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

DIEGO ALONSO DE ARMIÑO; MARIANO C. GONZÁLEZ LEBRERO; ADRIÁN ROITBERG; DARÍO A. ESTRIN; ROSA MARIA SUSANA ALVAREZ

Salta

Congreso; XXXIX Anual Meeting of the Argentinean Biophysical Society- 3rd Latin American Protein Society Meeting.; 2010

Sociedad Argentina de Biofísica

Vibrational spectroscopies, as well as molecular dynamics simulations, 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 of optimized structures obtained by molecular dynamics simulations1. 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), which was successfully applied  to small inorganic systems2, but seldom to biological ones3. The present study is intended as a preliminary work with the aim of establishing its validity for biological systems like proteins. With this purpose, hybrid QM/MM molecular dynamics calculations of tryptophan in explicit solvent were carried out, with the subsequent calculation of  the FTVACF,  in order to obtain the vibrational spectra. The results were compared to experimental data. References: 1. (a) J. Phys. Chem. A 2010, 114, 1212–1217 ; (b) J. Am. Chem. Soc., 2004, 126 (34), pp 10516–10517 2. (a)J. Phys. Chem. B, 2008, 112 (37), pp 11726–11733; (b) J. Phys. Chem. A, 1997, 101 (35), pp 6299–6309; (c) J. Phys. Chem. B, 2009, 113 (39), pp 13007–13013 3. (a)  J. Chem. Theory Comput., 2009, 5 (8), pp 2158–2172;  (b) J. Phys. Chem. B, 2007, 111 (48), pp 13626–13631 Acknowledgments: (Times New Roman, 8pt, Justified, single line spacing)