Simulations of amide I infrared band of proteins using classical molecular dynamics.

VILLAREAL, M; DECCA, M. B.; MONTICH, G

Los Cocos, Córdoba, Argentina

Congreso; XXXVIII Reunión Anual de la Sociedad Argentina de Biofísica.; 2009

The infrared spectrum of the amide I band is approximated by fourier-transforming the individual carbonyls vibrations obtained from classical molecular dynamics simulations. This approximation allows the calculation not only of the entire amide I band, but also the spectra of the different secondary structures in the protein. In this work we parametrize the bond and bond-angle constants of the GROMOS G53a6 force field to reproduce the experimental spectrum of ribonucleasa. After the parametrization the amide I band of myoblobin, lisozyme and BABP are calculated and the results of the simulation are compared with the corresponding experimental spectra. We observe a good agreement between the simulated and experimental amide I band, for myoglobin and lisosyme, but only a qualitative agreement for the protein BABP. We also compared the components of the amide I band. The simulations and the band analysis generally agree with the relative position of the bands, but differ in the shape. While in the traditional a gaussian or lorenzial function is assumed, the simulations show highly asymmetric curves for some components.