N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

• Published in: Journal of molecular biology 2012-02, Vol.416 (2), p.287-299
• Main Authors: Das, Rahul K., Crick, Scott L., Pappu, Rohit V.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; atomistic simulations; basic regions of bZIPs; Basic-Leucine Zipper Transcription Factors - chemistry; Basic-Leucine Zipper Transcription Factors - metabolism; Binding Sites; bioinformatics; Circular Dichroism; Computer Simulation; DNA; DNA-binding domains; evolution; genes; intrinsic disorder; Leucine Zippers; Molecular Sequence Data; prediction; Protein Conformation; Protein Structure, Secondary; proteins; Sequence Alignment; sequence design; sequence homology; spectroscopy; Structure-Activity Relationship; transcription factors; α-helicity
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2011.12.043

Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for α-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). [Display omitted] ► bZIP-bR transcription factors are assumed to be uniformly disordered. ► Contrary to this expectation, simulations and spectroscopy show that bZIP-bRs have quantifiable α-helicities as isolated unbound monomers. ► Simulations identify the eight-residue N-terminal segments in bZIP-bRs as the primary modulators of bZIP-bR helicities. ► This inference leads to the design of chimeras with either increased or decreased helicity. ► This work demonstrates the first ever design of the statistical properties of the conformational ensembles of IDRs. ► The quantitative agreement between simulation results and spectroscopic results augurs well for the continued use of joint computational and experimental investigations of IDRs.