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

Flexibility and molecular recognition in the immune system.

Ralph Jimenez1, Georgina Salazar, Kim K Baldridge

  • 1Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail Drop CVN22, La Jolla, CA 92037, USA.

Proceedings of the National Academy of Sciences of the United States of America
|January 9, 2003
PubMed
Summary

Antibody binding sites exhibit motions from femtoseconds to nanoseconds. One antibody, 4-4-20, has a rigid site due to its heavy chain complementarity-determining region 3 (HCDR3) loop and a critical tyrosine.

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

Long-term stabilization of intensity-difference squeezing from four-wave mixing in rubidium vapor.

Optics express·2026
Same author

Dark-State-Mediated Photobleaching in mCherry-Based Red Fluorescent Proteins.

The journal of physical chemistry letters·2026
Same author

Chiral Semibuckminsterfullerene: Synthesis, Resolution, and Chiroptical Properties.

Organic letters·2025
Same author

A Liquid-Core Fiber Platform for Classical and Entangled Two-Photon Absorption Measurements.

ACS photonics·2025
Same author

Surprising acidity for the methylene of 1,3-indenocorannulenes?

Beilstein journal of organic chemistry·2024
Same author

Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants.

The journal of physical chemistry letters·2024

Area of Science:

  • Biophysics
  • Immunology
  • Protein Dynamics

Background:

  • Antibody-antigen interactions are crucial for immune response.
  • Understanding the dynamic nature of antibody binding sites is key to deciphering recognition mechanisms.
  • Fluorescein is a common model antigen used in antibody studies.

Purpose of the Study:

  • To investigate the dynamic motions within antibody binding sites using photon echo spectroscopy.
  • To compare the flexibility of binding sites in three different antibodies raised against fluorescein.
  • To correlate structural features with observed binding site dynamics.

Main Methods:

  • Utilizing ultrafast laser spectroscopy, specifically photon echo spectroscopy.
  • Measuring the time-resolved response of antibody-fluorescein complexes to electronic excitation.

Related Experiment Videos

  • Analyzing the femtosecond to nanosecond timescale dynamics of antibody binding sites.

    • Main Results:

    • Observed motions in antibody binding sites spanning femtoseconds to nanoseconds.
    • Identified antibody 4-4-20 as having a rigid binding site, attributed to a short HCDR3 loop and a stabilizing tyrosine residue.
    • Demonstrated that antibodies 34F10 and 40G4 possess more flexible binding sites, linked to longer HCDR3 loops and a light chain deletion.

    Conclusions:

    • Binding site flexibility varies significantly among antibodies, even those targeting the same antigen.
    • Structural elements like HCDR3 loop length and specific residue interactions (e.g., tyrosine as a molecular splint) dictate binding site rigidity.
    • Differential binding site flexibility may lead to distinct antigen recognition mechanisms, including lock-and-key, induced-fit, and conformational selection.