Molecular dynamics of the α-helical hairpin and its surrounding inside the protein S16 from Thermus thermophilus

Dynamics of the α-helical hairpin inside the ribosomal protein S16 from Thermus thermophilus has been considered. The analysis of polypeptide chain dynamics was carried out on five independent trajectories with a total time of 370 ns. It was shown that relaxed fluctuations of Cα-atoms of the polypeptide backbone at the final part of the trajectory of 60–80 ns become constant: in the β-sheet – 0.4 Å, in helix1 – 0.8 Å, in helix2 – 0.6 Å, and in loops – 1.1 Å. The predicted dynamic profile of the Cα-atom shifts clearly indicates a decreasing in mobility of the α-hairpin in the regions where hydrophobic clusters are located. The restriction factor of such movements is directly related to the interaction of their residues with the other protein residues.