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

Equivalent binding sites reveal convergently evolved interaction motifs.

Andreas Henschel1, Wan Kyu Kim, Michael Schroeder

  • 1Bioinformatics Group, Biotechnological Centre TU Dresden, Germany. ah@biotec.tu-dresden.de

Bioinformatics (Oxford, England)
|November 17, 2005
PubMed
Summary

This study introduces a new method to find non-homologous protein domains binding at similar sites. This reveals convergent evolution of binding motifs, aiding in understanding interaction specificity and designing new ligands.

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

Much ado about nothing: modeling amino acid replacement with predicted protein structures.

Bioinformatics (Oxford, England)·2026
Same author

Robotic mini- or less open sublay for anterior abdominal wall hernia repair using the da Vinci single port robotic platform (SP MILOS): a preclinical feasibility study.

Hernia : the journal of hernias and abdominal wall surgery·2026
Same author

The structural basis of drugs targeting protein-protein interactions uncovered with the protein-ligand interaction profiler PLIP.

Expert opinion on drug discovery·2025
Same author

Improving T2D machine learning-based prediction accuracy with SNPs and younger age.

Computational and structural biotechnology journal·2025
Same author

Imaging-derived biomarkers from <sup>68</sup>Ga-DOTATOC PET/CT scans to predict survival of patients with neuroendocrine tumors after PRRT with <sup>177</sup>Lu-DOTATATE.

Cancer imaging : the official publication of the International Cancer Imaging Society·2025
Same author

PLIP 2025: introducing protein-protein interactions to the protein-ligand interaction profiler.

Nucleic acids research·2025

Area of Science:

  • Structural biology
  • Bioinformatics
  • Molecular evolution

Background:

  • Characterizing protein-protein interaction interfaces is crucial for understanding molecular recognition.
  • Interactions involving non-homologous domains at equivalent binding sites offer insights into convergent evolution and conserved binding motifs.

Purpose of the Study:

  • To develop a novel computational method for identifying non-homologous structural domains that bind to equivalent sites on a common partner.
  • To create a comprehensive database of such interactions and explore their implications in molecular mimicry and drug design.

Main Methods:

  • A novel computational approach was developed to systematically identify non-homologous domains interacting at equivalent binding sites.
  • The method was applied to all known protein complex structures to build a comprehensive database.

Related Experiment Videos

  • The database was utilized for screening viral protein mimicry and analyzing enzyme-inhibitor structural motifs.

    • Main Results:

    • A significant percentage of non-homologous domains (4.2% excluding immunoglobulins/proteases, 16% including them) utilize common binding interfaces.
    • Identified instances of viral protein mimicry, such as viral M3 protein mimicking chemokine dimers and HIV Nef mimicking kinases.
    • Elucidated conserved structural motifs in viral proteins and enzyme-inhibitor interactions, highlighting convergent evolution.

    Conclusions:

    • The developed method and database provide valuable resources for understanding protein interaction specificity and identifying potential drug targets.
    • Convergent evolution of binding interfaces is a recurring theme, particularly evident in viral strategies to interfere with host processes.
    • The findings have implications for designing novel ligands and understanding molecular mimicry in biological systems.