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 Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Recombinant Human Fab Antibodies Differentially Neutralize Shiga Toxin in Renal Epithelial and Endothelial Cells.

Toxins·2026
Same author

Clarifying Frizzled 2 function in development through genetically validated mouse models.

Disease models & mechanisms·2026
Same author

Dual targeting of inhibitory EGFR epitopes with synthetic antibodies in therapeutic-resistant cancers.

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

Structural Basis of Serine Protease Inhibition by Antibodies from Biased Fab Phage-Display Libraries.

bioRxiv : the preprint server for biology·2026
Same author

LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance.

Molecular & cellular proteomics : MCP·2026
Same author

Tetravalent antibodies are more potent and efficacious erythropoiesis-stimulating agents than erythropoietin in vivo.

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

Drugging the proteome via large-scale chemoproteomics.

Trends in biochemical sciences·2026
Same journal

Peptideins: Navigating the gray zone of the proteome.

Trends in biochemical sciences·2026
Same journal

A metabolon channels nicotine biosynthesis.

Trends in biochemical sciences·2026
Same journal

Better call chaperone.

Trends in biochemical sciences·2026
Same journal

Biochemistry at scale: Seeing both the forest and the trees.

Trends in biochemical sciences·2026
Same journal

Voices across Asia and Oceania: Biochemistry across borders.

Trends in biochemical sciences·2026
See all related articles

Related Experiment Video

Updated: Jun 5, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Evolving specificity from variability for protein interaction domains.

Tomonori Kaneko1, Sachdev S Sidhu, Shawn S C Li

  • 1Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.

Trends in Biochemical Sciences
|January 14, 2011
PubMed
Summary
This summary is machine-generated.

Protein domain interactions are key in biology. Different families like SH2, SH3, and PDZ domains use distinct mechanisms, such as loop configurations and binding site evolution, to achieve specific peptide interactions.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Related Experiment Videos

Last Updated: Jun 5, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Modular protein interaction domains are crucial for biological processes.
  • Understanding how these domains achieve specific interactions is a key question.
  • Diversity in specificity within domain families needs explanation.

Purpose of the Study:

  • To investigate the mechanisms by which modular protein domains encode diverse specificities.
  • To compare specificity determination strategies across different domain families.

Main Methods:

  • Analysis of the Src homology (SH) 2 domain family.
  • Comparative analysis of SH3 and PDZ domains.
  • Examination of surface loop configurations and binding site residue evolution.

Main Results:

  • SH2 domain specificity is largely determined by surface loop configurations controlling ligand access.
  • SH3 domains utilize loops for ligand recognition.
  • PDZ domains achieve specificity through co-evolution of binding-site residues.

Conclusions:

  • Conformational and sequence variability in surface loops and binding sites are general mechanisms for encoding domain-peptide interaction specificity.
  • Different domain families employ distinct strategies to achieve specific molecular recognition.