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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

You might also read

Related Articles

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

Sort by
Same author

Ligand-dependent reprogramming of HNF4A expression and function suppresses multistep hepatocarcinogenesis.

Molecular therapy. Oncology·2026
Same author

Convenient and sensitive detection of viable Escherichia coli employing a sequential reaction between antibody-enzyme complexes.

Biosensors & bioelectronics·2026
Same author

Rapid and convenient electrochemical hemoglobin detection in mouse feces employing a DNA aptamer to evaluate the severity of colitis in a mouse model.

Analytical methods : advancing methods and applications·2026
Same author

Design and Evaluation of Domain-Rearranged Bispecific Antibody Fragments for Functional Optimization.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Production of Bispecific Antibody Fragments from Fc Fusion.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Visualization of Immunological Synapse Formation by Intercellular Cross-Linking of T Cell-Dependent Bispecific Antibodies Using Fluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Related Experiment Video

Updated: Jun 13, 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

In Silico Screening Using Freely Available Computational Tools to Generate Novel Peptide/Protein Pairs

Haruka Kawai1, Daimei Miura1,2, Genki Kudo3

  • 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan.

Chembiochem : a European Journal of Chemical Biology
|June 12, 2026
PubMed
Summary

Computational screening of protein ligation mutants shows limitations in predicting covalent bond formation. While some SpyTag mutants retained binding to SpyCatcher, accurately predicting enhanced reactions remains challenging.

Keywords:
MD simulationdocking simulationin silico screeningtag/catcher

More Related Videos

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Related Experiment Videos

Last Updated: Jun 13, 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

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Protein-protein ligation technologies like SpyTag/SpyCatcher (ST/SC) are crucial for creating functional protein complexes and biosensors.
  • Developing orthogonal Tag/Catcher pairs is essential for constructing complex, controlled protein assemblies.
  • Improving the reaction rates of existing Tag/Catcher pairs often requires extensive and resource-intensive in vitro screening.

Purpose of the Study:

  • To explore the utility of in silico screening methods for identifying improved protein ligation mutants.
  • To assess the feasibility of using computational tools to predict mutations that enhance protein ligation efficiency.
  • To investigate the compatibility of engineered SpyTag mutants with SpyCatcher.

Main Methods:

  • In silico screening utilizing structural prediction, molecular docking, and molecular dynamics simulations.
  • Selection of four SpyTag (ST) mutants based on computational predictions.
  • In vitro testing of selected ST mutants for binding and reaction with SpyCatcher (SC) wild type and mutants.

Main Results:

  • None of the selected ST mutants reacted with a corresponding SC mutant, indicating challenges in predicting covalent bond formation computationally.
  • All tested ST mutants demonstrated retained binding affinity to the wild-type SC.
  • The study identified ST mutants with partial compatibility towards SC.

Conclusions:

  • General-purpose computational methods have limitations in designing proteins for specific molecular recognition and catalysis, particularly for covalent bond formation.
  • In silico screening can identify protein mutants with altered binding properties, even if reaction efficiency predictions are challenging.
  • Further refinement of computational approaches is needed for effective in silico design of protein ligation systems.