Induction of the tetracycline repressor: characterization by molecular-dynamics simulations.

Extensive molecular-dynamics simulations show that the distance between the centers of gravity of the two equivalent helices 3 in the DNA-binding heads of the dimer of the tetracycline-repressor protein (TetR) can be used as a reliable diagnostic of induction. This is not, however, true for X-ray structures, but only for molecular-dynamics simulations. This is suggested to be because TetR is inherently flexible along the coordinate of the allosteric change (as is always likely to be the case for allosteric proteins), so that crystal-packing forces can determine the conformation of the protein.

Molecular dynamics characterization of the structures and induction mechanisms of a reverse phenotype of the tetracycline receptor.

Molecular-dynamics simulations have been used to investigate the mechanism of induction of a mutant (revTetR) of the tetracycline repressor protein (TetR) that shows the reverse phenotype (i.e., it is induced in the absence of tetracyclines and not in their presence).