Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

PLoS Comput Biol. 2015 Jun 11;11(6):e1004287. doi: 10.1371/journal.pcbi.1004287. eCollection 2015 Jun.


Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • DNA / chemistry*
  • DNA / metabolism*
  • Molecular Dynamics Simulation
  • Octamer Transcription Factor-3 / chemistry*
  • Octamer Transcription Factor-3 / metabolism*
  • Pluripotent Stem Cells
  • Protein Binding
  • SOXB1 Transcription Factors / chemistry*
  • SOXB1 Transcription Factors / metabolism*


  • Octamer Transcription Factor-3
  • SOXB1 Transcription Factors
  • DNA

Grant support

FM and VC are financially supported by the Max Planck Society (MPSG) and the German Research Foundation (DFG) through the priority program “SPP1356—Pluripotency and Cellular Reprogramming” (grant number CO 975/1-1). BB is supported by the Agence Nationale de la Recherche (CHROME project, grant number ANR-12_BSV5-0017-01). Computer resources were provided by the MPSG and the Partnership for Advanced Computing in Europe (PRACE Project “LASIPROD”). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.