Discrete breathers in protein secondary structure

Details Discrete breathers in protein secondary structure Discrete breathers in protein secondary structure

2003-06-05

arxiv.org/abs/cond-mat/0306135v2

Soft Condensed Matter. New Research. Ed. K.I.Dillon, Ch. 5, pp. 157-172, Nova, 2007.

Physics

Condensed Matter

Soft Condensed Matter

LaTeX, 20 pages, 5 eps figures. Revised version. Invited contribution for the collection "Soft condensed matter. New research.

Scientific paper

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 alpha-helix and anti-parallel beta-sheet structures and attractive for parallel beta-sheet structure. The effective on-site potential is found to be a hard one for alpha-helix and anti-parallel beta-sheet and a soft one for parallel beta-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 alpha-helicies, then one can conclude that the excitation of a DB in such a way is possible in alpha-helix and seems to be hardly possible in beta-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 alpha-helix is obtained in the region of 115 cm^{-1} in accordance with these experiments.

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