Abstract
A central tenet of biology is that protein structure mediates the sequence-function relationship. Recently, there has been excitement about the promise of advances in protein structure modeling to generate hypotheses about sequence-structure-function relationships. Here, we leverage structural similarity to identify rapidly evolving proteasome assembly chaperones and characterize their function in Candidozyma (Candida) auris. Despite extensive sequence divergence, we demonstrate conservation of function, corroborating that specific folds, and not sequences, are required for function. This theoretical premise suggests that protein structures with certain properties should be functionally interchangeable, even if they were not products of a common evolutionary history. To reduce this theory to practice, we performed structure-informed protein design, exploring sequence space that is not accessible via stepwise evolution, and mutated more than 40 residues in the Poc4 proteasome assembly chaperone to demonstrate that artificial proteins can rescue complex biological processes in the context of the whole cell. This sequence-structure-function relationship expands our ability to use structure to identify deep evolutionary relationships between proteins and generate hypotheses about gene function in non-model organisms. Overall, this helps to define and understand functional constraints on protein evolution, with important implications for both future protein design and retrospective function prediction.
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All data generated in this study are provided in this study are provided in the Supplementary Information and/or Source Data files. Strain used in this will be sent following standard material transfer agreements (MTAs) Source data are provided with this paper.
Code availability
All original code has been deposited at Zenodo at DOI: 10.5281/zenodo.1905266577 and is publicly available as of the date of publication. The code is also developed openly at the GitHub repository (https://github.com/maomlab/Poc4).
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Acknowledgements
We thank the O’Meara Labs for helpful discussions. National Institutes of Health grant R35GM147894 (TRO), National Institutes of Health grant U19AI181767 (TRO). National Institutes of Health grant T32GM149391 (JRR). National Institutes of Health grant R35GM151129 (MJO). National Institutes of Health grant 5F32CA261115 (MS). National Institutes of Health grant R35 GM118073 (PJW). Michigan Postdoctoral Pioneer Fellowship (MS)
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Conceptualization: J.R.R., M.S., M.J.O., and T.R.O. Methodology: J.R.R., M.S., M.J.O. and T.R.O. Investigation: J.R.R., M.S., M.J.O. and T.R.O. Visualization: J.R.R., M.S., M.J.O. and T.R.O. Funding acquisition: J.R.R., M.S., P.J.W. and T.R.O. Project administration: T.R.O., M.J.O. Supervision: P.J.W., T.R.O. and M.J.O. Writing—original draft: J.R.R., M.S., M.J.O. and T.R.O. Writing—review and editing: J.R.R., M.S., P.J.W., M.J.O. and T.R.O.
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Rapala, J.R., Siddiq, M., Wittkopp, P.J. et al. Deep homology and design of proteasome chaperone proteins in Candidozyma auris. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71206-4
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DOI: https://doi.org/10.1038/s41467-026-71206-4
