RESUMO
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). Low-frequency, normal-mode analyses demonstrate that the reverse phenotype is reproduced by the simulations on the basis of criteria established for wild-type TetR. The reverse phenotype is caused by the fact that the DNA-binding heads in revTetR are closer than the ideal distance needed for DNA-binding when no inducer is present. This distance increases on binding an inducer. Whereas this distance increase makes the interhead distance too large in wild-type TetR, it increases to the ideal value in revTetR. Thus, the mechanism of induction is the same for the two proteins, but the consequences are reversed because of the smaller interhead distance in revTetR when no inducer is present.
Assuntos
Simulação por Computador , Modelos Biológicos , Proteínas Repressoras/química , DNA/química , Modelos Moleculares , Conformação Molecular , Mutação , Estrutura Secundária de Proteína , Proteínas Repressoras/efeitos dos fármacos , Relação Estrutura-Atividade , Tetraciclina/química , Tetraciclina/farmacologia , Tetraciclinas/química , Tetraciclinas/farmacologia , Fatores de TempoRESUMO
The binding motif (pharmacophore) for induction and the changes in the structure of the binding site that accompany induction have been determined from molecular-dynamics simulations on the tetracycline-repressor signal-transduction protein. The changes and the induction mechanism are discussed and compared with conclusions drawn from earlier X-ray structures. The differences in inducer strength of tetracycline and 5a,6-anhydrotetracycline are discussed with respect to their interaction in the MD simulations.
Assuntos
Modelos Moleculares , Proteínas Repressoras/química , Tetraciclinas/química , Regulação Alostérica , Antibacterianos/química , Sítios de Ligação , Cristalografia por Raios X , Ligação Proteica , Conformação Proteica , Inibidores da Síntese de Proteínas/química , Proteínas Repressoras/biossíntese , Tetraciclina/químicaRESUMO
Molecular dynamics simulations on the tetracycline-repressor (TetR) protein, both in the absence of an inducer and complexed with the inducers tetracycline and 5a,6-anhydrotetracycline, show significant differences in the structures and dynamics of the induced and non-induced forms of the protein. Calpha-density-difference plots, low-frequency normal vibrations and inter-residue interaction energies all point to a common mechanism of induction. The inducer displaces Asp156 from the magnesium ion in the binding pocket, leading to a short cascade of rearrangements of salt bridges that results in the allosteric change. The increased flexibility of the induced form of the protein is suggested to contribute to the decrease in binding affinity to DNA on induction.
