Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Ligand Binding Sites

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...

Protein-protein Interfaces

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...

Conserved Binding Sites

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...

Antibody Structure and Classes

Antibody Structure and Classes

Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.

Immunoprecipitation

Immunoprecipitation

Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...

Affinity and Avidity

Affinity and Avidity

You might also read

Related Articles

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

Sort by

Same author

Analysis of monoclonal antibodies against the malaria invasion complex protein RIPR reveals the structural basis for synergistic antibody protection.

Immunity·2026

Same author

Mapping Allergen B- and T-Cell Epitopes: Technological Advances and Their Role in Precision Allergy Therapy.

Allergy·2026

Same author

ANARCII enables alignment-free antigen receptor numbering using a generalised language model.

Communications biology·2026

Same author

Engineering of acidic pH-responsive anti-CD3 binding antibodies.

mAbs·2026

Same author

Convergent antigenic drift of the influenza hemagglutinin lateral patch across time and species.

bioRxiv : the preprint server for biology·2026

Same author

iNOS modulates inflammatory responses in an NO-independent manner through direct interaction with IRG1 in mitochondria.

Nature metabolism·2026

Search research articles

Related Experiment Video

Updated: Jul 11, 2025

Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag

Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag

Published on: January 16, 2012

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.

Valentin J Hoerschinger¹, Franz Waibl¹, Nancy D Pomarici¹

¹Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria.

Journal of Chemical Information and Modeling

|November 7, 2023

Summary

This summary is machine-generated.

We developed PEP-Patch, a new tool to visualize and quantify protein surface electrostatics. This method aids in understanding molecular interactions, antibody developability, and pharmacokinetic properties.

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy

Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy

Published on: August 6, 2018

Related Experiment Videos

Last Updated: Jul 11, 2025

Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag

Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag

Published on: January 16, 2012

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy

Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy

Published on: August 6, 2018

Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Protein electrostatic properties, determined by charged and polar residues, are crucial for biological functions.
These properties influence molecular recognition, solubility, viscosity, and antibody developability.
Accurate characterization of protein electrostatics is essential for understanding these processes.

Purpose of the Study:

To introduce PEP-Patch, a novel computational tool for visualizing and quantifying protein surface electrostatic potential.
To demonstrate the utility of PEP-Patch in analyzing key protein interactions and properties.

Main Methods:

Development of the PEP-Patch software tool.
Application of PEP-Patch to analyze electrostatic surface patches on proteins.
Validation of PEP-Patch by correlating predictions with experimental data.

Main Results:

PEP-Patch effectively visualizes and quantifies electrostatic potential as distinct surface patches.
The tool successfully elucidates protease substrate specificity and antibody-antigen recognition patterns.
PEP-Patch accurately predicts antibody heparin column retention times, correlating with pharmacokinetic behavior.

Conclusions:

PEP-Patch provides a valuable method for characterizing protein surface electrostatics.
The tool has broad applications in understanding protein function, drug design, and antibody engineering.
Quantifying electrostatic surface properties enhances predictions of protein behavior and interactions.