DNA Folding and Interactions in Complexes with Proteins The DNA structures in about 90 available crystals of DNA-protein complexes were analyzed. The ultimate goal has been to deduce sequence- dependent """"""""rules"""""""" governing DNA deformability in complexes (mostly, DNA bending and twisting). (i) Sequence-dependent energy functions for DNA. Novel theoretical formalism was developed to deduce the DNA energetics from its conformational variability in crystals. The knowledge-based parameters estimated in this way, demonstrate that the pyrimidine-purine YR dimers are the most flexible ones, and the purine-pyrimidine RY dimers are the most rigid. This result is entirely consistent with the theoretical results obtained by us earlier. Generally, the new energy parameters obtained here are important for evaluating the sequence-dependent deformability of DNA in complexes with proteins, and thus, for estimating quantitatively the impact of induced fit on the free energy of complex formation. In turn, this will be used for predicting the DNA- protein binding sites and for molecular design. (ii) Novel CH...O Interactions in Protein-DNA Complexes. In addition to conventional hydrogen bonds involving oxygens and nitrogens, numerous CH...O hydrogen bonds were observed in the DNA-protein interfaces in crystals. Considering these interactions in addition to classical hydrogen bonds, enables extraction of simple structural principles for amino acid-base recognition which was not possible before. Both items (i) and (ii) are useful for molecular modelling and have proven critical for the studies of the p53-DNA complex (see below). Overall Architecture of the Complex between DNA and Tumor Suppressor Protein p53 A detailed stereochemically feasible model was proposed for the complex between p53 tetramer and the cognate DNA sequence, consistent with X-ray and solution data. Our analysis shows that DNA has to be bent by about 50: to relieve the inter-protein steric clashes occurring when p53 tetramer binds the response element Waf1. The directionality and magnitude of DNA bending predicted by us has been confirmed experimentally. DNA is bent in the highly conserved CATG parts of the Waf1 site containing flexible CA:TG dimers (see item (i) above). The hydrogen bonding patterns discussed above were utilized to elucidate the p53 affinity to the consensus sequence YYYC(A/T) (Y = pyrimidines). This detailed model will be used for analyzing the human genome database aimed at establishing general mechanisms of p53 binding to chromatin DNA and subsequent trans-activation. Elucidating structural aspects of the p53-DNA complex becomes particularly important now, after the reported close similarities between the tumor suppressor proteins p53 and p73.
