ArticleJournal of chemical theory and computation2014
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 345 papers.
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Who cites it
345 citing papers in PubMed.
- Seeing the Chemistry of Biomolecular Condensates: In Situ Mapping of Composition and Water Content.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- Biomolecular Condensates Act as Distinct Solvation Environments That Reshape Amino Acid pJournal of the American Chemical Society · 2026Article
- The Monomeric Conformational Ensembles of Aβ40 and Aβ42 Encode Their Differential Amyloid Aggregation Propensity.The journal of physical chemistry. B · 2026Article
- Advancements in single-molecule fluorescence spectroscopy for probing conformations, dynamics, and interactions in disordered protein regions.Current opinion in structural biology · 2026Review
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration.Science (New York, N.Y.) · 2026Article
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- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Nearest neighbour interactions between amino acid residues in short peptides and coil libraries.RSC advances · 2026Article
- Determination of Nucleotide-Nucleotide and Nucleotide-Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations.ACS physical chemistry Au · 2026Article
- Evaluating the Impact of Phosphorylation on the Dynamics of the Tau Protein Proline-Rich Region.Journal of chemical theory and computation · 2026Article
- Residue-Specific Modulation of Aggregation-Associated Interactions by Spermine in Tau, α‑Synuclein, and Aβ40.JACS Au · 2026Article
- Article
285 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and average solvation free energies of model compounds which are more consistent with experiment. Most importantly, we show that this scaling is small enough not to affect adversely the stability of the folded state, with only a modest effect on the stability of model peptides forming α-helix and β-sheet structures. The proposed adjustment opens the way to more accurate atomistic simulations of proteins, particularly for intrinsically disordered proteins, protein-protein association, and crowded cellular environments.
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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.