ArticleCommunications biology2021
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation.Computational and structural biotechnology journal · 2026Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.Proteins · 2025Article
- Quality Evaluation Based Simulation Selection (QEBSS) for analysis of conformational ensembles and dynamics of multidomain proteins.Communications chemistry · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Sensing Protein Structural Transitions with Microfluidic Modulation Infrared Spectroscopy.Biosensors · 2025Article
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates.ACS central science · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0.Journal of structural biology · 2024Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Structure of Full-Length Src Kinase and Its Key Phosphorylated States: Molecular Dynamics Study.International journal of molecular sciences · 2024Article
- Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.Journal of chemical information and modeling · 2024Article
- Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities.Biophysical journal · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Conformational analysis of the IQSEC2 protein by statistical thermodynamics.Current research in structural biology · 2024Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.