Influence of the nonlinearity and dipole strength on the amide I band of protein α-helices
Abstract
Vibrational energy storage and propagation are simulated in a fully atomic model of an α-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 -30pN.
- Publication:
-
Journal of Chemical Physics
- Pub Date:
- December 2005
- DOI:
- 10.1063/1.2138705
- Bibcode:
- 2005JChPh.123w4909C
- Keywords:
-
- 87.15.By;
- 87.15.Kg;
- 87.15.Aa;
- 36.20.Ey;
- 87.15.He;
- Structure and bonding;
- Molecular interactions;
- membrane-protein interactions;
- Theory and modeling;
- computer simulation;
- Conformation;
- Dynamics and conformational changes