Structure-based prediction of DNA target sites by regulatory proteins

Abstract

Regulatory proteins play a critical role in controlling complex spatial and temporal patterns of gene expression in higher organism, by recognizing multiple DNA sequences and regulating multiple target genes. Increasing amounts of structural data on the protein-DNA complex provides clues for the mechanism of target recognition by regulatory proteins. The analyses of the propensities of base-amino acid interactions observed in those structural data show that there is no one-to-one correspondence in the interaction, but clear preferences exist. On the other hand, the analysis of spatial distribution of amino acids around bases shows that even those amino acids with strong base preference such as Arg with G are distributed in a wide space around bases. Thus, amino acids with many different geometries can form a similar type of interaction with bases. The redundancy and structural flexibility in the interaction suggest that there are no simple rules in the sequence recognition, and its prediction is not straightforward. However, the spatial distributions of amino acids around bases indicate a possibility that the structural data can be used to derive empirical interaction potentials between amino acids and bases. Such information extracted from structural databases has been successfully used to predict amino acid sequences that fold into particular protein structures. We surmised that the structures of protein-DNA complexes could be used to predict DNA target sites for regulatory proteins, because determining DNA sequences that bind to a particular protein structure should be similar to finding amino acid sequences that fold into a particular structure. Here we demonstrate that the structural data can be used to predict DNA target sequences for regulatory proteins. Pairwise potentials that determine the interaction between bases and amino acids were empirically derived from the structural data. These potentials were then used to examine the compatibility between DNA sequences and the protein-DNA complex structure in a combinatorial "threading" procedure. We applied this strategy to the structures of protein-DNA complexes to predict DNA binding sites recognized by regulatory proteins. To test the applicability of this method in target-site prediction, we examined the effects of cognate and noncognate binding, cooperative binding, and DNA deformation on the binding specificity, and predicted binding sites in real promoters and compared with experimental data. These results show that target binding sites for several regulatory proteins are successfully predicted, and our data suggest that this method can serve as a powerful tool for predicting multiple target sites and target genes for regulatory proteins.

The Nuclear Protein IκBζ Forms a Transcriptionally Active Complex with Nuclear Factor-κB (NF-κB) p50 and the Lcn2 Promoter via the N- and C-terminal Ankyrin Repeat Motifs

“…phate moiety of DNA but also via recognition of a DNA base, especially a guanine (39,40). In this context, it should be noted that the IB-responsive element (5Ј-YCCC-3Ј) of the Lcn2 promoter is abundant in the Lys/Arg-recognizing base guanine in the antisense strand.…”

“…Promoter and Not via p50 -It should be noted that the basic residues lysine and arginine are both capable of not only forming a salt bridge with a phosphate group of DNA but also of directly interacting with a base of DNA, especially guanine (39,40). Furthermore, we have shown recently that a cytosine-rich region downstream of the B site is involved in formation of the active three-species complex IBp50-DNA (23), suggesting that the extra-B site makes a direct contact with p50, IB, or both.…”

Individual Nucleotide Bases, Not Base Pairs, Are Critical for Triggering Site-specific DNA Cleavage by Vaccinia Topoisomerase

“…This result surprised us, as classical models of protein binding to specific sequences in double-stranded DNA highlight hydrogen-bonding interactions between amino acid side chains and the DNA base pairs as determinants of sequence specificity (32,33). Fig.…”

Computational redesign of endonuclease DNA binding and cleavage specificity

“…The nucleotide sequence specificity of DNA-binding proteins can not be deduced directly from amino acid sequence because the packing, hydrogen-bonding and electrostatic interactions responsible for nucleotide-specific recognition are dependent on the threedimensional structure of the protein-DNA complex 11,12 . While a number of canonical amino acid-nucleotide interaction motifs are observed in protein-DNA interfaces 13 , they are…”