ACS Publications. Most Trusted. Most Cited. Most Read

OR SEARCH CITATIONS

My Activity
Publications
CONTENT TYPES

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Theory Comput. 2018, 14, 1, 242-254
RETURN TO ISSUEPREVArticleNEXT

Extended Zinc AMBER Force Field (EZAFF)

View Author Information
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
*E-mail: [email protected]
Cite this: J. Chem. Theory Comput. 2018, 14, 1, 242–254
Publication Date (Web):November 17, 2017
https://doi.org/10.1021/acs.jctc.7b00773
Copyright © 2017 American Chemical Society
Request reuse permissions

    Article Views

    2046

    Altmetric

    -

    Citations

    30
    LEARN ABOUT THESE METRICS
    Read OnlinePDF (5 MB)
    Get e-Alerts
    Supporting Info (1)»
    SUBJECTS:

    Abstract

    Abstract Image

    An empirical approach based on the previously developed zinc AMBER force field (ZAFF) is proposed for the determination of the parameters for bonds and angles involving zinc. We call it the extended ZAFF (EZAFF) model because the original ZAFF model was only formulated for four-coordinated systems, while EZAFF additionally can tackle five- and six-coordinated systems. Tests were carried out for six metalloproteins and six organometallic compounds with different coordination spheres. Results validated the reliability of the current model to handle a variety of zinc containing complexes. Meanwhile, benchmark calculations were performed to assess the performance of three bonded molecular mechanics models (EZAFF, Seminario, and Z-matrix models), four nonbonded parameter sets (the HFE, IOD, CM, and 12-6-4 models), and four semiempirical quantum mechanical methods (AM1, PM3, PM6, and SCC-DFTB methods) for simulating zinc containing systems. The obtained results indicate that, even with their increased computational cost, the semiempirical quantum methods only offered slightly better accuracy for the computation of relative energies and only afforded similar molecular geometries, when compared to the investigated molecular mechanics models.

    Supporting Information

    ARTICLE SECTIONS
    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.7b00773.

    • Table S1 showing mean errors of relative energies for 12 zinc complexes investigated; Table S2 showing RMSDs of the optimized structure by various methods toward the DFT optimized geometry; Table S3 showing RMSDs of the optimized structure by various methods toward the crystal structure. (PDF)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 30 publications.

    1. Süleyman Selim Çınaroğlu, Philip C. Biggin. Computed Protein–Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. Journal of Chemical Information and Modeling 2023, Article ASAP.
    2. Mirko Paulikat, Daniele Vitone, Florian K. Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti, Giulia Rossetti, Adam H. Clark, Maarten Nachtegaal, Michael Haumann, Holger Dau, Paolo Carloni, Silvano Geremia, Rita De Zorzi, Liliana Quintanar, Fabio Arnesano. Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. Journal of Chemical Information and Modeling 2023, 63 (1) , 161-172. https://doi.org/10.1021/acs.jcim.2c01164
    3. Isabel Armour-Garb, In Sub Mark Han, Benjamin S. Cowan, Kelly M. Thayer. Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction. The Journal of Physical Chemistry B 2022, 126 (42) , 8495-8507. https://doi.org/10.1021/acs.jpcb.2c06229
    4. Angela Parise, Giada Ciardullo, Mario Prejanò, Aurélien de la Lande, Tiziana Marino. On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. Journal of Chemical Information and Modeling 2022, 62 (20) , 4916-4927. https://doi.org/10.1021/acs.jcim.2c01002
    5. Alexandre C. Oliveira, Hugo A. L. Filipe, João P. Prates Ramalho, Armindo Salvador, Carlos F. G. C. Geraldes, Maria João Moreno, Luís M. S. Loura. Modeling Gd3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents. Inorganic Chemistry 2022, 61 (30) , 11837-11858. https://doi.org/10.1021/acs.inorgchem.2c01597
    6. Dana L. Cruz, Nina Pipalia, Shu Mao, Deepti Gadi, Gang Liu, Michael Grigalunas, Matthew O’Neill, Taylor R. Quinn, Andi Kipper, Andreas Ekebergh, Alexander Dimmling, Carlos Gartner, Bruce J. Melancon, Florence F. Wagner, Edward Holson, Paul Helquist, Olaf Wiest, Frederick R. Maxfield. Inhibition of Histone Deacetylases 1, 2, and 3 Enhances Clearance of Cholesterol Accumulation in Niemann-Pick C1 Fibroblasts. ACS Pharmacology & Translational Science 2021, 4 (3) , 1136-1148. https://doi.org/10.1021/acsptsci.1c00033
    7. Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz, Jr.. Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of Chemical Theory and Computation 2021, 17 (4) , 2342-2354. https://doi.org/10.1021/acs.jctc.0c01320
    8. Florencia Klein, Daniela Cáceres, Mónica A. Carrasco, Juan Carlos Tapia, Julio Caballero, Jans Alzate-Morales, Sergio Pantano. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. Journal of Chemical Information and Modeling 2020, 60 (8) , 3935-3943. https://doi.org/10.1021/acs.jcim.0c00160
    9. Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. ACS Omega 2020, 5 (25) , 15301-15310. https://doi.org/10.1021/acsomega.0c01337
    10. Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci. Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. Journal of Chemical Information and Modeling 2019, 59 (9) , 3803-3816. https://doi.org/10.1021/acs.jcim.9b00407
    11. Antonija Tomić, Gordan Horvat, Michael Ramek, Dejan Agić, Hrvoje Brkić, Sanja Tomić. New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. Journal of Chemical Information and Modeling 2019, 59 (8) , 3437-3453. https://doi.org/10.1021/acs.jcim.9b00235
    12. A. Löhner, T. Kunsel, M. I. S. Röhr, T. L. C. Jansen, S. Sengupta, F. Würthner, J. Knoester, J. Köhler. Spectral and Structural Variations of Biomimetic Light-Harvesting Nanotubes. The Journal of Physical Chemistry Letters 2019, 10 (11) , 2715-2724. https://doi.org/10.1021/acs.jpclett.9b00303
    13. Searle S. Duay, Gaurav Sharma, Rajeev Prabhakar, Alfredo M. Angeles-Boza, Eric R. May. 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 2019, 123 (15) , 3163-3176. https://doi.org/10.1021/acs.jpcb.8b11496
    14. Julen Aduriz‐Arrizabalaga, Xabier Lopez, David De Sancho. Atomistic molecular simulations of Aβ‐Zn conformational ensembles. Proteins: Structure, Function, and Bioinformatics 2023, 12 https://doi.org/10.1002/prot.26590
    15. Simone Scrima, Matteo Tiberti, Ulf Ryde, Matteo Lambrughi, Elena Papaleo. Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2023, 1871 (4) , 140921. https://doi.org/10.1016/j.bbapap.2023.140921
    16. Éderson Sales Moreira Pinto, Mathias J. Krause, Márcio Dorn, Bruno César Feltes. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair 2023, 127 , 103510. https://doi.org/10.1016/j.dnarep.2023.103510
    17. Kerlen T. Korbeld, Maximilian J. L. J. Fürst. Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering. ChemBioChem 2023, 24 (12) https://doi.org/10.1002/cbic.202300192
    18. Amani A. Eshtiwi, Dan L. Rathbone. A modified bonded model approach for molecular dynamics simulations of New Delhi Metallo-β-lactamase. Journal of Molecular Graphics and Modelling 2023, 121 , 108431. https://doi.org/10.1016/j.jmgm.2023.108431
    19. Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias. Benchmarking biomolecular force field‐based Zn 2+ for mono‐ and bimetallic ligand binding sites. Journal of Computational Chemistry 2023, 44 (8) , 912-926. https://doi.org/10.1002/jcc.27052
    20. Senta Volkenandt, Petra Imhof. Comparison of Empirical Zn2+ Models in Protein–DNA Complexes. Biophysica 2023, 3 (1) , 214-230. https://doi.org/10.3390/biophysica3010014
    21. Varun Dewaker, Pratik Narain Srivastava, Saroj Verma, Ajay K. Srivastava, Yenamandra S. Prabhakar. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics 2022, 40 (24) , 13432-13455. https://doi.org/10.1080/07391102.2021.1989037
    22. Harpreet Kaur, Manmohit Kalia, Vikram Singh, Neelam Taneja. Identification of novel inhibitors against Escherichia coli utilizing HisC as a target from histidine biosynthesis pathway. Journal of Biomolecular Structure and Dynamics 2022, 295 , 1-8. https://doi.org/10.1080/07391102.2022.2148319
    23. Harpreet Kaur, Manmohit Kalia, Naveen Chaudhary, Vikram Singh, Vivek Kumar Yadav, Vinay Modgil, Vishal Kant, Balvinder Mohan, Alka Bhatia, Neelam Taneja. Repurposing of FDA approved drugs against uropathogenic Escherichia coli: In silico, in vitro, and in vivo analysis. Microbial Pathogenesis 2022, 13 , 105665. https://doi.org/10.1016/j.micpath.2022.105665
    24. Peter R. Fatouros, Urmi Roy, Shantanu Sur. Modeling Substrate Coordination to Zn-Bound Angiotensin Converting Enzyme 2. International Journal of Peptide Research and Therapeutics 2022, 28 (2) https://doi.org/10.1007/s10989-022-10373-6
    25. Silvia Gervasoni, James Spencer, Philip Hinchliffe, Alessandro Pedretti, Franco Vairoletti, Graciela Mahler, Adrian J. Mulholland. A multiscale approach to predict the binding mode of metallo beta‐lactamase inhibitors. Proteins: Structure, Function, and Bioinformatics 2022, 90 (2) , 372-384. https://doi.org/10.1002/prot.26227
    26. Claudio Perego, Luca Pesce, Riccardo Capelli, Subi J. George, Giovanni M. Pavan. Multiscale Molecular Modelling of ATP‐Fueled Supramolecular Polymerisation and Depolymerisation**. ChemSystemsChem 2021, 3 (2) https://doi.org/10.1002/syst.202000038
    27. Afrah Khairallah, Özlem Tastan Bishop, Vuyani Moses. AMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6‐pyruvoyl tetrahydropterin synthase. Journal of Biomolecular Structure and Dynamics 2020, 9 , 1-18. https://doi.org/10.1080/07391102.2020.1796800
    28. Varun Dewaker, Ajay K. Srivastava, Ashish Arora, Yenamandra S. Prabhakar. Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents. Journal of Biomolecular Structure and Dynamics 2020, 97 , 1-26. https://doi.org/10.1080/07391102.2020.1780940
    29. Berkley E. Gryder, Lei Wu, Girma M. Woldemichael, Silvia Pomella, Taylor R. Quinn, Paul M. C. Park, Abigail Cleveland, Benjamin Z. Stanton, Young Song, Rossella Rota, Olaf Wiest, Marielle E. Yohe, Jack F. Shern, Jun Qi, Javed Khan. Chemical genomics reveals histone deacetylases are required for core regulatory transcription. Nature Communications 2019, 10 (1) https://doi.org/10.1038/s41467-019-11046-7
    30. Victor De La Rosa, Ashley L. Bennett, Ian Scott Ramsey. Coupling between an electrostatic network and the Zn2+ binding site modulates Hv1 activation. Journal of General Physiology 2018, 150 (6) , 863-881. https://doi.org/10.1085/jgp.201711822
    Download PDF

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect