ArticleThe journal of physical chemistry. B2016
Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 33 citations in OpenAlex.
- In vitro and in vivo Evaluation on the Safety and Efficacy of a Brand-New Intracutaneous Filler with α1-R-Collagen.Clinical, cosmetic and investigational dermatology · 2021Trial
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
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- All-atom simulations of biomolecular condensates.Current opinion in structural biology · 2025Review
- Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.Journal of chemical theory and computation · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.Communications chemistry · 2022Review
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20.Journal of chemical theory and computation · 2021Article
- Toward an understanding of biochemical equilibria within living cells.Biophysical reviews · 2018Review
- New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.Physical chemistry chemical physics : PCCP · 2018Review
- Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium/carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by rederiving the partial charges for each peptide.
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