A Structural Model for the P53 Complex with DNA Response Elements
267
Finally, the molecular model requires that bend and twist angles be positively
correlated to optimize the antiparallel HI-HI interactions, and that bending into
the major groove in the CATG tetrads, therefore, be accompanied by an increase
in twisting as observed in the gel studies (Table 19.1). However, it is not known
precisely how the bend-twist correlation depends upon the specific sequence of
the bending tetrads. DNA bending in the complex is maximal for CATG and is
reduced in CAAG (Nagaich et aI., 1997a), which implies somewhat less twist in
the latter tetrad also because of the observed positive correlation. It is quite possible that differential twist-bend correlation effects among sequence tetrads
found in different p53 response elements may govern binding affinities, sequence
specificities, and the responses of these elements to local supercoiling effects in
promoter regions. Clearly, additional studies are required to more fully understand these complicated questions.
3
Implications of the Molecular Model to p53 Function
The basic structural model described here for a sequence specific nucleoprotein
complex between p53DBD and a response element is not a fully determined
structure but nevertheless is consistent with several types of independent biochemical experiments. These include ligase-mediated cyclization (Balagurumoorthy et aI., 1995), cyclic permutation (Nagaich et aI., 1997a), a variety of
chemical probes studies (Nagaich et aI., 1997b, 1998; Appella et ai., 1998), and the
use of A-tract phase sensitive detection analysis (Nagaich et ai., 1999). The latter
has allowed determination for the first time of both the magnitude and directionality of the DNA bend in the complex. The bending directionality confirms our
earlier prediction based on molecular modeling only (Nagaich et ai., 1997b, 1998;
Durell et aI., 1998) and follows the pattern of major groove bending at conserved
CATG sequence elements that has been observed in other nucleoprotein systems
(El Hassan and Calladine, 1998; Dickerson, 1998; Olson et aI., 1998) including
nucleosomes (Satchwell et aI., 1986).
An especially important observation from the phasing studies is that the DNA
bending and twisting angles are significantly larger in the wild type p53 complex
than in the complex with the p53 core domains only. This suggests that the p53
domains flanking the p53DBD are also involved in DNA binding, a reasonable
concept since p53 function depends upon its DNA binding properties, and these
domains retain a high level of evolutionary conservation. Such a view is also consistent with allosteric control in the binding of wild type p53 (Vojtesek et aI.,
1995; Waterman et aI., 1995) and offers another possible facet of indirect control
in the binding specificity of this protein (Lefstin and Yamamoto, 1998).
The model may also offer insights into the role of p53 in promoting DNA looping (Prives, 1994; Stenger et ai., 1994; Jackson et aI., 1998). This may occur
through N-terminal interactions, since these are exposed outside the DNA loops.
The model also suggests that direct binding of p53 to nucleosomes might occur,
and that p53 binding to unfolded chromatin might offer a possible mechanism
for the detection of DNA damage. The staggered external location of the p53DBD
moieties on the DNA, and the critical importance of the major groove bending
267
Finally, the molecular model requires that bend and twist angles be positively
correlated to optimize the antiparallel HI-HI interactions, and that bending into
the major groove in the CATG tetrads, therefore, be accompanied by an increase
in twisting as observed in the gel studies (Table 19.1). However, it is not known
precisely how the bend-twist correlation depends upon the specific sequence of
the bending tetrads. DNA bending in the complex is maximal for CATG and is
reduced in CAAG (Nagaich et aI., 1997a), which implies somewhat less twist in
the latter tetrad also because of the observed positive correlation. It is quite possible that differential twist-bend correlation effects among sequence tetrads
found in different p53 response elements may govern binding affinities, sequence
specificities, and the responses of these elements to local supercoiling effects in
promoter regions. Clearly, additional studies are required to more fully understand these complicated questions.
3
Implications of the Molecular Model to p53 Function
The basic structural model described here for a sequence specific nucleoprotein
complex between p53DBD and a response element is not a fully determined
structure but nevertheless is consistent with several types of independent biochemical experiments. These include ligase-mediated cyclization (Balagurumoorthy et aI., 1995), cyclic permutation (Nagaich et aI., 1997a), a variety of
chemical probes studies (Nagaich et aI., 1997b, 1998; Appella et ai., 1998), and the
use of A-tract phase sensitive detection analysis (Nagaich et ai., 1999). The latter
has allowed determination for the first time of both the magnitude and directionality of the DNA bend in the complex. The bending directionality confirms our
earlier prediction based on molecular modeling only (Nagaich et ai., 1997b, 1998;
Durell et aI., 1998) and follows the pattern of major groove bending at conserved
CATG sequence elements that has been observed in other nucleoprotein systems
(El Hassan and Calladine, 1998; Dickerson, 1998; Olson et aI., 1998) including
nucleosomes (Satchwell et aI., 1986).
An especially important observation from the phasing studies is that the DNA
bending and twisting angles are significantly larger in the wild type p53 complex
than in the complex with the p53 core domains only. This suggests that the p53
domains flanking the p53DBD are also involved in DNA binding, a reasonable
concept since p53 function depends upon its DNA binding properties, and these
domains retain a high level of evolutionary conservation. Such a view is also consistent with allosteric control in the binding of wild type p53 (Vojtesek et aI.,
1995; Waterman et aI., 1995) and offers another possible facet of indirect control
in the binding specificity of this protein (Lefstin and Yamamoto, 1998).
The model may also offer insights into the role of p53 in promoting DNA looping (Prives, 1994; Stenger et ai., 1994; Jackson et aI., 1998). This may occur
through N-terminal interactions, since these are exposed outside the DNA loops.
The model also suggests that direct binding of p53 to nucleosomes might occur,
and that p53 binding to unfolded chromatin might offer a possible mechanism
for the detection of DNA damage. The staggered external location of the p53DBD
moieties on the DNA, and the critical importance of the major groove bending