title: Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
abstract: The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Zhang
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Dantas Machado
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ding
authors.forename: Yongheng
authors.initials: Y
authors.lastname: Chen
authors.forename: Yan
authors.initials: Y
authors.lastname: Lu
authors.forename: Yankun
authors.initials: Y
authors.lastname: Duan
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Tham
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004578:Electron Spin Resonance Spectroscopy; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D020218:Response Elements; D013113:Spin Labels; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000378:metabolism*
chemical_list: D013113:Spin Labels; D016159:Tumor Suppressor Protein p53; D004247:DNA