Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains

Max V. Staller, Eddie Ramirez, Sanjana R. Kotha, Alex S. Holehouse, Rohit V. Pappu, Barak A. Cohen

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper's transparent peer review process is included in the supplemental information.

Original languageEnglish
Pages (from-to)334-345.e5
JournalCell Systems
Volume13
Issue number4
DOIs
StatePublished - Apr 20 2022

Keywords

  • activation domain
  • all-atom simulations
  • deep mutational scanning
  • genomic method development
  • high-throughput mutagenesis
  • intrinsically disordered protein
  • intrinsically disordered region
  • transcription factor

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