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

Prediction of binding energetics from structure using empirical parameterization

B M Baker1, K P Murphy

  • 1Department of Biochemistry, University of Iowa, Iowa City 52242, USA.

Methods in Enzymology
|September 29, 1998
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

Assessment of isocenter alignment during CT colonography: Implications for clinical practice.

Radiography (London, England : 1995)·2018
Same author

Radiation exposure from diagnostic imaging in young patients with testicular cancer.

European radiology·2014
Same author

Non-contrast CT at comparable dose to an abdominal radiograph in patients with acute renal colic; impact of iterative reconstruction on image quality and diagnostic performance.

Insights into imaging·2014
Same author

Single-chain VαVβ T-cell receptors function without mispairing with endogenous TCR chains.

Gene therapy·2011
Same author

The Arthritis of Bacillary Dysentery.

Transactions of the American Clinical and Climatological Association·2011
Same author

The Effect of Long-Continued Suppressive Atabrine Medication on Relapses of Vivax Malaria.

Transactions of the American Clinical and Climatological Association·2011
Same journal

1,2-Aminothiol-specific conjugation for dual-color fluorescent labeling via ultrafast TAMM conjugates.

Methods in enzymology·2026
Same journal

Nitrone dipoles in bioorthogonal chemistry applications.

Methods in enzymology·2026
Same journal

Bioorthogonal labeling of sialic acid isomers for detection of glycoconjugates by mass spectrometry imaging and microscopy.

Methods in enzymology·2026
Same journal

Bioorthogonal photocatalytic proximity labeling for quantitative mapping of cell-cell interactions.

Methods in enzymology·2026
Same journal

inCu-click: Enabling copper-catalyzed click chemistry inside living cells.

Methods in enzymology·2026
Same journal

Site-specific antibody labeling via endo-S2 mediated Fc glycan remodeling.

Methods in enzymology·2026
See all related articles

This study introduces a new empirical method to predict protein-protein and protein-peptide binding energetics. It provides a full thermodynamic profile, including heat capacity, enthalpy, and entropy changes, for better interaction analysis.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Predicting protein-protein and protein-peptide interactions is crucial in molecular biology.
  • Existing empirical methods often focus solely on binding free energy (delta G degree).
  • A comprehensive thermodynamic description offers deeper insights into binding mechanisms.

Purpose of the Study:

  • To present an empirical method for predicting binding energetics of protein-protein and protein-peptide interactions.
  • To provide a detailed thermodynamic profile (delta Cp, delta H degree, delta S degree) beyond delta G degree.
  • To highlight the need for integrated structural and thermodynamic data for improved accuracy.

Main Methods:

  • Development of an empirical computational method based on 3D structures.

Related Experiment Videos

  • Prediction of thermodynamic parameters: heat capacity (delta Cp), enthalpy change (delta H degree), and entropy change (delta S degree).
  • Comparison with experimental data for validation and assessment of accuracy.

    • Main Results:

    • The method successfully predicts a comprehensive thermodynamic signature of binding.
    • The inclusion of delta Cp, delta H degree, and delta S degree provides richer detail than delta G degree alone.
    • Accuracy is enhanced with sufficient experimental binding and linked equilibria data.

    Conclusions:

    • The presented empirical method offers a detailed thermodynamic description of biomolecular interactions.
    • More comprehensive experimental data, including linked equilibria, are essential for method refinement and validation.
    • Future parameterization with diverse binding data will expand the method's applicability to various interaction types.