Structural Differences Associated with DNA Binding of p53 Family Member Proteins

Graduate #2
Discipline: Biological Sciences
Subcategory: Biochemistry (not Cell and Molecular Biology and Genetics)

Grace R. Mavodza - Howard University
Co-Author(s): Yayin Fang and Zaki Sherif, Howard University, Washington, DC

Introduction: p53 family member proteins, which are made up of p53, p63, and p73, have long been presumed to function as tumor suppressors. They possess significant structural homology, including the presence of a transactivation domain, a DNA-binding domain, and an oligomerization domain. In spite of their structural similarities there is growing evidence that p63 and p73 initiate unique pathways, which play larger roles in development rather than in tumor suppression. This study seeks to further highlight the structural differences between the DNA-binding regions of the three proteins and how those structural differences may translate into the functional differences observed for each protein.
Methods: The structure of the DNA binding domain of each protein was obtained from the RCSB Protein Data Bank. The final structures used for protein p53, p63 and p73 were PDB ID 2ADY, 3US0 and 4G82 respectively. MOE 2013 was utilized to visualize the structure of the DNA binding domain of each protein and it was then used to perform a sequence and structural alignment of the three proteins. The three structures were compared at the atomic level, and the amino acids in contact with the DNA were selected for further analysis.
Results: The six regions of interest, which are all in contact with DNA, have been identified. Five of the areas were verifications of information previously published. The region of greatest interest was a conserved arginine, whose guanidinium group had a noticeably different orientation and an equally unique electrostatic map in all three structures. Arg248, Arg279, and Arg268 correspond to the arginine of interest in p53, p63, and p73 respectively.
Conclusion: The presence of a conserved arginine within the p53 family of proteins does not guarantee the proteins will interact with DNA in the same manner. This is highlighted by the unique orientation observed in the arginine of each family member protein and may contribute to the diversity in their ability to initiate the activation of various proteins. Future experiments include the mutation of arginine 248/279/268 in p53/p63/p73 in order to determine how much binding ability is affected and the creation of a complete protein structure for each p53 family member.

Funder Acknowledgement(s): This work was supported by grant #G12 MD007597 from NIMHD, NIH to RCMI program at Howard University, HUMAA (Howard University Medicine Alumni Association) Endowed Founder's Chair in Basic Science, and grant #U01 CA185188-01A1 from NCI/NIH to Zaki Sherif.

Faculty Advisor: Zaki Sherif, zaki.sherif@howard.edu

Role: I, Grace Mavodza, completed the whole project myself. I received assistance in learning the program and in the interpretation of data collected, but the bulk of the work was done by me.