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Related Experiment Videos

Structural basis for cooperative DNA binding by CAP and lac repressor.

Alexander Balaeff1, L Mahadevan, Klaus Schulten

  • 1Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Structure (London, England : 1993)
|January 17, 2004
PubMed
Summary

This study models how transcription factors catabolite gene activator protein (CAP) and lac repressor (LR) bind DNA. The model reveals DNA loop overwinding and extension in the ternary complex, explaining protein cooperativity.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • Transcription-regulating proteins like CAP and LR bind DNA cooperatively.
  • These proteins form a ternary complex with a promoter loop, crucial for gene regulation.

Purpose of the Study:

  • To develop a multiscale model of the ternary complex formed by CAP, LR, and a DNA loop.
  • To elucidate the structural dynamics and energetic basis of cooperative DNA binding.

Main Methods:

  • Utilized crystal structures of CAP and LR.
  • Employed the theory of elasticity to model the DNA loop structure.
  • Developed a multiscale and all-atom model of the ternary complex.

Main Results:

  • Predicted DNA loop underwinding in the binary LR-DNA complex.

Related Experiment Videos

  • Predicted DNA loop overwinding and extension in the ternary LR-CAP-DNA complex.
  • Computed DNA binding hand relocation distance consistent with experimental data.

    • Conclusions:

    • The multiscale model accurately explains the cooperativity effect in transcription factor binding.
    • The study provides an all-atom model suggesting avenues for further experimental validation.
    • Structural dynamics of DNA loops are critical for cooperative protein binding.