In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent

Vinodhkuma Vijayakumar, Ramadoss Vijayaraj, Günther H. Peters

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

    Resumé

    The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(d-Trp-l-Gln-d-Trp-l-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone–backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain–side chain hydrogen bonds.
    OriginalsprogEngelsk
    Artikelnummer264
    TidsskriftJournal of Molecular Modeling
    Vol/bind22
    ISSN1610-2940
    DOI
    StatusUdgivet - 2016

    Emneord

    • Peptide conformation
    • In silico modelling
    • Simulation techniques
    • Free energy calculations
    • Steered molecular dynamics simulations
    • Cyclic peptide nanotubes

    Citer dette

    Vijayakumar, Vinodhkuma ; Vijayaraj, Ramadoss ; Peters, Günther H. / In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent. I: Journal of Molecular Modeling. 2016 ; Bind 22.
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    title = "In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent",
    abstract = "The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(d-Trp-l-Gln-d-Trp-l-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone–backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain–side chain hydrogen bonds.",
    keywords = "Peptide conformation, In silico modelling, Simulation techniques, Free energy calculations, Steered molecular dynamics simulations, Cyclic peptide nanotubes",
    author = "Vinodhkuma Vijayakumar and Ramadoss Vijayaraj and Peters, {G{\"u}nther H.}",
    year = "2016",
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    In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent. / Vijayakumar, Vinodhkuma; Vijayaraj, Ramadoss; Peters, Günther H.

    I: Journal of Molecular Modeling, Bind 22, 264, 2016.

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

    TY - JOUR

    T1 - In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent

    AU - Vijayakumar, Vinodhkuma

    AU - Vijayaraj, Ramadoss

    AU - Peters, Günther H.

    PY - 2016

    Y1 - 2016

    N2 - The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(d-Trp-l-Gln-d-Trp-l-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone–backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain–side chain hydrogen bonds.

    AB - The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(d-Trp-l-Gln-d-Trp-l-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone–backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain–side chain hydrogen bonds.

    KW - Peptide conformation

    KW - In silico modelling

    KW - Simulation techniques

    KW - Free energy calculations

    KW - Steered molecular dynamics simulations

    KW - Cyclic peptide nanotubes

    U2 - 10.1007/s00894-016-3122-x

    DO - 10.1007/s00894-016-3122-x

    M3 - Journal article

    VL - 22

    JO - Journal of Molecular Modeling

    JF - Journal of Molecular Modeling

    SN - 1610-2940

    M1 - 264

    ER -