One of the basic and most important processes,
required for the function of cells (for example cell division or start of
protein synthesis) is interactions between proteins and DNA.
two modes of protein::DNA interactions: direct readout that relies on specific
hydrogen bonds between protein side chains and the donor and acceptor in DNA
major groove; and indirect readout that relies on structural recognition of DNA
by proteins. p53 is a tumor suppressor
protein that is responsible for genome stability. It acts as a
transcription factor and relies on both modes of protein::DNA interactions.
p53 consensus binding site consist of two half
sites. The DNA sequence for each half site is R1R2R3C4W5W6G7Y8Y9Y10
(R = A/G; W = A/T; Y = C/T) and p53 has been shown to act as an activator in
such sites. The main focus of my research was on bases 5 and 6 - W5W6.
It was previously shown in the crystal structure of p53
to its DNA consensus sequence, that only 3 base pairs (bp) of the pentamer (R2R3C4)
play a role in forming hydrogen bonds with p53 monomer. The central W5W6
is uncontacted. Nevertheless, most p53 binding sites contain AT or AA step, and
not TA steps. I found that the stoichiometry of p53::DNA complexes is dependent
on these bases; there are two complexes (tetramer and dimer) for sequences with
W5W6 = AT and one complex for sequences with W5W6
= TA or AA. The difference in binding patterns comes from the difference
in structural properties of these sequences. The GATC sequence is much more
flexible than GTAC or the GAAC sequence. This flexibility ensures that two
monomers of p53 are in the right orientation that permits creation of stable
bonds between them, therefore stabilizing the dimer.
Furthermore, in my studies I found that
base-pairing in W5W6
bases is not obligatory for binding and
that binding can occur even without Watson-Crick base pairing, however
insertion of even 1 bp spacer between W5
and W6 nullify
the binding of p53 to such sequence. Other experiments were performed with
different sequences that contain only one half / quarter site. Those
experiments proved that the structure of W5W6 is more
important than the actual sequence of this site.