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

Free energy calculations for the relative binding affinity between DNA and lambda-repressor.

Minoru Saito1, Akinori Sarai

  • 1Faculty of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan. msaito@si.hirosaki-u.ac.jp

Proteins
|July 2, 2003
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

Local synthesis and function of neuro-estrogen and neuro-androgen: impact on the hippocampus-related cognition and neuronal plasticity.

Frontiers in cellular neuroscience·2026
Same author

Miyako <i>Bidens pilosa</i> Extract Ameliorates Allodynia and Suppresses Spinal Microglial Activation in Mice with Partial Sciatic Nerve Ligation.

Current issues in molecular biology·2025
Same author

Autophagy Regulator Rufy 4 Promotes Osteoclastic Bone Resorption by Orchestrating Cytoskeletal Organization via Its RUN Domain.

Cells·2024
Same author

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study.

International journal of molecular sciences·2023
Same author

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community.

Scientific reports·2022
Same author

Translating and validating a Japanese version of the instrument for patient assessment of medical professionalism (J-IPAMP): a cross-sectional survey.

BMC medical education·2022

DNA base modification from thymine (T) to deoxyuracil (U) significantly alters binding free energy. Molecular dynamics revealed T-U substitution impacts hydration and van der Waals interactions, affecting DNA-lambda-repressor complex stability.

Area of Science:

  • Molecular biology
  • Biophysics
  • Computational chemistry

Background:

  • The lambda-repressor protein binds to specific DNA sequences, regulating gene expression.
  • Understanding the energetic basis of DNA-protein interactions is crucial for molecular biology.
  • Base modifications can alter DNA-protein binding affinity and specificity.

Purpose of the Study:

  • To quantify the binding free energy change between DNA and lambda-repressor upon thymine (T) to deoxyuracil (U) substitution.
  • To elucidate the molecular mechanisms underlying the observed binding free energy changes.
  • To investigate the role of hydration and van der Waals interactions in DNA-lambda-repressor recognition.

Main Methods:

  • Free energy perturbation method applied to molecular dynamics simulations.

Related Experiment Videos

  • Simulations conducted on the DNA-lambda-repressor complex in explicit water.
  • Inclusion of all degrees of freedom and long-range Coulomb interactions.

    • Main Results:

    • Calculated binding free energy change of 1.47 +/- 0.40 kcal/mol, consistent with experimental values (1.8 kcal/mol).
    • Thymine (T) to deoxyuracil (U) substitution lowered the dissociated-state free energy due to increased hydration.
    • The T to U change raised the associated-state free energy by reducing favorable van der Waals interactions with lambda-repressor.

    Conclusions:

    • The methyl group (CH3) on thymine is critical for favorable van der Waals interactions with lambda-repressor amino acid residues.
    • The hydrophobic nature of the methyl group enhances its preference for the protein over water, strengthening binding.
    • This study highlights the sensitivity of DNA-protein interactions to subtle base modifications and the importance of specific molecular recognition mechanisms.