MOLECULAR-DYNAMICS SIMULATION OF THE PROLINE CONFORMATIONAL EQUILIBRIUM AND DYNAMICS IN ANTAMANIDE USING THE GROMOS FORCE-FIELD

Molecular dynamics simulations of the proline-containing cyclic peptide antamanide using the GROMOS force field have been performed in order to compare the conformational equilibrium and dynamics of the four proline residues with experimental data originating from NMR spectroscopy. J-coupling constants, order parameters, and conformational populations are well-reproduced. The average simulated conformational residence times of 4 ps are shorter than the measured ones which are on the order of 30 ps, implying a somewhat too flexible force field for proline rings. The proline dynamics seems to be insensitive to the observed conformational dynamics of the peptide ring and to the solvent viscosity.