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Título

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

Autor D'Ovidio, Francesco; Bohr, Henrik Georg; Lindgaard, Per-Anker
Palabras clave Solitons
Lennard-Jones potential
Proteins
Hydrogen bonds
Vibrational modes
Phonons
Microorganisms
Molecular biophysics
Fecha de publicación 15-feb-2005
EditorAmerican Physical Society
Citación Physical Review E 71, 026606 (1-9) (2005)
ResumenWe 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.
Descripción 9 pages, 13 figures.-- PACS nrs.: 05.45.Yv, 87.15.-v.-- PMID: 15783440 [PubMed].
Versión del editorhttp://dx.doi.org/10.1103/PhysRevE.71.026606
URI http://hdl.handle.net/10261/7476
DOI10.1103/PhysRevE.71.026606
ISSN1539-3755
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