Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1

Levani Zandarashvili, Dana Vuzman, Alexandre Esadze, Yuki Takayama, Debashish Sahu, Yaakov Levy, Junji Iwahara

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Abstract

Egr-1 is an inducible transcription factor that recognizes 9-bp target DNA sites via three zinc finger domains and activates genes in response to cellular stimuli such as synaptic signals and vascular stresses. Using spectroscopic and computational approaches, we have studied structural, dynamic, and kinetic aspects of the DNAscanning process in which Egr-1 is nonspecifically bound to DNA and perpetually changes its location on DNA. Our NMR data indicate that Egr-1 undergoes highly dynamic domain motions when scanning DNA. In particular, the zinc finger 1 (ZF1) of Egr-1 in the nonspecific complex is mainly dissociated fromDNA and undergoes collective motions on a nanosecond timescale, whereas zinc fingers 2 and 3 (ZF2 and ZF3, respectively) are bound to DNA. This was totally unexpected because the previous crystallographic studies of the specific complex indicated that all of Egr-1's three zinc fingers are equally involved in binding to a target DNA site. Mutations that are expected to enhance ZF1's interactions with DNA and with ZF2 were found to reduce ZF1's domain motions in the nonspecific complex suggesting that these interactions dictate the dynamic behavior of ZF1. By experiment and computation, we have also investigated kinetics of Egr-1's translocation between two nonspecific DNA duplexes. Our data on the wild type and mutant proteins suggest that the domain dynamics facilitate Egr-1's intersegment transfer that involves transient bridging of two DNA sites. These results shed light on asymmetrical roles of the zinc finger domains for Egr-1 to scan DNA efficiently in the nucleus.

Original languageEnglish (US)
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number26
DOIs
StatePublished - Jun 26 2012

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Zinc Fingers
Transcription Factors
DNA
Mutant Proteins
Blood Vessels
Mutation

Keywords

  • Interdomain dynamics
  • NMR spectroscopy
  • Protein-DNA interactions
  • Simulation
  • Target search process

ASJC Scopus subject areas

  • General

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Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1. / Zandarashvili, Levani; Vuzman, Dana; Esadze, Alexandre; Takayama, Yuki; Sahu, Debashish; Levy, Yaakov; Iwahara, Junji.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 26, 26.06.2012.

Research output: Contribution to journalArticle

Zandarashvili, Levani ; Vuzman, Dana ; Esadze, Alexandre ; Takayama, Yuki ; Sahu, Debashish ; Levy, Yaakov ; Iwahara, Junji. / Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1. In: Proceedings of the National Academy of Sciences of the United States of America. 2012 ; Vol. 109, No. 26.
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