Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices

Bercem Dutagaci, Maryam Sayadi, Michael Feig

    Research output: Contribution to journalArticle

    • 2 Citations

    Abstract

    The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) by combining separate contributions from each of the membrane components. The HDGBvdW model is validated with a series of test cases ranging from membrane insertion and pair association profiles of amino acid side chain analogs and transmembrane helices. Overall, the HDGBvdW model leads to increased agreement with explicit membrane simulation results and experimental data.

    Original languageEnglish (US)
    Pages (from-to)1308-1320
    Number of pages13
    JournalJournal of Computational Chemistry
    Volume38
    Issue number16
    DOIs
    StatePublished - Jun 15 2017

    Profile

    Membrane
    Bronchiolo-Alveolar Adenocarcinoma
    Membranes
    Model
    Anthralin
    Van der Waals
    Term
    Helix
    Hexosaminidase A
    Association reactions
    Energy estimates
    Insertion
    Amino acids
    Free energy
    Interior
    Experimental data
    Analogue
    Series
    Interaction
    Simulation

    Keywords

    • generalized Born formalism
    • implicit membrane model
    • transmembrane helix dimers

    ASJC Scopus subject areas

    • Chemistry(all)
    • Computational Mathematics

    Cite this

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    abstract = "The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al. (J. Comput. Chem. 2004, 25, 479) by combining separate contributions from each of the membrane components. The HDGBvdW model is validated with a series of test cases ranging from membrane insertion and pair association profiles of amino acid side chain analogs and transmembrane helices. Overall, the HDGBvdW model leads to increased agreement with explicit membrane simulation results and experimental data.",
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    T1 - Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices

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    AU - Sayadi,Maryam

    AU - Feig,Michael

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