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

Dynamics of the $\alpha$-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 C$\alpha$-atoms of the polypeptide backbone at the final part of the trajectory of 60–80 ns become constant: in the $\beta$-sheet – 0.4 $\mathring{\mathrm{A}}$, in helix1 – 0.8 $\mathring{\mathrm{A}}$, in helix2 – 0.6 $\mathring{\mathrm{A}}$, and in loops – 1.1 $\mathring{\mathrm{A}}$. The predicted dynamic profile of the C$\alpha$-atom shifts clearly indicates a decreasing in mobility of the $\alpha$-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.