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

Keywords

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

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