How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
Open accessAbstract
Phosphorylation of intrinsically disordered proteins (IDPs) can produce changes in structural and dynamical properties and thereby mediate critical biological functions. How phosphorylation effects intrinsically disordered proteins has been studied for an increasing number of IDPs, but a systematic understanding is still lacking. Here, we compare the collapse propensity of four disordered proteins, Ash1, the C-terminal domain of RNA polymerase (CTD2’), the cytosolic domain of E-Cadherin, and a fragment of the p130Cas, in unphosphorylated and phosphorylated forms using extensive all-atom molecular dynamics (MD) simulations. We find all proteins to show V-shape changes in their collapse propensity upon multi-site phosphorylation according to their initial net charge: phosphorylation expands neutral or overall negatively charged IDPs and shrinks positively charged IDPs. However, force fields including those tailored towards and commonly used for IDPs overestimate these changes. We find quantitative agreement of MD results with SAXS and NMR data for Ash1 and CTD2’ only when attenuating protein electrostatic interactions by using a higher salt concentration ( e . g . 350 mM), highlighting the overstabilization of salt bridges in current force fields. We show that phosphorylation of IDPs also has a strong impact on the solvation of the protein, a factor that in addition to the actual collapse or expansion of the IDP should be considered when analyzing SAXS data. Compared to the overall mild change in global IDP dimension, the exposure of active sites can change significantly upon phosphorylation, underlining the large susceptibility of IDP ensembles to regulation through post-translational modifications.
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Disordered proteins and regions are characterized by broad and heterogeneous ensembles with small differences in relative conformational stabilities and low barriers.
“Disordered proteins (regions) are characterized by broad and heterogeneous ensembles where the differences in the relative conformational stabilities are small, or even minor and the barriers are low.”
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- Authors
- Jin, F., & Gräter, F.
- Affiliations
- Heidelberg University (DE)
- Corresponding author
- Gräter, Frauke
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2021-05-04
- Volume
- 17
- Issue
- 5
- Pages
- e1008939
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC8148376
- OpenAlex
- W3157400614
- Cited by
- 77
- References
- 48
- Citations by year
- 2026: 15 · 2025: 20 · 2024: 16 · 2023: 10 · 2022: 13 · 2021: 3
- FWCI
- 3.30
- Type
- journal article
- Language
- en
- Update notices
- new_version (2021-05-25)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Baden-Württemberg
- Deutsche Forschungsgemeinschaft (INST 35/1134-1 FUGG, SPP1782)
- Gauss Centre for Supercomputing e.V.
- Klaus Tschira Foundation
- Heidelberg University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- intrinsically disordered proteins, multisite phosphorylation, protein conformation, electrostatic interactions, salt bridges, protein solvation, active site exposure, post-translational modification, ASH1, p130Cas, net charge
- MeSH terms
- Amino Acid Sequence, Phosphorylation, Protein Conformation, Protein Processing, Post-Translational, Reproducibility of Results, Nuclear Magnetic Resonance, Biomolecular, Molecular Dynamics Simulation, Intrinsically Disordered Proteins
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