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

Protein-DNA interactions: A structural analysis.

S Jones1, P van Heyningen, H M Berman

  • 1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London, WC1E 6BT, England.sue@biochem.ucl.ac.uk

Journal of Molecular Biology
|May 1, 1999
PubMed
Summary
This summary is machine-generated.

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

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Journal of cheminformatics·2024
Same author

Resolvin D2 promotes host defense in a 2 - hit model of sepsis with secondary lung infection.

Prostaglandins & other lipid mediators·2022
Same author

Lipoxin A4 promotes reduction and antibiotic efficacy against Pseudomonas aeruginosa biofilm.

Prostaglandins & other lipid mediators·2020
Same author

Clinical management of Brucella suis infection in dogs and implications for public health.

Australian veterinary journal·2017
Same author

Modeling birds on wires.

Journal of theoretical biology·2016
Same author

HydroCoils, occlusion rates, and outcomes: a large single-center study.

AJNR. American journal of neuroradiology·2010
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. Elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

This study analyzed protein-DNA binding sites, revealing common features like hydrophilic surfaces and identifying three binding modes. DNA distortions, including helix bending, were observed, leading to proposed rules for DNA bending in protein-DNA complexes.

Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • Protein-DNA interactions are fundamental to cellular processes.
  • Understanding these interactions requires detailed structural analysis.

Purpose of the Study:

  • To analyze the structural and chemical properties of protein-DNA binding sites.
  • To identify common features and modes of DNA binding by proteins.
  • To investigate DNA structural changes upon protein binding.

Main Methods:

  • Analysis of 26 protein-DNA complex structures from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB).
  • Examination of chemical and physical properties at the protein-DNA interface.
  • Identification and classification of protein-DNA interaction footprints.

Related Experiment Videos

  • Evaluation of DNA structural distortions using root-mean-square deviation.

    • Main Results:

    • Protein-DNA interfaces are characterized by hydrophilic surfaces and numerous hydrogen bonds, distinct from protein-protein interfaces.
    • Three DNA binding modes were identified: single-headed, double-headed, and enveloping, with the latter being common in enzymes.
    • Bound DNA exhibits structural distortions, including altered helical parameters and bending, influenced by specific DNA sequences.
    • Helix bending modifies DNA groove dimensions, facilitating protein element binding.

    Conclusions:

    • Protein-DNA binding sites share conserved features facilitating specific interactions.
    • The identified binding modes provide a framework for classifying protein-DNA recognition.
    • DNA bending is a key mechanism in protein-DNA complex formation, influenced by sequence-specific distortions.
    • A preliminary set of rules governing DNA bending in these complexes has been proposed.