Specificity determinants for the abscisic acid response element

Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences. We have also examined the variation in the stability of the protein–DNA complex upon mutating ABRE sequences using the protein design algorithm FoldX. The high throughput free energy calculations successfully predicted the ability of ABF1 to bind to alternative core motifs like GCGT or AAGT and also rationalized the role of the flanking sequences in determining the specificity of the protein-DNA interaction.

▸ Abscisic acid response elements (ABREs) are bound by ABFs, a class of bZIP transcription factor. ▸ We examined the recognition of ABRE DNA sequences by ABF1 protein from A. thaliana. ▸ An initial model was constructed by comparative modeling and protein DNA docking. ▸ Relative binding affinities of the protein for mutated DNA sequences were calculated. ▸ The approach explains much of the experimental data at a low computational cost.