Conformational tuning of a DNA-bound transcription factor

Abstract

Transcription factors are involved in many cellular processes that take place remote from their cognate DNA sequences. The efficiencies of these activities are thus in principle counteracted by high binding affinities of the factors to their cognate DNAs. Models such as facilitated diffusion or dissociation address this apparent contradiction. We show that the MYC associated transcription factor X (MAX) undergoes nanoscale conformational fluctuations in the DNA-bound state, which is consistent with facilitated dissociation from or diffusion along DNA strands by transiently reducing binding energies. An integrative approach involving EPR, NMR, crystallographic and molecular dynamics analyses demonstrates that the N-terminal domain of MAX constantly opens and closes around a bound DNA ligand thereby dynamically tuning the binding epitope and the mode of interaction.

A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix–Loop–Helix Transcription Factor

“…Finally, in our earlier work we could show that MAX 2 ’s NTD undergoes substantial internal motions even when in the stable DNA-bound helical state. A comparison of the data 16 for MAX 2 bound to a DNA ligand with the results obtained here on DNA-free MAX 2 shows that the range of end-to-end distances sampled by MAX 2 ’s NTD is similarly broad (1.5–4.5 nm) in both the DNA-free and DNA-bound states. ( Figure 4 b,c shows DEER-derived distance distributions and form factors before (red) and after (blue) binding of DNA to MAX 2 for the R5C-R5C double mutant.)…”

Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA

“…In such an open state, the two BRs bind into the neighboring major and minor grooves on the DNA, respectively, with a distance in between (~33 Å) almost the length of a full DNA helical pitch. In a recent NMR integrated structural dynamics study which measured the Max-Max homodimer conformational fluctuations in association with DNA, it is found that the opening of the binding cleft varies in width by about 2-5 nm [40]. Such an opening of Max-Max may also apply for Myc-Max.…”

How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations

“…Recently, approaches based on the site-specific introduction of paramagnetic labels could characterize the DNA-binding sites of (partially) disordered TFs [61] , [62] , [63] , [64] , [65] . These approaches employed the so-called paramagnetic relaxation enhancement (PRE) technique [66] .…”

“…Recently, putting the combination of PRE-based relaxometry and MD simulations to use, the intrinsically disordered DNA-binding interface of the important transcription factor MAX (MYC-associated factor X) has been investigated [61] , [63] , [77] . It could be shown that its conformational space is not merely void of long-lived structural elements.…”

“…To study the structural dynamics involved in facilitated diffusion, experimental observations of PRE data have been reported [61] , [63] in combination with ensemble-averaged conformations obtained from MD trajectories. Thus, models of the conformational space of the MAX:MAX-DNA complex could be inferred and it was found that the DNA-binding site undergoes substantial (i.e., spanning several nanometers) structural fluctuations on the nanoseconds timescale that are likely underlying a facilitated diffusion mechanism ( Fig.…”