The NMR Solution Structure of a Mutant of the Max b/HLH/LZ Free of DNA: Insights into the Specific and Reversible DNA Binding Mechanism of Dimeric Transcription Factors

Basic region-helix1-loop-helix2-leucine zipper (b/H1LH2/LZ) transcription factors bind specific DNA sequence in their target gene promoters as dimers. Max, a b/H1LH2/LZ transcription factor, is the obligate heterodimeric partner of the related b/H1LH2/LZ proteins of the Myc and Mad families. These heterodimers specifically bind E-box DNA sequence (CACGTG) to activate (e.g. c-Myc/Max) and repress (e.g. Mad1/Max) transcription. Max can also homodimerize and bind E-box sequences in c-Myc target gene promoters. While the X-ray structure of the Max b/H1LH2/LZ/DNA complex and that of others have been reported, the precise sequence of events leading to the reversible and specific binding of these important transcription factors is still largely unknown. In order to provide insights into the DNA binding mechanism, we have solved the NMR solution structure of a covalently homodimerized version of a Max b/H1LH2/LZ protein with two stabilizing mutations in the LZ, and characterized its backbone dynamics from 15N spin-relaxation measurements in the absence of DNA. Apart from minor differences in the pitch of the LZ, possibly resulting from the mutations in the construct, we observe that the packing of the helices in the H1LH2 domain is almost identical to that of the two crystal structures, indicating that no important conformational change in these helices occurs upon DNA binding. Conversely to the crystal structures of the DNA complexes, the first 14 residues of the basic region are found to be mostly unfolded while the loop is observed to be flexible. This indicates that these domains undergo conformational changes upon DNA binding. On the other hand, we find the last four residues of the basic region form a persistent helical turn contiguous to H1. In addition, we provide evidence of the existence of internal motions in the backbone of H1 that are of larger amplitude and longer time-scale (nanoseconds) than the ones in the H2 and LZ domain. Most interestingly, we note that conformers in the ensemble of calculated structures have highly conserved basic residues (located in the persistent helical turn of the basic region and in the loop) known to be important for specific binding in a conformation that matches that of the DNA-bound state. These partially prefolded conformers can directly fit into the major groove of DNA and as such are proposed to lie on the pathway leading to the reversible and specific DNA binding. In these conformers, the conserved basic side-chains form a cluster that elevates the local electrostatic potential and could provide the necessary driving force for the generation of the internal motions localized in the H1 and therefore link structural determinants with the DNA binding function. Overall, our results suggests that the Max homodimeric b/H1LH2/LZ can rapidly and preferentially bind DNA sequence through transient and partially prefolded states and subsequently, adopt the fully helical bound state in a DNA-assisted mechanism or induced-fit.