ArticleThe journal of physical chemistry. B2014
Force field independent metal parameters using a nonbonded dummy model.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Lenalidomide Stabilizes Protein-Protein Complexes by Turning Labile Intermolecular H-Bonds into Robust Interactions.Journal of medicinal chemistry · 2023Article
- Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.Nature communications · 2022Article
- Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors.Journal of chemical information and modeling · 2022Article
- Unlocking the computational design of metal-organic cages.Chemical communications (Cambridge, England) · 2022Review
- A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.Proteins · 2022Article
- Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study.Frontiers in molecular biosciences · 2022Article
- Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [MJournal of chemical information and modeling · 2021Article
- Probing the Suitability of Different CaMolecules (Basel, Switzerland) · 2021Article
- A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase.Nucleic acids research · 2021Article
- Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.The Journal of general physiology · 2021Article
- Analysis of Kojic Acid Derivatives as Competitive Inhibitors of Tyrosinase: A Molecular Modeling Approach.Molecules (Basel, Switzerland) · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.
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