p53 DNA-binding domain (p53DBD) plays crucial roles in domain stability, DNA binding and dimerization. In this article, we analyze the motion mode of p53DBD using the Gaussian network model and anisotropy elastic network model. For each structure, the calculated B-factors by two models obtain good agree with the experimentally determined B-factors in x-ray crystal structures. The results show that the four CRs (conserved regions) in the p53DBD have small fluctuation in the slowest mode of GNM, but the same regions lay the peaks of the fast modes. With the aid of the anisotropy elastic network mode, we analyze the motion directions of this domain. The first slowest mode of ANM for both structures mainly corresponds to the rotational motion. However, the CR V (N-terminal) shows an opposite direction with the other parts of structure. Through this motion, p53DBD will bind to its consensus sequence DNA in a highly cooperative manner. By analyzing cross-correlations between residue fluctuations of p53DBD, the results indicate that residues involved in similar functions are fluctuating in a cooperative manner.
p53 DNA-binding domain (p53DBD), Motion Mode, Elastic Network Model
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