Molecular dynamics of α-hairpin motif in globular proteins: hydrophobic factor restricts the mobility of the peptide chain

Molecular dynamics of the α-helical hairpin structural motifs in five selected globular proteins were considered. The dynamics of each polypeptide chain were investigated on four independent trajectories with total time of 400 ns. A decrease in the dynamic mobility of α-helical hairpins was clearly observed in the regions containing certain amino acid residues. And that phenomena depends on the contacts of non-polar atoms of the hairpin residues with the other surrounding residues. This was demonstrated for α-helical hairpin motif but may also be applicable to the other structural motifs of the protein molecules. As a result, it is possible to estimate the dynamic behavior of any protein in aqueous solution and even predict structural changes of the polypeptide chain.