ArticleScientific reports2020
Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Hierarchical multi-timescale structural dynamics of the disordered N-terminal of p53.Nature communications · 2026Article
- Quantum medicine: A quantum-mechanical framework for redox biology, disease and precision medicine.Clinical and translational medicine · 2026Review
- Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations.ACS omega · 2024Article
- Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins.PloS one · 2024Article
- Article
- Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model.bioRxiv : the preprint server for biology · 2023Article
- Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.PLoS computational biology · 2022Article
- Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.Journal of chemical theory and computation · 2022Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- An integrated view of p53 dynamics, function, and reactivation.Current opinion in structural biology · 2021Review
- Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide.The journal of physical chemistry. B · 2021Article
- Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway.Chemical science · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for [Formula: see text] 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel [Formula: see text]-sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.
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