Stereochemistry in the disorder–order continuum of protein interactions

Estella A. Newcombe, Amanda D. Due, Andrea Sottini, Steffie Elkjær, Frederik Friis Theisen, Catarina B. Fernandes, Lasse Staby, Elise Delaforge, Christian R. O. Bartling, Inna Brakti, Katrine Bugge, Benjamin Schuler, Karen Skriver, Johan G. Olsen () and Birthe B. Kragelund ()
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Estella A. Newcombe: Department of Biology, University of Copenhagen
Amanda D. Due: Department of Biology, University of Copenhagen
Andrea Sottini: University of Zurich
Steffie Elkjær: Department of Biology, University of Copenhagen
Frederik Friis Theisen: Department of Biology, University of Copenhagen
Catarina B. Fernandes: Department of Biology, University of Copenhagen
Lasse Staby: Department of Biology, University of Copenhagen
Elise Delaforge: Department of Biology, University of Copenhagen
Christian R. O. Bartling: University of Copenhagen
Inna Brakti: Department of Biology, University of Copenhagen
Katrine Bugge: Department of Biology, University of Copenhagen
Benjamin Schuler: University of Zurich
Karen Skriver: Department of Biology, University of Copenhagen
Johan G. Olsen: Department of Biology, University of Copenhagen
Birthe B. Kragelund: Department of Biology, University of Copenhagen

Nature, 2024, vol. 636, issue 8043, 762-768

Abstract: Abstract Intrinsically disordered proteins can bind via the formation of highly disordered protein complexes without the formation of three-dimensional structure1. Most naturally occurring proteins are levorotatory (l)—that is, made up only of l-amino acids—imprinting molecular structure and communication with stereochemistry2. By contrast, their mirror-image dextrorotatory (d)-amino acids are rare in nature. Whether disordered protein complexes are truly independent of chiral constraints is not clear. Here, to investigate the chiral constraints of disordered protein–protein interactions, we chose as representative examples a set of five interacting protein pairs covering the disorder–order continuum. By observing the natural ligands and their stereochemical mirror images in free and bound states, we found that chirality was inconsequential in a fully disordered complex. However, if the interaction relied on the ligand undergoing extensive coupled folding and binding, correct stereochemistry was essential. Between these extremes, binding could be observed for the d-ligand with a strength that correlated with disorder in the final complex. These findings have important implications for our understanding of the molecular processes that lead to complex formation, the use of d-peptides in drug discovery and the chemistry of protein evolution of the first living entities on Earth.

Date: 2024
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DOI: 10.1038/s41586-024-08271-6

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