Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

DNA deformation energetics and protein binding.

K Zakrzewska1

  • 1Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005 Paris, France.

Biopolymers
|October 28, 2003
PubMed
Summary

Protein-DNA interactions require DNA helix deformation, with backbone changes accounting for most energy costs. Alpha angle transitions significantly contribute to this energetic cost in protein-DNA complexes.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

TiO<sub>2</sub>-Based Nanomaterials for Gas Sensing-Influence of Anatase and Rutile Contributions.

Nanoscale research letters·2017
Same author

Thin films of TiO2:N for photo-electrochemical applications.

Journal of nanoscience and nanotechnology·2012
Same author

TiO2-based nanopowders and thin films for photocatalytical applications.

Journal of nanoscience and nanotechnology·2010
Same author

Effectiveness of nanofiltration in removing small non-enveloped viruses from three different plasma-derived products.

Transfusion medicine (Oxford, England)·2009
Same author

Conformational analysis of nucleic acids revisited: Curves+.

Nucleic acids research·2009
Same author

The process of active rehabilitation for SCI patients.

Ortopedia, traumatologia, rehabilitacja·2007

Area of Science:

  • Structural biology
  • Biophysics
  • Computational chemistry

Background:

  • Protein-DNA complex formation frequently necessitates DNA double helix deformation.
  • Understanding the energetic costs of DNA deformation is crucial for deciphering protein-DNA interactions.

Purpose of the Study:

  • To quantify the energetic cost of DNA deformation in protein-DNA complexes.
  • To analyze the relationship between deformation energy and structural changes.

Main Methods:

  • Calculated deformation energy for 71 crystallographic protein-DNA complexes.
  • Utilized JUMNA program for internal coordinate energy optimization.
  • Employed generalized Born continuum solvent treatment.

Main Results:

  • Approximately 60% of deformation energy in most complexes arises from backbone distortion.
  • Large stacking and pairing energy changes are often offset by long-range stabilizing factors.
  • Alpha angle transitions represent the most energetically significant backbone distortion.

Conclusions:

  • DNA deformation energy is primarily associated with backbone structural changes.
  • Specific backbone distortions, like alpha angle transitions, are energetically costly.
  • Local deformations such as base opening have limited energetic impact.

Related Experiment Videos