ERG, a transcription factor of the Ets family, is known for its role in embryonic development, vascular health and disease as well as aberrant expression in a number of cancers. ERG has been shown to bind a GGAA DNA-motif and thereby activate or repress certain gene targets. Mechanistic details of the DNA-binding process including discrimination of activated or repressed targets, regulation of ERG's activity as well as DNA-sequence recognition outside the core GGAA-sequence are still open areas of investigation. DNA binding of ERG has been proposed to be regulated through autoinhibition mediated by two conformations of Tyr371 and conformational dynamics of the Ets domain region. We have used molecular dynamics simulations in combination with available crystallographic data to address some of these open questions <i>in silico</i>. In particular we were able to reproduce the ERG DNA-complex with a DNA-binding simulation start- ing in an unbound state with a final RMSD of 2.1 Å to the core Ets domain DNA-complex crystal structure. This allowed us to elucidate the relevance of amino acids involved in the formation of the ERG DNA-complex. These studies highlight Arg385 as a novel key residue in the DNA-binding process. In terms of the DNA-sequence recognition mechanism of ERG we were able to show that water mediated hydrogen bonds, which have recently been proposed to be important in the sequence recognition of Ets transcription factors, are present between ERG and DNA in our simulations and that those interactions have the potential to achieve sequence recognition outside the GGAA core DNA-sequence. In the course of the bridged hydrogen bonding analysis Asp363 emerged as a novel player in the DNA-sequence recognition of ERG. For the role of Tyr371 in the autoinhibitory regulation of ERG we show a different preferred orientation in the DNA-bound form due to interactions with the DNA-backbone and π-stacking interactions. This report presents both novel mechanis- tic aspects for the role of Asp363, Tyr371, Arg385 and water mediated hydrogen bonding in the function of ERG as well as an interesting proof of concept study for the utility of molecular dynamics in protein-DNA interactions.

Molecular dynamics studies targeting the DNA-binding process of ERG focusing on autoinhibition and sequence recognition

251st National Meeting (2016)

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