Conformational Dynamics of Trialanine in Water: A Molecular Dynamics Study

Abstract

Classical molecular dynamics (MD) studies of trialanine in aqueous solution are presented. The investigations have been inspired by recent 2D vibrational spectroscopy experiments of Woutersen and Hamm (J. Phys. Chem. B 2000, 104, 11316), who determined the structure and the conformational fluctuations of trialanine. The MD studies include various unbiased 20-ns simulations as well as umbrella sampling calculations of the potential of mean force along the central dihedral angles of trialanine. By employing the GROMOS96 force field, it is predicted that solvated trialanine is predominantly (∼80%) found in the extended conformations β and PII and is also (∼16%) found in the helix conformation αR. The results are explained by analyzing the free-energy contributions of intra- and intermolecular interactions, calculating the absolute entropy of the trialanine molecule, investigating the solvation and hydrogen bonding of the peptide, and studying the transitions between the extended and helix conformations. Moreover, the vibrational cross-relaxation rates associated with the two amide I modes of trialanine are calculated. The conformational structures and dynamics obtained from the MD studies are shown to be in good overall agreement with experimental data.