Nucleic Acids Research, 2002, Vol. 30, No. 7 1563-1574
© 2002 Oxford University Press
Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain
1Institute of Biomedical Sciences, Academia Sinica, 11529 Taipei, Taiwan and 2Department of Chemistry, National Tsing-Hua University, 300 Hsinchu, Taiwan
The mutation of R273
H in the p53 core domain (p53-CD) is one of the most common mutations found in human cancers. Although the 273H p53-CD retains the wild-type conformation and stability, it lacks sequence-specific DNA binding, a transactivation function and growth suppression. However, mutating T284R in the 273H p53-CD restores the DNA binding affinity, and transactivation and tumour suppressor functions. Since X-ray/NMR structures of DNA-free or DNA-bound mutant p53-CD molecules are unavailable, the factors governing the loss and rescue of sequence-specific DNA binding in the 273H and 273H+284R p53-CD, respectively, are unclear. Hence, we have carried out molecular dynamics (MD) simulations of the wild-type, single mutant and double mutant p53-CD, free and DNA bound, in the presence of explicit water molecules. Based on the MD structures, the DNA-binding free energy of each p53 molecule has been computed and decomposed into component energies and contributions from the interface residues. The wild-type and mutant p53-CD MD structures were found to be consistent with the antibody-binding, X-ray and NMR data. The predicted DNA binding affinity and specificity of both mutant p53-CDs were also in accord with experimental data. The non-detectable DNA binding of the 273H p53-CD is due mainly to the disruption of a hydrogen-bonding network involving R273, D281 and R280, leading to a loss of major groove binding by R280 and K120. The restoration of DNA binding affinity and specificity of the 273H+284R p53-CD is due mainly to the introduction of another DNA-binding site at position 284, leading to a recovery of major groove binding by R280 and K120. The important role of water molecules and the DNA major groove conformation as well as implications for structure-based linker rescue of the 273H p53-CD DNA-binding affinity are discussed.
* To whom correspondence should be addressed at: Institute of Biomedical Sciences, Academia Sinica, 11529 Taipei, Taiwan. Tel: +886 2 2652 3031; Fax: +886 2 2788 7641; Email: carmay{at}gate.sinica.edu.tw Permanent address: Sergey Yu Noskov, Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya str., 1, 153045 Ivanovo, Russia The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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