ArticleThe journal of physical chemistry. B2009
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 388 papers.
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Who cites it
388 citing papers in PubMed.
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- Molecular determinants of arginine versus lysine cation-π interactions in biomolecular condensates.Communications chemistry · 2026Article
- Hierarchical multi-timescale structural dynamics of the disordered N-terminal of p53.Nature communications · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- How to Use Quantum Computers for Biomolecular Free Energies.Journal of chemical theory and computation · 2026Article
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- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Nearest neighbour interactions between amino acid residues in short peptides and coil libraries.RSC advances · 2026Article
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- USP1 driven mitotic dysregulation and PLK1 stabilization confer Lenvatinib resistance in hepatocellular carcinoma.Journal of experimental & clinical cancer research : CR · 2026Article
- Contact Cluster Modeling of Allosteric Communication in PDZ Domains.The journal of physical chemistry. B · 2026Review
- Biomolecular Condensates Dictate the Folding Landscape of Proteins.bioRxiv : the preprint server for biology · 2026Article
- Proton-selective conductance and gating of the lysosomal cation channel TMEM175.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
328 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
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