Functional Implications of Intrinsic Helicities within Basic Regions of bZIP Transcription Factors

Abstract

Eukaryotic transcription factors (TFs) including basic leucine zippers (bZIPs) are enriched in disorder promoting residues. In contrast to the presumption that monomeric unbound bZIP basic regions (bRs) are uniformly disordered, recent studies have shown that unbound monomeric bRs have quantifiable -helicity. The 8-residue segments, directly N-terminal to DNA-binding motifs are primary modulators of intrinsic helicities. It is conceivable that observed intrinsic helicities and their variation with bR sequences are inconsequential given that sequences of disordered regions change rapidly. Our sequence analysis of bZIPs, however, demonstrates that bRs show a high degree of conservation across orthologs and considerable variation among paralogs. Based on this, we predict that bRs from similar sequence families and different organisms are likely to have equivalent intrinsic helicities and propose that this reflects a mechanistic conservation across orthologs with implications for search process for cognate DNA half sites. To test our predictions we have performed lattice-based kinetic Monte Carlo simulations to quantify the impact of variations in intrinsic helicities on the process of DNA binding. DNA is modeled as a wormlike chain and a randomly chosen site is designated as the cognate site. We model the interplay of three-dimensional diffusion of free TF molecules in solution, binding and unbinding of TF to the non-cognate sites, and one-dimensional sliding along the DNA. The effects of intrinsic helicity on these processes are investigated through systematic titrations in a multidimensional parameter space and quantifying their effects on the first passage time distribution for TF to find its cognate site. The search time has a non-monotonic dependence on bR helicity such that the search process is optimized within a limited regime of bR helicity. We also quantify effects of bZIP dimerization as a secondary modulator of TF-DNA interactions.