ArticleThe journal of physical chemistry. B2015
Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 131 citations in OpenAlex.
- Lipid gating of BK channels and activation mechanism by negatively charged lipids.Communications chemistry · 2026Article
- Calcium activation mechanism of a noncanonical aromatic L-amino acid decarboxylase from psilocybin mushroom Psilocybe cubensis.Communications biology · 2026Article
- The Role of Architectural Forces in Ion Selectivity.Advances in experimental medicine and biology · 2026Article
- Calcium dissociation with carbonate ions from Pf-SCP, sarcoplasmic calcium-binding protein in Pinctada fucata, contributes to calcium mineralization for shell formation.Protein science : a publication of the Protein Society · 2025Article
- Deciphering CaProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ion-Induced Dipole Interactions Matter in Metadynamics Simulation of Transition Metal Ion Transporters.Journal of chemical theory and computation · 2025Article
- Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors.Nature communications · 2025Article
- Do selectivity filter carbonyls in KJournal of structural biology: X · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions.Journal of chemical information and modeling · 2024Article
- A non-B DNA binding peptidomimetic channel alters cellular functions.Nature communications · 2024Article
- FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation.The journal of physical chemistry. B · 2024Article
- Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.Journal of chemical theory and computation · 2024Article
- A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.Journal of chemical theory and computation · 2024Article
- System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Polarizable AMOEBA Model for Simulating MgJournal of chemical information and modeling · 2024Article
- Water inside the Selectivity Filter of a KJournal of the American Chemical Society · 2024Article
- Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.Journal of the American Chemical Society · 2023Article
- A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.The Journal of general physiology · 2023Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K(+), Na(+), Ca(2+), and Cl(-)) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca(2+) binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.