Uncovering the complete 3D structure of p53 protein

By inducing cell repair or self-destruction, the tumor suppressor protein p53, often known as “the guardian of the genome,” shields the body’s DNA from daily stress or long-term damage. But, changes in the p53 gene, which produces the protein, can prevent it from carrying out its function, causing inaccuracies in the genetic code to accumulate and resulting in diseases like cancer.

Using patient samples, a team of scientists led by Penn State was able to determine the full structure of the p53 protein for the first time. They also looked at the potential effects on various tumors of changes in p53 structure spurred by mutations. ChemBioChem and the International Journal of Molecular Sciences published the results.

We defined the full-length structure of p53, opening the door to understanding the 3D arrangements that can used to inform new therapeutics. Scientists have previously identified p53 as an important focal point in the origin of tumors, and much has been investigated on its function in cells. However, without understanding the complete structure of the p53, our knowledge of how to deal with it in diseased cells was incomplete.”

Maria Solares, Study First Author and Doctoral Student, Molecular, Cellular and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University

Researchers detected individual p53 proteins extracted from brain tumor cells using cryo-electron microscopy (cryo-EM). The team’s utilization of semi-conductor materials to thoroughly capture the isolated p53 proteins before imaging is unique to their study, according to Solares.

The proteins are held in these silicon-based microchips in a way that allowed the researchers to clarify hitherto unobserved molecular features.

Seeing the complete structure of the p53 was like finally seeing the whole human body after only viewing limited parts or limbs for so long. It is hard to understand how things work without knowledge of their entire physical makeup.”

Deb Kelly, Professor, Biomedical Engineering, Pennsylvania State University

Kelly is also the director of the Penn State Center for Structural Oncology and Huck Chair in Molecular Biophysics.

The p53 protein is composed of small building blocks known as monomers that can join together to form larger structures known as dimers and tetramers.

Solares added, “We found a mixture of monomers, dimers, and tetramers were present inside cancer cells, each of which serve different purposes based on events happening inside the cell’s nucleus. Results of the dimer structure revealed, for the first time, a ‘closed’ configuration of the molecule. This form of p53 is like being at the starting blocks before a race, primed and ready to run toward DNA when notified by other cellular signals that there’s a problem.”

Other forms of p53, like monomers, are regarded as “open” since they have to first connect with another unit before proceeding to the starting line and carrying out their functions.

According to Kelly, disruptions in the process are associated with the causes of diseases, including cancer, and proper communication is crucial to controlling the time and volume of p53 deployment to the nucleus of cells, where DNA is located.

Kelly added that defective p53 proteins can result from mutations in the p53 gene. After revealing the 3D structure, the researchers looked at how structural modifications to p53 lead to molecules that behave improperly inside cells.

“It is well known that half of all cancers contain p53 gene mutation. To take a closer look at how these mutations impact the p53 protein structure, we used molecular modeling software to simulate changes in the p53 monomer structure,” Solares further stated.

The seven “hotspots” where mutations in the protein structure are most frequently associated with cancer were examined by the researchers. According to Kelly, individuals with these seven p53 protein mutations often experience worse cancer progression and chemoresistance outcomes.

A modified p53’s surface charges, which function to reject and attract the charges of other molecular units, were discovered to be affected by small changes in the protein’s 3D structure.

According to Kelly, this can obstruct the protein's ability to bind properly with DNA, impairing p53’s capacity to help regulate or repair processes that are crucial for maintaining healthy cells.

Solares further added, “Under healthy conditions, p53 uses zinc ions to tightly hold genetic material. When the protein’s surface charge remains properly balanced, zinc ions can assume the correct position to help p53 grasp DNA. But when mutations in the p53 gene lead to changes in the protein’s surface, zinc ions are not properly placed, and p53 loses its grip on DNA. This effect is further exacerbated in disease.”

The researchers stated that they intend to broaden their research in the future to examine p53 mutations’ significant role in pancreatic and ovarian cancers. Based on their newfound knowledge of the whole 3D structure of p53, they are also researching novel therapeutic strategies.

Solares concluded, “One patient’s cancer is not the same as another patient’s cancer. We need to keep gathering experimental data from different patients and different cancers to test our models. Without the complete picture, we can’t completely understand cancer.”