-Gly sequence is the defining motif of CMPs and is critical to their triple-helical structure and stability. Substitutions to the residues occupying the x and y positions present a means to modulate the CMP structure and properties. Peptoid residues-N-substituted glycine derivatives-present an attractive potential substitution due to their thermal stability, proteolytic resistance, biocompatibility, and diverse palette of non-natural side chains, but also tend to introduce a high degree of backbone flexibility that can diminish the stability of the triple helix. In this work, we report a computational active learning cycle comprising molecular dynamics simulation, Gaussian process regression, and Bayesian optimization to computationally identify a number of promising peptoid substitutions predicted to stabilize the desired quaternary structure through side chain interactions and produce stable peptoid-based collagen-like triple helices. To experimentally test the computational predictions, a top candidate identified by the screen was synthesized and imaged using scanning electron microscopy to resolve fibril-like bundles consistent with collagen-like triple helices. This work predicts a number of CMP peptoid substitutions capable of forming stable triple-helical structures, presents a generalizable design strategy for engineering desired peptoid structures, and opens new avenues for the design of peptoid-based biomimetic materials.