National Centre for Biomolecular Research,
Faculty of Science, Masaryk University, 611 37 Brno
Investigation of
the protein of mouse urine has shown that it consists predominantly of a group
of closely related proteins termed the Major Urinary Proteins (MUPs). These are
acidic proteins (pI values from 4.2 to 4.7) with molecular masses of
approximately 19 kDa. The MUPs are associated with pheromonally active ligands
including relatively tightly bound 2-sec-butyl-4,5-dihydrothiazole. Thus MUPs
may serve as a model of proteins binding small, hydrophobic ligands that are
known to possess the capability of chemical signaling. Structure of MUP-I was
determined crystallographically.
The X-ray
structures of MUP-I with and without ligand were taken and hydrogens,
counter-ions and box of explicit water molecules were added. The system was
minimized, heated and equilibrated and then the molecular dynamics was ran.
From whole trajectory a 6ns-long part was taken and used for further analysis
of internal motions of MUP-I. Correlation functions and frequency dependent
order parameters have been calculated.All molecular dynamics was performed with
AMBER7 software package.
This work was
supported by Grant No. 203/00/0511 from Grant Agency of the Czech Republic.