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Conformational flexibility and transient structure of the proline-rich domain in p53

Berggren, Agnes LU ; Bakker, Michael LU ; Fisher, Hayden and Skepö, Marie LU orcid (2026) In Biophysical Journal 125(8). p.1914-1925
Abstract

The proline-rich domain (PRD) of the tumor suppressor p53 plays a central role in modulating conformational dynamics and molecular interactions, yet its intrinsic structural behavior remains incompletely understood. Here, we combine extensive all-atom molecular dynamics simulations with biophysical validation to characterize the conformational ensemble of the p53 PRD. The domain behaves as an intrinsically disordered region, sampling a highly heterogeneous ensemble with average end-to-end distance and radius of gyration of 52.5 Å and 21.8 Å, respectively. Despite this disorder, transient local structure is prominent: unordered conformations dominate, followed by substantial polyproline II (PPII) content, with β-bends and turns linking... (More)

The proline-rich domain (PRD) of the tumor suppressor p53 plays a central role in modulating conformational dynamics and molecular interactions, yet its intrinsic structural behavior remains incompletely understood. Here, we combine extensive all-atom molecular dynamics simulations with biophysical validation to characterize the conformational ensemble of the p53 PRD. The domain behaves as an intrinsically disordered region, sampling a highly heterogeneous ensemble with average end-to-end distance and radius of gyration of 52.5 Å and 21.8 Å, respectively. Despite this disorder, transient local structure is prominent: unordered conformations dominate, followed by substantial polyproline II (PPII) content, with β-bends and turns linking conserved PXXP motifs. Circular dichroism and small-angle X-ray scattering experiments corroborate the largely disordered yet partially structured nature of the PRD. Ramachandran and contact analyses reveal that consecutive prolines, particularly Pro71-Pro72, impose steric constraints that stabilize locally extended conformations and restrict backbone collapse. To approximate the PRD within full-length p53, additional simulations were performed with restrained terminal distances, yielding reduced conformational variability and improved agreement with small-angle X-ray scattering data while preserving secondary-structure propensities. PPII helices emerge as particularly robust features, acting as stiff spacers linking the transactivation domain to downstream regions. Finally, simulations of clinically relevant variants reveal mutation-specific local perturbations: P72R disrupts consecutive proline rigidity and increases flexibility, whereas P82L abolishes a PXXP motif and its associated PPII helix. These results identify proline-mediated rigidity and transient PPII structure as key determinants of the dynamic conformational landscape of the p53 PRD.

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author
; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biophysical Journal
volume
125
issue
8
pages
12 pages
publisher
Cell Press
external identifiers
  • pmid:41832603
  • scopus:105036736727
ISSN
1542-0086
DOI
10.1016/j.bpj.2026.03.024
language
English
LU publication?
yes
id
657a38c7-73b0-41e0-aca9-3bbc904cb9d0
date added to LUP
2026-05-25 09:12:59
date last changed
2026-09-01 23:16:48
@article{657a38c7-73b0-41e0-aca9-3bbc904cb9d0,
  abstract     = {{<p>The proline-rich domain (PRD) of the tumor suppressor p53 plays a central role in modulating conformational dynamics and molecular interactions, yet its intrinsic structural behavior remains incompletely understood. Here, we combine extensive all-atom molecular dynamics simulations with biophysical validation to characterize the conformational ensemble of the p53 PRD. The domain behaves as an intrinsically disordered region, sampling a highly heterogeneous ensemble with average end-to-end distance and radius of gyration of 52.5 Å and 21.8 Å, respectively. Despite this disorder, transient local structure is prominent: unordered conformations dominate, followed by substantial polyproline II (PPII) content, with β-bends and turns linking conserved PXXP motifs. Circular dichroism and small-angle X-ray scattering experiments corroborate the largely disordered yet partially structured nature of the PRD. Ramachandran and contact analyses reveal that consecutive prolines, particularly Pro71-Pro72, impose steric constraints that stabilize locally extended conformations and restrict backbone collapse. To approximate the PRD within full-length p53, additional simulations were performed with restrained terminal distances, yielding reduced conformational variability and improved agreement with small-angle X-ray scattering data while preserving secondary-structure propensities. PPII helices emerge as particularly robust features, acting as stiff spacers linking the transactivation domain to downstream regions. Finally, simulations of clinically relevant variants reveal mutation-specific local perturbations: P72R disrupts consecutive proline rigidity and increases flexibility, whereas P82L abolishes a PXXP motif and its associated PPII helix. These results identify proline-mediated rigidity and transient PPII structure as key determinants of the dynamic conformational landscape of the p53 PRD.</p>}},
  author       = {{Berggren, Agnes and Bakker, Michael and Fisher, Hayden and Skepö, Marie}},
  issn         = {{1542-0086}},
  language     = {{eng}},
  number       = {{8}},
  pages        = {{1914--1925}},
  publisher    = {{Cell Press}},
  series       = {{Biophysical Journal}},
  title        = {{Conformational flexibility and transient structure of the proline-rich domain in p53}},
  url          = {{http://dx.doi.org/10.1016/j.bpj.2026.03.024}},
  doi          = {{10.1016/j.bpj.2026.03.024}},
  volume       = {{125}},
  year         = {{2026}},
}