ArticleJournal of chemical theory and computation2019
Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- Novel bioactive peptides targeting Keap1-Nrf2 interaction for combating UVA-induced skin aging: Computational discovery and experimental validation.Journal of pharmaceutical analysis · 2026Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
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- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.The journal of physical chemistry. B · 2024Article
- Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation.Journal of the American Chemical Society · 2024Article
- Machine Learning Generation of Dynamic Protein Conformational Ensembles.Molecules (Basel, Switzerland) · 2023Review
- The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control.bioRxiv : the preprint server for biology · 2023Article
- Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.Journal of chemical theory and computation · 2023Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Coupled binding and folding of disordered SPIN N-terminal region in myeloperoxidase inhibition.Frontiers in molecular biosciences · 2023Article
- Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.Journal of chemical information and modeling · 2022Article
- Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.PLoS computational biology · 2022Article
- Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners.The journal of physical chemistry. B · 2022Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain.Journal of molecular biology · 2021Article
- Folding and self-assembly of short intrinsically disordered peptides and protein regions.Nanoscale advances · 2021Review
- Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores.Chemical science · 2021Article
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2 authors.
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Abstract
Molecular dynamics simulations using physics-based atomistic force fields have been increasingly used to characterize the heterogeneous structural ensembles of intrinsically disordered proteins (IDPs). To evaluate the accuracy of the latest atomistic explicit-solvent force fields in modeling larger IDPs with nontrivial structural features, we focus on the 61-residue N-terminal transactivation domain (TAD) of tumor suppressor p53, an important protein in cancer biology that has been extensively studied, and abundant experimental data is available for evaluation of simulated ensembles. We performed extensive replica exchange with solute tempering simulations, in excess of 1.0 μs/replica, to generate disordered structural ensembles of p53-TAD using six latest explicit solvent protein force fields. Multiple local and long-range structural properties, including chain dimension, residual secondary structures, and transient long-range contacts, were analyzed and compared against available experimental data. The results show that IDPs such as p53-TAD remain highly challenging for atomistic simulations due to conformational complexity and difficulty in achieving adequate convergence. Structural ensembles of p53-TAD generated using various force fields differ significantly from each other. The a99SB-disp force field demonstrates the best agreement with experimental data at all levels and proves to be suitable for simulating unbound p53-TAD and how its conformational properties may be modulated by phosphorylation and other cellular signals or cancer-associated mutations. Feasibility of such detailed structural characterization is a key step toward establishing the sequence-disordered ensemble-function-disease relationship of p53 and other biologically important IDPs.
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