Abstract
The human mediator subunit MED25 acts as a coactivator that binds the transcriptional activation domains (TADs) present in various cellular and viral gene-specific transcription factors. Previous studies, including on NMR measurements and site-directed mutagenesis, have only yielded low-resolution models that are difficult to refine further by experimental means. Here, we apply computational molecular dynamics simulations to study the interactions of two different TADs from the human transcription factor ETV5 (ERM) and herpes virus VP16-H1 with MED25. Like other well-studied coactivator-TAD complexes, the interactions of these intrinsically disordered domains with the coactivator surface are temporary and highly dynamic (‘fuzzy’). Due to the fact that the MED25 TAD-binding region is organized as an elongated cleft, we specifically asked whether these TADs are capable of binding in either orientation and how this could be achieved structurally and energetically. The binding of both the ETV5 and VP16-TADs in either orientation appears to be possible but occurs in a conformationally distinct manner and utilizes different sets of hydrophobic residues present in the TADs to drive the interactions. We propose that MED25 and at least a subset of human TADs specifically evolved a redundant set of molecular interaction patterns to allow binding to particular coactivators without major prior spatial constraints.
Highlights
The regulated expression of the human genome results from the interplay between epigenetic processes and the activity of gene-specific transcription factors (GSTFs) [1]
In order to explore the full innate secondary structure potential of ETV538–68 and VP16-H1413–452 transactivation domains (TADs) in the absence of any coactivator binding, we carried out Markov chain Monte Carlo (MCMC) simulations that allow for the comprehensive exploration of conformational states without entrapment in local minima (Figure 2a,b)
Traditional models envisaged that local interactions between GSTFs and members of the basal transcriptional machinery assembled at the transcription start site provide a relatively confined environment for TADs to bind to coactivators due to the high-density, synergistic binding of transcription factors to enhancers [49], allowing even brief contacts [7] and energetically weak interactions (KD in micromolar range; e.g.) [7,12,13,14,16,50]
Summary
The regulated expression of the human genome results from the interplay between epigenetic processes and the activity of gene-specific transcription factors (GSTFs) [1]. Specific parts of GSTFs, the transactivation domains (TADs) [2] are responsible for stimulating the expression of nearby genes by interacting dynamically with coactivators that are typically part of the invariant basal transcriptional machinery. Some of the best understood coactivators are present in the basal factor TFIID and in the Mediator complex that associate with RNA polymerase II during transcription initiation [3,4]. Discovered more than three decades ago, the structural and functional basis of coactivator-TAD interactions is still poorly understood. This is mostly because these interactions are relatively weak (micro-/high nanomolar affinities), short-lived (characterized by high association and dissociation rate constants) and structurally highly dynamic [5,6,7,8]. Computational simulation techniques, especially atomistic molecular dynamics (MD) simulations, are ideally suited to provide new insights into such complex interaction patterns [9]
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