MOLECULAR-DYNAMICS SIMULATIONS OF THE CONFORMATIONAL DYNAMICS OF TRYPTOPHAN

Molecular dynamics simulations of a single tryptophan molecule were performed using CHARMm-parametrized potential functions, where both explicit molecular and dielectric continuum models were used for the solvent. When all hydrogens were modeled explicitly, rotations about the chi(2) dihedral were more frequent than about the chi(1) dihedral. The presence of a molecular solvent damped librational motion about both dihedral angles. Conversely, when a united atom representation for hydrogen was used, rotations about the chi(1) dihedral were more frequent than about the chi(2) dihedral. We show that conflicting rotamer models for the biexponential fluorescence of tryptophan zwitterion can be supported, depending on the model for hydrogen representation in the simulation. We also show that the predicted relative populations of trytophan rotamers are not consistent with the available experimental data. Simulators are thus warned not to impute universal applicability to empirical potential energy functions found in biomacromolecular molecular mechanics packages.