Mapping cryptic phosphorylation sites in the human proteome
Open accessPublished version of a preprint
Abstract
Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the protein’s inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphorylation in health and disease.
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“17 A key challenge in biophysics is to obtain precise, proteome-wide measurements of the energetic contributions of phosphorylation to protein stability.”
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“Higher RSA values indicate greater exposure to the solvent surface, correlating with a higher likelihood of PTM occurrence 31 .”
- Authors
- Gasparotto, D., Zanon, A., Bonaldo, V., Marchiori, E., Casagranda, M., Di Domenico, E., Copat, L., Asquini, T. F., Rigoli, M., Feltrin, S. V., Lopez Lorenzo, N., Lolli, G., Pennuto, M., Requena, J. R., Rota Stabelli, O., Minervini, G., Micheletti, C., Spagnolli, G., Faccioli, P., & Biasini, E.
- Affiliations
- University of Trento (IT)
- University of Padua (IT)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- Istituto Nazionale di Fisica Nucleare, Trento Institute for Fundamental Physics And Applications (IT)
- Corresponding author
- Gasparotto, Dino
- Zanon, Annarita
- Bonaldo, Valerio
- ORCID
- Venue
- The EMBO Journal
- Published
- 2025-10-03
- Volume
- 44
- Issue
- 22
- Pages
- 6704-6731
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC12624043
- OpenAlex
- W4414777747
- Cited by
- 9
- References
- 60
- Citations by year
- 2026: 6 · 2025: 3
- FWCI
- 2.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- The EMBO Journal (publishedVersion, cc-by)
- Qeios (acceptedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion, cc-by)
- SDL (submittedVersion, cc-by)
- Iris (University of Trento) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by)
- Funders
- Fondazione Telethon (GGP20043, GMR24T2072)
- Ministero dell'Istruzione, dell'Università e della Ricerca (H53D23000860006)
- Spanish National Research Agency (AEI) and EU Feder Funds (PID2020-117465GB-I00)
- Ministero dell'Istruzione, dell'Università e della Ricerca and Sibylla Biotech (NRRP)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
- Keywords
- protein phosphorylation, folding intermediates, solvent accessibility, post-translational modification, protein stability, protein degradation, phosphomimetic mutations, tumor fitness, human proteome
- MeSH terms
- Humans, Phosphoproteins, Phosphorylation, Protein Processing, Post-Translational, Protein Folding, Proteome
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