On using oscillating time-dependent restraints in MD simulation

Bettina Keller, Markus Christen, Chris Oostenbrink, Wilfred F. van Gunsteren*

*Corresponding author for this work

    Research output: Contribution to JournalArticleAcademicpeer-review

    Abstract

    The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average 3J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating 3J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a 3J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling.

    Original languageEnglish
    Pages (from-to)1-14
    Number of pages14
    JournalJournal of Biomolecular NMR
    Volume37
    Issue number1
    DOIs
    Publication statusPublished - 1 Jan 2007

    Funding

    Financial support by the National Centre of Competence in Research (NCCR) Structural Biology and by grant 200021-109227 of the Swiss National Science Foundation (SNSF) is gratefully acknowledged.

    Keywords

    • J-coupling constants
    • Molecular modeling
    • NMR data
    • Restrained MD
    • Structure refinement

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