ArticleNature communications2025
Optimized protein-water interactions and torsional refinements yield balanced atomistic protein force fields.
Article in Nature communications, 2025. 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 5 papers.
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Who cites it
5 citing papers in PubMed.
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- Multiscale Neural Network Potential with Anisotropic Message Passing for the Fast and Accurate Simulation of Protein Dynamics and Enzymatic Reactions.Journal of the American Chemical Society · 2026Article
- CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field Compatibility and Robust Dense-Phase Relaxation.Journal of chemical information and modeling · 2026Article
- Biomolecular Condensates Act as Distinct Solvation Environments That Reshape Amino Acid pJournal of the American Chemical Society · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
3 authors.
Funding
Abstract
All-atom molecular dynamics (MD) simulations based on physics-based force fields serve as an essential complement to experiments for investigating protein structure, dynamics, and interactions. Despite significant advances in force field parameterization, achieving a consistent balance of molecular interactions that stabilize folded proteins while accurately capturing the conformational dynamics of intrinsically disordered polypeptides in solution remains challenging. In this work, we introduce two refined force fields which incorporate either a selective upscaling of protein-water interactions or targeted improvements to backbone torsional sampling: (i) amber ff03w-sc, and (ii) amber ff99SBws-STQ'. Extensive validation against small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy observables revealed that both force fields accurately reproduced the chain dimensions and secondary structure propensities of IDPs. Importantly, both force fields also maintained the stability of single-chain folded proteins and protein-protein complexes over microsecond-timescale simulations. Overall, our refinement strategies result in transferable force fields with improved accuracy for simulating diverse protein systems, ranging from folded domains to IDPs and protein-protein complexes.
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