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    Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ–carboxyglutamic acid: revised CHARMM22* parameters

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    Publication date
    2015
    Author
    Church, A.T.
    Hughes, Zak E.
    Walsh, T.R.
    Keyword
    Force-field development
    Amino-acids
    Molecular simulation
    CHARMM
    Rights
    © 2015 RSC. Full-text reproduced in accordance with the publisher’s self-archiving policy.
    Peer-Reviewed
    Yes
    
    Metadata
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    Abstract
    A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca2+, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca2+ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22*, substantially over-estimates the binding strength between Ca2+ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium–acetate and calcium–malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard–Jones interaction between Ca2+ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate–Ca2+ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22* parameter set.
    URI
    http://hdl.handle.net/10454/15911
    Version
    Accepted manuscript
    Citation
    Church AT, Hughes ZE and Walsh TR (2015) Improving the description of interactions between Ca2+ and protein carboxylate groups, including [gamma]-carboxyglutamic acid: revised CHARMM22* parameters. RSC Advances. 2015(83): 67820-67828.
    Link to publisher’s version
    https://doi.org/10.1039/C5RA11268K
    Type
    Article
    Collections
    Life Sciences Publications

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