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J Phys Chem B

Title:		Backbone motions of free and pheromone-bound major urinary protein I studied by molecular dynamics simulation
Author(s):		Macek P; Novak P; Zidek L; Sklenar V;
Address:		"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, KotlArskA 2, CZ-611 37 Brno, Czech Republic"
Journal Title:		J Phys Chem B
Year:		2007
Volume:		20070428
Issue:		20
Page Number:		5731 - 5739
DOI:		10.1021/jp0700940
ISSN/ISBN:		1520-6106 (Print) 1520-5207 (Linking)
Abstract:		"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. 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 '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 a larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in 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"
Keywords:		"Computer Simulation Models, Molecular Motion Pheromones/*chemistry Protein Conformation Proteins/*chemistry Thiazoles/*chemistry;"
Notes:		"MedlineMacek, Pavel Novak, Petr Zidek, Lukas Sklenar, Vladimir eng Research Support, Non-U.S. Gov't 2007/05/01 J Phys Chem B. 2007 May 24; 111(20):5731-9. doi: 10.1021/jp0700940. Epub 2007 Apr 28"