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

Finding biologically relevant protein domain interactions: conserved binding mode analysis.

Benjamin A Shoemaker1, Anna R Panchenko, Stephen H Bryant

  • 1Computational Biology Branch, National Center for Biotechnology Information, Building 38A, National Institutes of Health, Bethesda, MD 20894, USA. shoemake@mail.nih.gov

Protein Science : a Publication of the Protein Society
|December 31, 2005
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

MD2NMR: Linking molecular dynamics with NMR relaxation.

Biophysical journal·2026
Same author

Integrating evidence from protein domains to identify cancer driver mutations.

Protein science : a publication of the Protein Society·2026
Same author

G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.

Nucleic acids research·2026
Same author

Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability.

Nucleic acids research·2025
Same author

G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.

bioRxiv : the preprint server for biology·2025
Same author

Deciphering Allosteric Modulation of Cancer-Associated Histone Missense Mutations.

Journal of molecular biology·2025
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Researchers developed a method to identify biologically relevant protein domain interactions by classifying conserved binding modes (CBMs) from structural data. This approach helps discover significant protein connections and predict unknown binding surfaces.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Proteins evolve via domain shuffling, leading to conserved domains across species.
  • Interactions between conserved domains are crucial for cellular function and involve specific binding surfaces.

Purpose of the Study:

  • To develop a systematic method for comparing and classifying protein domain interactions from structural data.
  • To identify biologically relevant interactions and distinguish them from non-specific associations.

Main Methods:

  • Developed a method to classify protein domain interactions using structural alignment data and domain databases.
  • Defined Conserved Binding Modes (CBMs) inferred from superimposed structural complexes of interacting domain families.
  • Applied the method to analyze oligomeric interactions of globins.

Related Experiment Videos

Main Results:

  • Created a set of CBMs, identifying 1000-2000 types of interacting domain pairs in the structure database.
  • Constructed domain interaction networks highlighting functionally significant connections by filtering infrequent links.
  • Demonstrated the method's utility in inferring unknown binding surfaces using CBMs as docking templates.

Conclusions:

  • The CBM approach effectively identifies biologically relevant protein-protein interactions.
  • This method provides a valuable tool for predicting protein structures and functions.
  • Conserved domain interactions play a significant role in protein evolution and function.