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

Facilitated diffusion of DNA-binding proteins.

Konstantin V Klenin1, Holger Merlitz, Jörg Langowski

  • 1Division of Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany.

Physical Review Letters
|February 21, 2006
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

Efficient and reversible chirality induction between protein and achiral plasmonic assemblies.

Nature materials·2026
Same author

Tuning nuclear rheology through transient chromatin cross-links.

Physical review. E·2026
Same author

A Self-Organized Liquid Reaction Container for Cellular Memory.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Molecular dynamics investigation of polymer-decorated nanoparticles with co-nonsolvent: Structural transitions from isotropic layers to heterogeneous patches.

The Journal of chemical physics·2025
Same author

An Analytical Understanding of Reentrant Condensation of a Polyelectrolyte in the Presence of an Oppositely Charged Surfactant.

Langmuir : the ACS journal of surfaces and colloids·2025
Same author

CHMP6 as a novel prognostic biomarker in bladder cancer: insights from a comprehensive cell death-related gene risk model.

Frontiers in oncology·2025

Protein search times on DNA are significantly reduced by combining 3D diffusion with 1D sliding along the DNA. This theoretical model, verified by simulations, explains faster DNA-binding protein reactions.

Area of Science:

  • Biophysics
  • Molecular Biology
  • Computational Biology

Background:

  • Site-specific DNA-binding proteins are crucial for genetic processes.
  • Understanding protein-DNA interactions, including search mechanisms, is fundamental.
  • Previous models often simplify protein movement along DNA.

Purpose of the Study:

  • To derive the diffusion-controlled limit of reaction times for site-specific DNA-binding proteins from first principles.
  • To theoretically model protein propagation via simultaneous 3D diffusion and 1D sliding.
  • To analyze how these combined mechanisms affect protein search efficiency on DNA.

Main Methods:

  • Developed a novel analytical model based on first principles.
  • Incorporated two competitive protein propagation modes: 3D spatial diffusion and 1D DNA sliding.

Related Experiment Videos

  • Verified the analytical model's accuracy using numerical simulations.

    • Main Results:

    • The theoretical model accurately predicts reaction times for DNA-binding proteins.
    • Unspecific binding combined with 1D sliding significantly reduces protein search times.
    • Simulations confirmed the model's predictions regarding reaction time reduction.

    Conclusions:

    • The interplay between 3D diffusion and 1D sliding is a key factor in efficient DNA target searching.
    • Unspecific DNA interactions enhance the speed of site-specific protein binding.
    • This theoretical framework provides new insights into protein-DNA recognition dynamics.