Structural Basis for Cooperative DNA Binding by CAP and Lac Repressor

Alexander Balaeff, L. Mahadevan, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

Catabolite gene activator protein (CAP) and lac repressor (LR) are celebrated transcription-regulating proteins that bind to DNA cooperatively forming a ternary complex with the promoter loop. Here we present a multiscale model of the ternary complex derived from crystal structures of the proteins and a continuous structure of the DNA loop built using the theory of elasticity. We predict that the loop is underwound in the binary complex with the LR, whereas in the ternary complex with the LR and CAP, the loop is overwound and extended due to an upstream relocation of a DNA binding hand of LR. The computed relocation distance matches the experimental observations and the energy balance of the system explains the cooperativity effect. Using the multiscale approach, we build an all-atom model of the ternary complex that suggests a series of further experimental investigations.

Original languageEnglish (US)
Pages (from-to)123-132
Number of pages10
JournalStructure
Volume12
Issue number1
DOIs
StatePublished - Jan 2004

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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