Discrete breathers in protein secondary structure

The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction characterizing the chain rigidity and the effective on-site potentials are calculated for three main types of protein secondary structure. The coupling interaction is found to be surprisingly weak for all of them but different in character: repulsive for α-helix and anti-parallel β-sheet structures and attractive for parallel β-sheet structure. The effective on-site potential is found to be a hard one for α-helix and anti-parallel β-sheet and a soft one for parallel β-sheet. In all three types of protein secondary structures a stable zig-zag shape discrete breather (DB) associated with the oscillations of torsional (dihedral) angles can exist due to weakness of the coupling interaction. However, since the absorption of far infrared radiation (IR) by proteins is known to require the existence of rather long chains of hydrogen bonds that takes place only in α-helicies, then one can conclude that the excitation of a DB in such a way is possible in α-helix and seems to be hardly possible in β-sheet structures. The interpretation of the recent experiments of Xie et al. on far IR laser pulse spectroscopy of proteins is suggested. The frequency of a DB in an the α-helix is obtained in the region of 115 cm−1 in accordance with these experiments.