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

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...

Conserved Binding Sites

Conserved Binding Sites

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...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding and Linkage

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

You might also read

Related Articles

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

Sort by

Same author

Increased Selfness in the Tumor Emerges as a Possible Immune Sculpting Mechanism.

JCO precision oncology·2026

Same author

A new algorithm Precision OncoPanels (PrOPs) identifies short individualized actionable panels that can guide cancer treatment: a pan-cancer analysis of TCGA cohorts.

NAR genomics and bioinformatics·2025

Same author

Computational Analyses of Bifurcated Inter-Protein Interactions in Protein-Protein Assemblies Reveal Their Pivotal Role in Conferring Stability.

Proteins·2025

Same author

SIRT2 attenuates stress-induced skeletal muscle atrophy by inhibiting glucocorticoid receptor signalling.

bioRxiv : the preprint server for biology·2025

Same author

Understanding the Roles of Secondary Shell Hotspots in Protein-Protein Complexes.

Proteins·2025

Same author

TinyHLAnet: A Light-Weight 3D Structure-Aware Architecture for Rapid and Explainable Identification of CD8+ T-Cell Antigens.

HLA·2025

Same journal

BioMatics 1.0: A Wasserstein Distance Approach for Next-Generation Multiple Sequence Alignment.

Proteins·2026

Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026

Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026

Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026

Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026

Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.

Richa Mudgal¹, Narayanaswamy Srinivasan², Nagasuma Chandra³

¹IISc Mathematics Initiative, Indian Institute of Science, Bangalore, Karnataka, 560 012, India.

|March 26, 2017

Summary

This summary is machine-generated.

Accurate protein function annotation is challenging. This study uses binding site data to build a network revealing complex fold-function relationships, improving annotation and enzyme design.

Keywords:

binding site similarity network enzyme fold structure-function relationship sub-structures

More Related Videos

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

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

Published on: July 16, 2017

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

Related Experiment Videos

Last Updated: Mar 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: July 16, 2017

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

Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Protein functional annotation is complex due to divergence and convergence, and multi-domain proteins.
Existing methods struggle with nuanced fold-function relationships.

Purpose of the Study:

To develop a more accurate method for protein functional annotation.
To systematically map fold-function-binding site relationships.
To leverage binding site information for resolving protein function.

Main Methods:

Generated a comprehensive database of 2,020 fold-function-binding site relationships.
Employed a network-based approach integrating binding site, fold, function, and ligand similarity.
Analyzed network properties to identify versatile protein families and functional relationships.

Main Results:

Deciphered diverse associations: versatile folds with multiple functions, shared functions across folds, and one-to-one relationships.
Identified protein families with dissimilar binding sites performing similar functions.
Observed continuity in functional site space and evolution of protein functions.

Conclusions:

Binding site information refines fold-function relationships for accurate annotation.
Network analysis reveals protein functional versatility and evolutionary insights.
Findings support improved annotation, poly-pharmacology, and enzyme design.