ArticlePeerJ2018
How well do force fields capture the strength of salt bridges in proteins?
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 75 citations in OpenAlex.
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- Role of charges in a dynamic disordered complex between an IDP and a folded domain.Nature communications · 2025Article
- Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.The journal of physical chemistry. B · 2024Article
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- Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide.Proteins · 2024Article
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- Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers.The journal of physical chemistry. B · 2023Article
- TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins.Cell death & disease · 2023Article
- FERM domains recruit ample PI(4,5)PBiophysical journal · 2023Article
- Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein.Computational and structural biotechnology journal · 2023Article
- Physical Characteristics of von Willebrand Factor Binding with Platelet Glycoprotein Ibɑ Mutants at Residue 233 Causing Various Biological Functions.TH open : companion journal to thrombosis and haemostasis · 2022Article
- Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogenous Amyloid Oligomers.Journal of computational biophysics and chemistry · 2022Article
- Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants.Journal of the American Chemical Society · 2022Article
- The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.
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