Calculation of the Vibrational Spectra of Tryptophan from QM/MM Molecular Dynamics Simulations

DIEGO JAVIER ALONSO DE ARMIÑO; MARIANO C. GONZÁLES LEBRERO; ADRIAN E. ROITBERG; DARIO A. ESTRÍN; R. M. S. ALVAREZ

Salta

Congreso; 3rd Latin American Protein Society Meeting; 2010

Latin American Protein Society

Vibrational spectroscopies, as well as molecular dynamics simulations (MD), are valuable tools for the study of structure and dynamics of proteins. There are two general approaches for the calculation of vibrational spectra on the basis of molecular dynamics simulations. The first is based on the calculation of harmonic vibrational frequencies through normal modes analysis of selected portions of snapshots of a classical MD simulation1. The second method, simpler and more natural than the former, consists in obtaining the vibrational spectra from the Fourier transform of the velocities autocorrelation function (FTVACF). This method has been successfully applied to small inorganic systems2,3, but has been seldom applied to biological ones4. The present study has the objective of establishing the validity of this method for biological systems like proteins. With this purpose, hybrid QM/MM molecular dynamics calculations of tryptophan in explicit solvent and in different environments were carried out, with the subsequent calculation of the FTVACF in order to obtain the vibrational spectra. Results were compared to experiment.