Publication details

Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation



Year of publication 2007
Type Article in Periodical
Magazine / Source Journal of Physical Chemistry B
MU Faculty or unit

Faculty of Science

Field Biophysics
Keywords Molecular dynamics; order parameter; NMR relaxation; motional analysis
Description Molecular motions of free and pheromone-bound mouse major urinary protein~I, previously investigated by NMR relaxation, were simulated in 30-ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. A special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances and a "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in a general agreement with the NMR results. The higher flexibility observed on the fast (fs--ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.
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