Structural and Thermodynamic Insights into Competitive Binding of the EGR1 and Sp1 Zinc Finger Class of Transcription Factors with a GC-Rich DNA Motif

Transcriptional control of gene regulation in eukaryotes is primarily associated with the binding of transcription factors (TFs) to a particular motif sequence in genomic DNA, among the vast number of identical or highly similar sequences in the genome. The cooperative as well as competitive interactions among the paralogous TFs are believed to play an important role in this aspect to control precise gene regulatory functions. So far, the molecular mechanism of competitive TF binding is obscured, and due to a lack of molecular insights, it is difficult to predict how competitive interaction influences the genomic binding of individual TFs. Using microsecond atomistic simulations together with structural and functional bioinformatics data, here, we report the competitive binding nature of two biologically important zinc finger (ZF) class of pioneer TFs, namely, early growth response protein 1 (EGR1) and specificity protein 1* (Sp1), with highly similar GC-rich motif sequences. We show that the conformational entropy of protein and DNA components makes a substantial contribution in binding to a specific DNA motif and illustrate the roles of DNA shape features in competitive binding. The intrinsic shape features, along with local shape deformability of the DNA binding site motif, are found to facilitate sequence-specific recognition and binding of EGR1/Sp1 through the ZF domains by giving access to the base atoms of the specific bases along the grooves to form major contacts with the conserved residues in the canonical recognition positions in ZFs. Base-specific contacts of the functional key conserved charged residues of the ZFs in the DBD of EGR1/Sp1, along the major grooves of the DNA motif, further modulate the binding interactions, dynamics, and dissociation free energy. In general, this study provides microscopic insights into how the complex patterns of competitive TFs are intrinsically encoded in the DNA binding motif and help to design custom ZF nucleases for site-specific genome editing machinery.