Alika Parks proposed testing whether mutant p53 unfolds faster than normal p53 under weak tension
Alika Parks proposed testing whether mutant p53 unfolds faster than normal p53 under weak tension
On July 29, independent researcher Alika Parks published calculations and code for such an experiment. She proposes applying a constant weak force to a single molecule of mutant p53 and measuring how quickly the protein loses its folded structure.
p53 responds to DNA damage. It can stop a cell from dividing while the cell repairs its genome, or it can trigger cell death. p53 mutations occur in about half of all tumors. Some of these mutations make the protein's DNA-binding domain less stable. In a 1997 study, several tumor-associated variants of this domain were less stable in solution than normal p53.
In the Y220C variant, a single amino acid substitution creates a cavity on the protein surface and reduces its stability. In a 2008 study, researchers screened small molecules against this cavity. The molecules bound to the mutant, increased its melting temperature, and slowed denaturation. Parks proposes exploiting the same vulnerability in a different way by keeping the protein under tension until the less stable variant unfolds.
In Parks's calculation, two linked traps apply a constant force of 3–5 piconewtons, which corresponds to trillionths of a newton. According to her model, Y220C unfolds about one hundred times faster than the normal domain under this force. The force is applied for several seconds, so the difference in unfolding rates produces a difference in the fractions of molecules that unfold.
Parks built the “one hundred times” figure into the initial parameters of the calculation. For Y220C and normal p53, she assumes the same transition geometry but different initial unfolding rates: 0.1 and 0.001 per second. The experiment would compare the unfolding times of the two domain variants under constant force.
Parks proposes distinguishing p53 variants by measuring how many seconds their folded structures withstand tension. Conventional drug development looks for a chemical pocket or surface region on a mutant that a molecule can bind. Here, selection is based on the difference between the unfolding rates of the two variants under the same force.