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.