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

Allosteric Regulation

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...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Assembly of Signaling Complexes

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,...

GPCR Desensitization

GPCR Desensitization

G protein-coupled receptor (GPCR) signaling plays a crucial role in cell functioning. GPCR desensitization is an equally essential process. It allows cells to respond to changing environments and regain sensitivity to new stimuli while preventing unnecessary stimulation when no longer needed. Prolonged exposure to stimuli leads to GPCR desensitization. It involves blocking the receptors from binding and activating additional G proteins. This inhibits activation of downstream effectors, thereby...

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...

Allosteric Proteins-ATCase

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...

You might also read

Related Articles

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

Sort by

Same author

Directional information flow as a tool for analyzing protein allostery.

bioRxiv : the preprint server for biology·2026

Same author

Mechanisms of Ion Permeation in the AMPA Receptor Ion Channel.

bioRxiv : the preprint server for biology·2025

Same author

Allosteric competition and inhibition in AMPA receptors.

Nature structural & molecular biology·2024

Same author

SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling.

bioRxiv : the preprint server for biology·2024

Same author

Allosteric Competition and Inhibition in AMPA Receptors.

bioRxiv : the preprint server for biology·2023

Same author

Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism.

Nature communications·2023

Search research articles

Related Experiment Video

Updated: May 24, 2025

Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.

Daniel Evans¹, Samreen Sheraz¹, Albert Y Lau^1,2

¹Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

|March 3, 2025

Summary

This study introduces a new computational method to understand how signals travel in allosteric proteins, like the SARS-CoV-2 main protease (Mpro). The research highlights the C-terminal tail

Keywords:

SARS‐CoV‐2 computational chemistry coronavirus 3C proteases molecular dynamics simulation protein conformation

More Related Videos

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

Published on: January 9, 2019

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Related Experiment Videos

Last Updated: May 24, 2025

Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

Published on: January 9, 2019

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

Biochemistry and structural biology
Computational biophysics
Drug discovery and development

Background:

Allosteric proteins transmit signals between binding sites, crucial for biological regulation.
Understanding these allosteric pathways is key for drug development, particularly for viral targets like SARS-CoV-2 main protease (Mpro).
Current methods face challenges in accurately characterizing allosteric signal transmission.

Purpose of the Study:

To develop and apply a novel computational method for characterizing allosteric pathways in proteins.
To investigate the allosteric mechanisms of the SARS-CoV-2 main protease (Mpro).
To identify potential pitfalls in studying allosteric signal transmission via protein dihedral angles.

Main Methods:

Development of a computational approach to map allosteric signal pathways.
Application of the method to study the SARS-CoV-2 main protease (Mpro).
Analysis of the role of protein dihedral angles in allosteric communication.

Main Results:

The study proposes a significant role for the C-terminal tail in the allosteric modulation of Mpro.
The computational method successfully characterized allosteric signal pathways in Mpro.
Identified non-intuitive challenges associated with analyzing dihedral angles in allosteric signal transmission.

Conclusions:

The developed computational method provides a valuable tool for studying protein allostery.
The C-terminal tail of Mpro is implicated as a key player in its allosteric regulation.
Caution is advised when interpreting the role of dihedral angles in allosteric mechanisms due to potential complexities.