ArticleBiophysical journal2014
Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Hybrid deep learning with protein language models and dual-path architecture for predicting IDP functions.Briefings in bioinformatics · 2026Article
- Time-Resolved Single-Molecule FRET Reveals Length-Dependent Nucleosome Decompaction by Poly(ADP-ribose).bioRxiv : the preprint server for biology · 2026Article
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.The journal of physical chemistry. B · 2021Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.Acta crystallographica. Section D, Structural biology · 2017Article
- Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.Journal of computational chemistry · 2016Article
- Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations.Scientific reports · 2016Article
- Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.Biophysical journal · 2016Article
- Allosteric Interactions by p53 mRNA Govern HDM2 E3 Ubiquitin Ligase Specificity under Different Conditions.Molecular and cellular biology · 2016Article
- Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.The Biochemical journal · 2016Review
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- p53 dynamics upon response element recognition explored by molecular simulations.Scientific reports · 2015Article
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3 authors.
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Abstract
In eukaryotic proteins, intrinsically disordered regions (IDRs) are ubiquitous and often exist in linker regions that flank the functional domains of modular proteins, regulating their functions. For detailed structural ensemble modeling of IDRs, we propose a multiscale method for IDRs that possess significant long-range order in modular proteins and apply it to the eukaryotic transcription factor p53 as an example. First, we performed all-atom (AA) molecular dynamics (MD) simulations of the explicitly solvated p53 linker region, without experimental restraint terms, finding fractional long-range contacts within the linker. Second, we fed this AA MD ensemble into a coarse-grained (CG) model, finding an optimal set of contact potentials. The optimized CG MD simulations reproduced the contact probability map from the AA MD simulations. Finally, we performed the CG MD simulation of the tetrameric p53 fragments including the core domains, the linker, and the tetramerization domain. Using the obtained ensemble, we theoretically calculated the small angle x-ray scattering (SAXS) profile of this fragment. The obtained SAXS profile agrees well with the experiment. We also found that the long-range contacts in the p53 linker region are required to reproduce the experimental SAXS profile. The developed framework in which we calculate the long-range contact probability map from the AA MD simulation and incorporate it to the CG model can be applied to broad range of IDRs.
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