Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

Jacob Sonne, Morten Østergaard Jensen, Flemming Y. Hansen, Lars Hemmingsen, Günther H. Peters

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.
    Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.
    LanguageEnglish
    JournalBiophysical Journal
    Volume92
    Issue number12
    Pages4157-4167
    Number of pages11
    ISSN0006-3495
    DOIs
    StatePublished - 2007

    Keywords

    • ensemble
    • force field
    • lipid bilayers
    • molecular dynamics

    Cite this

    Sonne, Jacob ; Jensen, Morten Østergaard ; Hansen, Flemming Y. ; Hemmingsen, Lars ; Peters, Günther H./ Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. In: Biophysical Journal. 2007 ; Vol. 92, No. 12. pp. 4157-4167
    @article{3fdaf8f0a40111dcaf2d000ea68e967b,
    title = "Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension",
    abstract = "Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 {\AA}2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 {\AA}2. Compared to the 48 {\AA}2, the new value of 60.4 {\AA}2 is in fair agreement with the experimental value of 64 {\AA}2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright {\circledC} 2007 by the Biophysical Society.",
    keywords = "ensemble, force field, lipid bilayers, molecular dynamics",
    author = "Jacob Sonne and Jensen, {Morten {\O}stergaard} and Hansen, {Flemming Y.} and Lars Hemmingsen and Peters, {G{\"u}nther H.}",
    year = "2007",
    doi = "10.1529/biophysj.106.087130",
    language = "English",
    volume = "92",
    pages = "4157--4167",
    journal = "Biophysical Journal",
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    publisher = "Cell Press",
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    Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension. / Sonne, Jacob; Jensen, Morten Østergaard; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

    In: Biophysical Journal, Vol. 92, No. 12, 2007, p. 4157-4167.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

    AU - Sonne,Jacob

    AU - Jensen,Morten Østergaard

    AU - Hansen,Flemming Y.

    AU - Hemmingsen,Lars

    AU - Peters,Günther H.

    PY - 2007

    Y1 - 2007

    N2 - Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.

    AB - Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (N PT) ensemble give highly ordered, gel-like bilayers (20) with an area per lipid of ~48 Å2 (31). To obtain fluid (L) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid head group and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential (RESP) fitting method (5). We tested the derived charges in MD simulations of a fully hydrated DPPC bilayer. Only the simulation with the new RESP charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2 (43). Also the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the N PT ensemble by employing our modified CHARMM27 force field. Copyright © 2007 by the Biophysical Society.

    KW - ensemble

    KW - force field

    KW - lipid bilayers

    KW - molecular dynamics

    U2 - 10.1529/biophysj.106.087130

    DO - 10.1529/biophysj.106.087130

    M3 - Journal article

    VL - 92

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    EP - 4167

    JO - Biophysical Journal

    T2 - Biophysical Journal

    JF - Biophysical Journal

    SN - 0006-3495

    IS - 12

    ER -