ArticleJournal of chemical theory and computation2011
A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.
Article in Journal of chemical theory and computation, 2011. 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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Who cites it
16 citing papers in PubMed, 52 citations in OpenAlex.
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- Design, Synthesis, and Biological Evaluation of Novel Triazine-Based Dual Histone Deacetylase/phosphatidylinositol 3-kinase Inhibitors for Breast Cancer Therapy.ChemMedChem · 2026Article
- Automatically Constructed Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins.Frontiers in chemistry · 2021Article
- Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A.The journal of physical chemistry. B · 2019Article
- Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications.Molecular informatics · 2018Article
- Force Field Parametrization of Metal Ions from Statistical Learning Techniques.Journal of chemical theory and computation · 2018Article
- Metal Ion Modeling Using Classical Mechanics.Chemical reviews · 2017Review
- Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study.Journal of computational chemistry · 2015Article
- Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect.The journal of physical chemistry letters · 2015Article
- Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications.The journal of physical chemistry. B · 2015Article
- AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.Journal of chemical information and modeling · 2014Article
- Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions.Journal of chemical theory and computation · 2014Article
- Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.Journal of chemical theory and computation · 2013Article
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.Journal of biomolecular NMR · 2013Article
- Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- Simulations of allosteric motions in the zinc sensor CzrA.Journal of the American Chemical Society · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Herein we introduce a novel practical strategy to overcome the well-known challenge of modeling the divalent zinc cation in metalloproteins. The main idea is to design short-long effective functions (SLEF) to describe charge interactions between the zinc ion and all other atoms. This SLEF approach has the following desired features: (1). It is pairwise, additive and compatible with widely used atomic pair-wise force fields for modeling biomolecules; (2). It only changes interactions between the zinc ion and other atoms, and does not affect force field parameters that model other interactions in the system; (3). It is a non-bonded model that is inherently capable to describe different zinc ligands and coordination modes. By optimizing two SLEF parameters as well as zinc vdW parameters through force matching based on Born-Oppenheimer ab initio QM/MM molecular dynamics simulations, we have successfully developed the first SLEF force field (SLEF1) to describe zinc interactions. Extensive molecular dynamics simulations of seven zinc enzyme systems with different coordination ligands and distinct chelation modes (4-,5-,6-fold), including the binuclear zinc active site, yielded zinc coordination numbers and binding distances in good agreement with the corresponding crystal structures as well as ab initio QM/MM MD results. This not only demonstrates the transferability and adequacy of the new SLEF1 force field in describing a variety of zinc proteins, but also indicates that this novel SLEF approach is a promising direction to explore for improving force field description of metal ion interactions.
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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.