|Title||Influence of the nonlinearity and dipole strength on the amide I band of protein alpha-helices.|
|Publication Type||Journal Article|
|Year of Publication||2005|
|Journal||J Chem Phys|
|Date Published||2005 Dec 15|
|Keywords||Absorption, Amides, Carbon, Chemistry, Physical, Models, Statistical, Molecular Conformation, Oxygen, Peptides, Protein Conformation, Protein Structure, Secondary, Proteins, Temperature|
Vibrational energy storage and propagation are simulated in a fully atomic model of an alpha-helix by combining the AMBER force field for proteins with an extended version of the Davydov/Scott model for amide I vibrational transfer [A. Scott, Phys. Rep. 217, 1 (1992)]. Dipole-dipole interactions between transition dipole moments of amide I and its on-site energies are calculated from the corresponding three-dimensional atomic positions. The comparison of the theoretically calculated absorption line shapes with the experimentally measured ones leads to a putative value of the nonlinearity parameter of -30 pN.
|Alternate Journal||J Chem Phys|