ArticleThe journal of physical chemistry. B2020
Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins.
Article in The journal of physical chemistry. B, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- Site-specific methionine oxidation alters structure and phase separation of TDP-43 C-terminal domain.bioRxiv : the preprint server for biology · 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
- Current practices in the study of biomolecular condensates: a community comment.Nature communications · 2025Article
- All-atom simulations of biomolecular condensates.Current opinion in structural biology · 2025Review
- Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates.Cell · 2025Article
- Transient Interdomain Interactions Modulate the Monomeric Structural Ensemble and Self-Assembly of Huntingtin Exon 1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Expanding the molecular language of protein liquid-liquid phase separation.Nature chemistry · 2024Article
- Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization.eLife · 2024Article
- Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS.Journal of the American Chemical 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
- "Boundary residues" between the folded RNA recognition motif and disordered RGG domains are critical for FUS-RNA binding.The Journal of biological chemistry · 2023Article
- Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.The journal of physical chemistry letters · 2023Review
- Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation.The journal of physical chemistry. B · 2023Article
- Insights into Molecular Diversity within the FET Family: Unraveling Phase Separation of the N-Terminal Low Complexity Domain from RNA-Binding Protein EWS.bioRxiv : the preprint server for biology · 2023Article
- A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding.Journal of chemical theory and computation · 2023Article
- Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation.JACS Au · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Significant efforts in the past decade have given us highly accurate all-atom protein force fields for molecular dynamics (MD) simulations of folded and disordered proteins. These simulations, complemented with experimental data, provide new insights into molecular interactions that underlie the physical properties of proteins, especially for intrinsically disordered proteins (IDPs) for which defining the heterogeneous structural ensemble is hugely challenging by experiments alone. Consequently, the accuracy of these protein force fields is of utmost importance to ensure reliable simulated conformational data. Here, we first assess the accuracy of current state-of-the-art force fields for IDPs (ff99SBws and ff03ws) applied to disordered proteins of low amino acid sequence complexity that can undergo liquid-liquid phase separation. On the basis of a detailed comparison of NMR chemical shifts between simulation and experiment on several IDPs, we find that regions surrounding specific polar residues result in simulated ensembles with exaggerated helicity when compared to experiment. To resolve this discrepancy, we introduce residue-specific modifications to the backbone torsion potential of three residues (Ser, Thr, and Gln) in the ff99SBws force field. The modified force field, ff99SBws-STQ, provides a more accurate representation of helical structure propensity in these LC domains without compromising faithful representation of helicity in a region with distinct sequence composition. Our refinement strategy also suggests a path forward for integrating experimental data in the assessment of residue-specific deficiencies in the current physics-based force fields and improves these force fields further for their broader applicability.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.