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Biophysical Journal 91:421-432 (2006)
© 2006 The Biophysical Society

Cooperative Fluctuations Point to the Dimerization Interface of P53 Core Domain

Nigar Kantarci, Pemra Doruker and Turkan Haliloglu

Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey

Correspondence: Address reprint requests to Turkan Haliloglu, Tel.: 90-212-359-7002; Fax: 90-212-257-5032; E-mail: halilogt{at}boun.edu.tr.

Elastic network models are used for investigation of the p53 core domain functional dynamics. Global modes of motion indicate high positive correlations for residue fluctuations across the A-B interface, which are not observed at the B-C interface. Major hinge formation is observed at the A-B interface upon dimerization indicating stability of the A-B dimer. These findings imply A-B as the native dimerization interface, whereas B-C is the crystal interface. The A-B dimer exhibits an opening-closing motion about DNA, supporting the previously suggested clamp-like model of nonspecific DNA binding followed by diffusion. Monomer A has limited positive correlations with DNA, while monomer B exhibits high positive correlations with DNA in the functionally significant slow modes. Thus, monomer B might seem to maintain the stability of the dimer-DNA complex by forming the relatively fixed arm of the dimer clamp, whereas the other arm of the clamp, monomer A, might allow sliding via continuous association/dissociation mechanisms.




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B. Ma and A. J. Levine
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements
Nucleic Acids Res., December 3, 2007; 35(22): 7733 - 7747.
[Abstract] [Full Text] [PDF]


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