Molecular Dynamics Characterization of the Structures and Induction Mechanisms of a Reverse Phenotype of the Tetracycline Receptor

• Published in: The journal of physical chemistry. B 2007-05, Vol.111 (21), p.6006-6014
• Main Authors: Seidel, Ute, Othersen, Olaf G, Haberl, Florian, Lanig, Harald, Beierlein, Frank R, Clark, Timothy
• Format: Article
• Language: English
• Subjects: Computer Simulation; DNA - chemistry; Models, Biological; Models, Molecular; Molecular Conformation; Mutation; Protein Structure, Secondary; Repressor Proteins - chemistry; Repressor Proteins - drug effects; Structure-Activity Relationship; Tetracycline - chemistry; Tetracycline - pharmacology; Tetracyclines - chemistry; Tetracyclines - pharmacology; Time Factors
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp0674468

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.