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

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...

You might also read

Related Articles

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

Sort by
Same author

Epidemiology, clinical management, and outcomes in patients with eosinophilic granulomatosis with polyangiitis in England: A retrospective observational cohort study.

The journal of allergy and clinical immunology. Global·2026
Same author

Seven Years of Complaints from Patients in Plastic Surgery Hospitals About Autologous Fat Transfer Procedures.

Aesthetic plastic surgery·2026
Same author

Toward molecular and pathology-confirmed completeness in advanced ovarian cancer cytoreduction: Intraoperative molecular imaging and integrated theranostic strategies.

Molecular aspects of medicine·2026
Same author

Design, Synthesis, and Antiviral Evaluation of Novel 3,4-Dihydropyrimidin-2(1<i>H</i>)-one Derivatives.

Microorganisms·2026
Same author

Comprehensive 3D Analysis of Condyle After BSSRO in Surgery-First Approach Among Mandibular Prognathism Patients With and Without Asymmetry.

The Journal of craniofacial surgery·2026
Same author

Association between exposure to perfluoroalkyl ether sulfonate F-53B and cervical cancer risk and its mechanisms of cervical toxicity in Chinese women.

Ecotoxicology and environmental safety·2026

Related Experiment Video

Updated: May 29, 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

Characterization of PDZ domain-peptide interaction interface based on energetic patterns.

Nan Li1, Tingjun Hou, Bo Ding

  • 1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0359, USA.

Proteins
|September 20, 2011
PubMed
Summary

We developed a new computational method, MIEC-SVM, to predict how PDZ domains bind to peptides. This approach accurately identifies key interactions, improving our understanding of protein-protein binding specificity.

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

Related Experiment Videos

Last Updated: May 29, 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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • PDZ domains are crucial modular domains mediating protein-protein interactions by recognizing short peptide sequences.
  • Understanding the binding specificity of PDZ domains is essential for deciphering complex cellular signaling pathways.

Purpose of the Study:

  • To develop and validate a computational method for predicting PDZ domain-peptide binding specificity.
  • To differentiate between interactions contributing to binding specificity versus affinity.

Main Methods:

  • Utilized the MIEC-SVM method, which employs molecular interaction energy components (MIECs) and support vector machine (SVM) for energetic characterization and prediction.
  • Analyzed interactions between 11 mouse PDZ domains and 217 peptides.
  • Performed cross-validation and leave-one-domain-out tests.

Main Results:

  • The MIEC-SVM method demonstrated superior performance compared to existing sequence-based methods in predicting PDZ-peptide binding specificity.
  • Identified 28 informative residue pairs crucial for binding specificity, distinguishing them from 16 uninformative pairs that contributed significantly to binding energy.
  • The method showed improved prediction accuracy when using only the informative residue pairs.

Conclusions:

  • The MIEC-SVM method provides a robust framework for characterizing protein-peptide interactions, applicable to PDZ domains and potentially other protein families like SH3 domains.
  • Distinguishing between informative and uninformative residue interactions offers insights into the distinct contributions to binding specificity and affinity.
  • This approach enhances the understanding of protein recognition mechanisms from structural and energetic perspectives.