A Structural Model for the P53 Complex with DNA Response Elements
261
A relatively detailed model for the tetrameric p53DBD complex with the p211
WafllCipl DNA response element has been proposed recently (Durell et aI., 1998;
Nagaich et al., 1998). To develop this model, chemical probe analysis (Nagaich et
aI., 1997b, 1998; Appella et aI., 1998), cyclic permutation studies (Nagaich et aI.,
1997a), and advanced phasing studies (Nagaich et al., 1999) were combined with
sophisticated molecular modeling that preserved the dynamical character of the
DNA response element (Nagaich et aI., 1997b, 1999; Durell et aI., 1998). The
chemical probe methods can assign protein-DNA contacts at single base resolution as well as identify certairi bases involved in the specific protein-DNA recognition. Both cyclic permutation (Wu and Crothers, 1984) and A-tract-based
phase sensitive detection (Zinkel and Crothers, 1987; Niederweis and Hillen,
1993) are robust methods for identifying and locating bent DNA, and the latter is
especially powerful for the determination and quantitation of DNA twist changes
associated with complex formation. The tetrameric structural model based upon
these biochemical methods (Durell et aI., 1998; Nagaich et aI., 1999) is significantly more detailed than that obtained directly from the co-crystal study (Cho et
aI., 1994), and it offers further insights into a number of additional structural and
functional properties of the wild type p53 complex.
2.3
A Structural Model for the Tetrameric p53-DNA Complex
The structural model for the p53DBD complex developed as discussed above is
shown in Fig. 19.3a. All nomenclature associated with structural features of the
p53DBD used subsequently in this review is taken from the co-crystal structure
(Cho et aI., 1994). The response element used for the modeling was a symmetric
site in which both half sites were obtained from the p53 consensus response element (EI-Deiry et al., 1992). This site symmetry was necessary in order to keep
the modeling within tractable bounds but does not affect seriously the generality
of the model structure itself. In the development of the model, protein -DNA contacts were determined from high resolution chemical probes studies on the p211
WafllCipl sequence. These contacts were used along with the crystallographic
coordinates of the DNA -bound p53DBD (Cho et aI., 1994) to assemble a molecular model for the tetrameric complex that was energetically reasonable and preserved known energy constraints upon the DNA. The DNA is assumed to be in a
B-conformation (Olson et aI., 1998). The studies illustrate how limited co-crystal
structural data can be combined with relatively low resolution solution results to
develop a simple mechanistic model that can rationalize a wide variety of experimental findings.
Four p53DBD peptides are arranged in a staggered array along the 20 base
pair response element with each peptide bound to a single pentameric element
using its H2 recognition helix and other protein-DNA contacts as shown in the
co-crystal structure (Cho et al., 1994). Peptides immediately adjacent along the
response element are bound in opposite (antiparallel) orientations whereas nonadjacent peptides bind in the same (parallel) orientation. Energetic considerations dictate that the binding of four p53DBD peptides to each of the four
response element pentamers requires an overall bending of the DNA through
261
A relatively detailed model for the tetrameric p53DBD complex with the p211
WafllCipl DNA response element has been proposed recently (Durell et aI., 1998;
Nagaich et al., 1998). To develop this model, chemical probe analysis (Nagaich et
aI., 1997b, 1998; Appella et aI., 1998), cyclic permutation studies (Nagaich et aI.,
1997a), and advanced phasing studies (Nagaich et al., 1999) were combined with
sophisticated molecular modeling that preserved the dynamical character of the
DNA response element (Nagaich et aI., 1997b, 1999; Durell et aI., 1998). The
chemical probe methods can assign protein-DNA contacts at single base resolution as well as identify certairi bases involved in the specific protein-DNA recognition. Both cyclic permutation (Wu and Crothers, 1984) and A-tract-based
phase sensitive detection (Zinkel and Crothers, 1987; Niederweis and Hillen,
1993) are robust methods for identifying and locating bent DNA, and the latter is
especially powerful for the determination and quantitation of DNA twist changes
associated with complex formation. The tetrameric structural model based upon
these biochemical methods (Durell et aI., 1998; Nagaich et aI., 1999) is significantly more detailed than that obtained directly from the co-crystal study (Cho et
aI., 1994), and it offers further insights into a number of additional structural and
functional properties of the wild type p53 complex.
2.3
A Structural Model for the Tetrameric p53-DNA Complex
The structural model for the p53DBD complex developed as discussed above is
shown in Fig. 19.3a. All nomenclature associated with structural features of the
p53DBD used subsequently in this review is taken from the co-crystal structure
(Cho et aI., 1994). The response element used for the modeling was a symmetric
site in which both half sites were obtained from the p53 consensus response element (EI-Deiry et al., 1992). This site symmetry was necessary in order to keep
the modeling within tractable bounds but does not affect seriously the generality
of the model structure itself. In the development of the model, protein -DNA contacts were determined from high resolution chemical probes studies on the p211
WafllCipl sequence. These contacts were used along with the crystallographic
coordinates of the DNA -bound p53DBD (Cho et aI., 1994) to assemble a molecular model for the tetrameric complex that was energetically reasonable and preserved known energy constraints upon the DNA. The DNA is assumed to be in a
B-conformation (Olson et aI., 1998). The studies illustrate how limited co-crystal
structural data can be combined with relatively low resolution solution results to
develop a simple mechanistic model that can rationalize a wide variety of experimental findings.
Four p53DBD peptides are arranged in a staggered array along the 20 base
pair response element with each peptide bound to a single pentameric element
using its H2 recognition helix and other protein-DNA contacts as shown in the
co-crystal structure (Cho et al., 1994). Peptides immediately adjacent along the
response element are bound in opposite (antiparallel) orientations whereas nonadjacent peptides bind in the same (parallel) orientation. Energetic considerations dictate that the binding of four p53DBD peptides to each of the four
response element pentamers requires an overall bending of the DNA through