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

Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence 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...
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...
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...
Allosteric Regulation01:08

Allosteric Regulation

Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...

You might also read

Related Articles

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

Sort by
Same author

An anhydrous carboxymethyl chitosan/amorphous calcium phosphate nanocomposite toothpaste promotes enamel surface remineralization.

Journal of dentistry·2026
Same author

PuMYB40 and PuWRKY75 synergistically enhance phosphate uptake and organic phosphorus hydrolysis under phosphate deficiency in poplar.

Plant physiology·2026
Same author

ZHMolTopoRPI: A Commutative Algebra-Driven Deep Learning Framework for Robust RNA-Protein Interaction Prediction.

Journal of chemical information and modeling·2026
Same author

Regulation mechanism study of residues E318/319 for KaiC protein phosphorylation.

Biophysical journal·2026
Same author

Exploring ligand flexibility in nucleic acid scaffolds using graph neural networks.

Biophysical journal·2026
Same author

Association between circulating biomarkers of one-carbon metabolism and glymphatic system function in cognitive decline of Alzheimer's disease.

Frontiers in neurology·2026

Related Experiment Video

Updated: May 10, 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

ZHMolEReP: An Energy Response Strategy for Protein Allosteric Site Prediction.

Xing Ke1, Haoquan Liu1, Jian Wang2

  • 1Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.

Journal of Chemical Information and Modeling
|May 8, 2026
PubMed
Summary

A new tool, ZHMolEReP, accurately identifies protein allosteric sites beyond pockets using physically grounded features. This advances understanding of allosteric regulation and aids allosteric drug design.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: May 10, 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

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology and Cheminformatics

Background:

  • Accurate identification of protein allosteric sites is crucial for understanding biological regulation and developing targeted therapies.
  • Current methods often fail by focusing solely on pocket geometry, neglecting the broader network of interactions involved in allosteric regulation.

Purpose of the Study:

  • To develop a novel, residue-level computational tool, ZHMolEReP, for predicting allosteric sites with enhanced physical interpretability and accuracy.
  • To overcome the limitations of existing pocket-centric methods by considering energy propagation and cooperative effects.

Main Methods:

  • Integration of perturbation response scanning (PRS) with free energy response approximation to create a physically grounded, seven-feature representation.
  • Development of a residue-level model combining mechanical descriptors and local structural features to capture allosteric signals.

Main Results:

  • ZHMolEReP significantly outperforms existing methods on the ASBench dataset, achieving a recall of 0.7037 and an AUC of 0.7858.
  • The tool successfully identified allosteric sites in 33 out of 40 proteins, demonstrating substantial improvements over baseline approaches.
  • Performance advantages were validated on an independent test set, highlighting the model's generalization ability.

Conclusions:

  • ZHMolEReP offers a physically interpretable and generalizable framework for allosteric site identification.
  • The findings support advancements in understanding allosteric mechanisms and facilitate the design of novel allosteric drugs.