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Open Access item Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

Authors:d'Ovidio, Francesco
Bohr, Henrik Georg
Lindgaard, Per-Anker
Keywords:Solitons, Lennard-Jones potential, Proteins, Hydrogen bonds, Vibrational modes, Phonons, Microorganisms, Molecular biophysics
Issue Date:15-Feb-2005
Publisher:American Physical Society
Citation:Physical Review E 71, 026606 (1-9) (2005)
Abstract:We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons. The soliton phenomena described in the simulations of alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed.
Description:9 pages, 13 figures.-- PACS nrs.: 05.45.Yv, 87.15.-v.-- PMID: 15783440 [PubMed].
Publisher version (URL):http://dx.doi.org/10.1103/PhysRevE.71.026606
Appears in Collections:(IFISC) Artículos

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