ArticleJournal of computational chemistry2020
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Molecular Dynamics Reveals Unique Distal Histidine Positions and Interfacial Transitions of Fish and Mammalian Deoxyhemoglobin at Post-mortem pH.Journal of agricultural and food chemistry · 2025Article
- Cation-π Interactions in Biomolecular Contexts by Neutron Scattering and Molecular Dynamics: A Case Study of the Tetramethylammonium Cation.The journal of physical chemistry. B · 2025Article
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClJournal of chemical theory and computation · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Electronic Polarizability Tunes the Function of the Human Bestrophin 1 ClbioRxiv : the preprint server for biology · 2024Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Article
- Ion permeation, selectivity, and electronic polarization in fluoride channels.Biophysical journal · 2022Article
- Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.Communications chemistry · 2022Review
- Article
- Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC.Nature communications · 2021Article
- Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization.Computational and structural biotechnology journal · 2021Article
- Explicit Representation of Cation-π Interactions in Force Fields with 1/Journal of chemical theory and computation · 2020Article
- New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology.Journal of chemical theory and computation · 2020Article
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.Journal of chemical theory and computation · 2020Article
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2 authors.
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Abstract
Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.
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