Structural and Affinity Insight into the Sequence-Specific Interaction of Transcription Factors DEC1 and DEC2 with E-box DNA: A Novel Model Peptide Approach

The basic helix-loop-helix (bHLH) family members DEC1 and DEC2 function as transcription factors by directly binding to class B E-box region in the proximal promoter of target genes, and have recently been reported to play important roles in many human physiological and pathological processes such as cancer. However, it is a great challenge to quantitatively analyze the binding affinity and selectivity of sequence-specific interaction in DEC1/DEC2–E-box recognition since there are numerous potential competitive DNA binders of the transcription factors in cellular context. In the present study, we describe a novel model peptide approach to fast and reliably characterize the interaction behavior of DEC1 and DEC2 with DNA. In the procedure, a series of peptides that mimic the DNA recognition helices of DEC1 and DEC2 as well as other bHLH proteins are derived, and their binding potencies to cognate E-box and noncognate DNA decoys are evaluated using a residue-level affinity predictor built upon a distinct set of structure-solved, affinity-known protein–DNA complexes. By systematically examining the affinity distribution profiles of different peptides binding to the E-box and to a large number of decoys it is found that single-point mutations on peptide key residues such as H6A and R14A can significantly reduce both the affinity and selectivity of DEC1 and DEC2 toward E-box, but the mutations do not substantially influence their binding capability to most decoys, and a fraction (~22 %) of DNA decoys exhibit stronger interaction potency with DEC peptide as compared to E-box, suggesting that the DEC1 and DEC2 possess a moderate specificity that allows the transcription factors to bind, and regulate, a number of potential target genes.