Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand-protein interaction

Molecular dynamics simulations of the apo- and holo-forms of the trp-repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand-protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X-ray temperature factors. Distance, distance fluctuation, and dynamic cross-correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three-domain format has been proposed for the crystal structure (Zhang et al., Nature 327:591-597, 1987); namely, helices A-C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three-domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix-turn-helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA-binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments.