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Related Experiment Videos

Computer simulation of protein-induced structural changes in closed circular DNA

P Zhang1, I Tobias, W K Olson

  • 1Department of Chemistry, Wright-Rieman Laboratories, Rutgers, State University of New Jersey, New Bruswick 08903.

Journal of Molecular Biology
|September 23, 1994
PubMed
Summary

Computer simulations reveal how proteins alter DNA folding. Wrapping DNA around proteins causes sudden structural collapse, offering insights into supercoil regulation and DNA deformation mechanisms.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • Proteins play a crucial role in DNA folding and organization within cells.
  • Understanding protein-DNA interactions is key to deciphering gene regulation and DNA replication.
  • The supercoiling of DNA is a fundamental aspect of its structure and function.

Purpose of the Study:

  • To investigate the impact of protein-induced DNA wrapping on DNA folding using computational methods.
  • To develop a novel modeling scheme for simulating DNA configurations around protein cores.
  • To explore how proteins influence DNA supercoiling and structural transitions.

Main Methods:

  • Monte Carlo computer simulations were employed to model DNA-protein complexes.
  • A new modeling scheme represented DNA as a wrapped fragment and a free loop with single-stranded scission.

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  • The DNA loop's configuration and energy (elastic bending, twisting, excluded volume) were analyzed using Fourier series and Bézier curves.

    • Main Results:

    • Minimum energy structures were identified by varying DNA-protein complex proportions, superhelical turns, and linking number.
    • A sudden collapse in DNA's three-dimensional structure was observed with incremental protein wrapping.
    • Simulated configurations provided insights into the "linking number paradox" and protein-mediated supercoil changes.

    Conclusions:

    • Protein wrapping induces significant, sometimes abrupt, changes in DNA's three-dimensional structure.
    • These findings offer new perspectives on the mechanisms by which proteins manage DNA supercoiling.
    • The study provides a foundational understanding of how local molecular changes translate to large-scale DNA structural alterations.