ArticleThe journal of physical chemistry letters2019
Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.
Article in The journal of physical chemistry letters, 2019. 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.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration.Science (New York, N.Y.) · 2026Article
- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain.Nature communications · 2025Article
- Optimized protein-water interactions and torsional refinements yield balanced atomistic protein force fields.Nature communications · 2025Article
- Elucidation of the Molecular Interaction Network Underlying Full-Length FUS Conformational Transitions and Its Phase Separation Using Atomistic Simulations.The journal of physical chemistry. B · 2025Article
- Transient Interdomain Interactions Modulate the Monomeric Structural Ensemble and Self-Assembly of Huntingtin Exon 1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Martini3-IDP: improved Martini 3 force field for disordered proteins.Nature communications · 2025Article
- Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale.The journal of physical chemistry. B · 2025Article
- RNA binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs.Biophysical journal · 2024Article
- Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.The journal of physical chemistry. B · 2024Article
- The molecular basis for cellular function of intrinsically disordered protein regions.Nature reviews. Molecular cell biology · 2024Review
- Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable.Protein science : a publication of the Protein Society · 2024Article
- A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP-43 and modulates its phase behavior.Protein science : a publication of the Protein Society · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- "Boundary residues" between the folded RNA recognition motif and disordered RGG domains are critical for FUS-RNA binding.The Journal of biological chemistry · 2023Article
- Water molecule ordering on the surface of an intrinsically disordered protein.Biophysical journal · 2023Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to a combination of experimental data providing information about both local and global structure formation.
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