p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains

Abstract

The tumor suppressor p53 is a transcription factor that searches its cognate sites on DNA. During the search, the roles and interplay of its two DNA binding domains, the folded core domain and the disordered C-terminal domain (CTD), have been controversial. Here, we performed molecular simulations of p53 at various salt concentrations finding that, at physiological salt concentration, p53 diffuses along nonspecific DNA via rotation-uncoupled sliding with its CTD, whereas the core domain repeats dissociation and association. This is in perfect agreement with a recent single molecule experiment. In the simulation of tetrameric full-length p53, two DNA binding domains both bound to nonspecific DNA in a characteristic form at low salt concentration, whereas at physiological salt concentration, only CTD kept bound to DNA and the core domain frequently hopped on DNA. Simulations of a construct that lacks the core domain (TetCD) clarified rotation-uncoupled diffusion on nonspecific DNA. At low salt concentration, the diffusion constant due to sliding was dependent on the salt concentration, which differs from the prediction of a classic theory of transcription factors. At physiological salt concentration, it was independent of the salt concentration, in harmony with experiments. Moreover, we found that the sliding via the CTD follows the helical pitch of DNA (i.e., rotation-coupled sliding) at low salt concentration while it is virtually uncoupled to the helical pitch, a hallmark of rotation-uncoupled sliding at physiological salt concentration.

One-Dimensional Sliding of p53 Along DNA Is Accelerated in the Presence of Ca2+ or Mg2+ at Millimolar Concentrations

“…In 50% of human cancers, the mutations of p53 gene are found, which are located in the core domain and prevent the specific binding to DNA [3]. Due to its importance, the mechanism by which p53 searches for its binding sites among huge DNA has been the focus of intensive investigations [4][5][6][7][8].…”

Fluorescence Study Gives a Hint to Understand How the p53 DNA Binding Domain Recognizes Its Specific Binding Site on DNA Fragments

“…For this reason, it is still highly controversial how p53 recognizes its specific target site on DNA. 6,15,[17][18][19] According to the previously reported data, G245, R248, and R249 residues on wild-type p53DBD might be able to form well-defined hydrogen bonds, and then R248 could interact with DNA at the minor groove properly.…”

DNA repair systems

“…When bound to DNA, the p53 protein acts in different cis/trans interac ons with its target sequences, modula ng the transcrip on of various target genes [695,696]. Rela vely recently it was found that the p53 molecule may ac vely slide along the length of the DNA molecule, searching for its cognate control elements [697,698]. p53 is capable of ac va ng both the ini a on and the elonga on from promoters for RNA polymerase II, as it can bind directly to TFIIH [699,700].…”