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bioRxiv · 10.64898/2026.10.10.757878

Buried Ion-Pairs Reshape Folding Pathways of Artificial Proteins

Liebau, J.·Kemp, G.·Auman, D.·Hoja, N.·Jussupow, A.·Baumgart, M.·von Heijne, G.·Kaila, V. R. I.
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Abstract

Ion-pairs are central charged motifs that control the biological function of several proteins. Yet, the physical principles linked to the formation of ion-pairs during protein folding remain poorly understood. Here, we show that buried ion-pairs of de novo-designed helical bundle proteins reshape the folding pathways by introducing kinetic barriers that are overcome by a hydrophobic collapse linked to packing of the protein core. By combining protein design with co-translational folding studies, nuclear magnetic resonance (NMR) spectroscopy, and molecular dynamics simulations, we show that introduction of a buried ion-pair leads to a shifted folding transition that balances desolvation and electrostatic interactions within the protein and the bulk solvent. Moreover, we find that the folding pathway is sensitive to modifications in non-polar interactions and motifs that electrostatically shield the ion-pair from its surroundings. Our combined findings provide a blueprint for understanding how functional motifs affect protein folding and how mutation of charged networks alter the stability of proteins.

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Liebau, J., Kemp, G., Auman, D., Hoja, N., Jussupow, A., Baumgart, M., von Heijne, G., Kaila, V. R. I.. 2026-10-10. Buried Ion-Pairs Reshape Folding Pathways of Artificial Proteins. https://doi.org/10.64898/2026.10.10.757878

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