title: p53 dynamics upon response element recognition explored by molecular simulations.
abstract: p53 is a representative transcription factor that activates multiple target genes. To realize stimulus-dependent specificities, p53 has to recognize targets with structural variety, of which molecular mechanisms are largely unknown. Here, we conducted a series of long-time scale (totally more than 100-ms) coarse-grained molecular dynamics simulations, uncovering structure and dynamics of full-length p53 tetramer that recognizes its response element (RE). We obtained structures of a full-length p53 tetramer that binds to the RE, which is strikingly different from the structure of p53 at search. These structures are not only consistent with previous low-resolution or partial structural information, but also give access to previously unreachable detail, such as the preferential distribution of intrinsically disordered regions, the contacts between core domains, the DNA bending, and the connectivity of linker regions. We also explored how the RE variation affects the structure of the p53-RE complex. Further analysis of simulation trajectories revealed how p53 finds out the RE and how post-translational modifications affect the search mechanism.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Terakawa
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan.
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D001665:Binding Sites; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D020218:Response Elements; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry*
chemical_list: D016159:Tumor Suppressor Protein p53