Mapping cryptic phosphorylation sites in the human proteome

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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Publication Details

Journal
The EMBO Journal
Published
2025-10-03
DOI
https://doi.org/10.1038/s44318-025-00567-1
Citations
2
Primary Topic
Advanced Proteomics Techniques and Applications
Type
article
Field-Weighted Citation Impact
1.51

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article

Mapping cryptic phosphorylation sites in the human proteome

Alessia Zanon, Graziano Lolli, Omar Rota‐Stabelli, Elisa Marchiori et al.
2 citations
The EMBO Journal
Advanced Proteomics Techniques and Applications
1.51
article

Mapping cryptic phosphorylation sites in the human proteome

Alessia Zanon, Graziano Lolli, Omar Rota‐Stabelli, Elisa Marchiori, M. Dolores Casagranda, Valerio Bonaldo, Dino Gasparotto, Marta Rigoli, Giovanni Minervini, Jesús R. Requena, Maria Pennuto, Emiliano Biasini, Giovanni Spagnolli, Cristian Micheletti, Nuria L. Lorenzo, Pietro Faccioli, Erika Di Domenico, Sirio Vittorio Feltrin, Laura Copat, Tommaso Fortunato Asquini
article en
2 citations

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.

The EMBO JournalVol. 44(22)
Fondazione Edmund Mach (IT), Scuola Internazionale Superiore di Studi Avanzati (IT), University of Padua (IT), University of Trento (IT), Universidade de Santiago de Compostela (ES), Veneto Institute of Molecular Medicine (IT), Istituto Nazionale di Fisica Nucleare, Trento Institute for Fundamental Physics And Applications (IT), Center for Research in Molecular Medicine and Chronic Diseases (ES), Instituto de Investigación Sanitaria de Santiago (ES), University of Milano-Bicocca (IT)
European Commission, Fondazione Telethon, Agencia Estatal de Investigación
Openalex Percentile: Top 16%
Advanced Proteomics Techniques and Applications
1.51
DOIOpen Access PDFOpenAlex
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