Related Experiment Video
Updated: Sep 24, 2025
05:12
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
Published on: February 2, 2024
920
Quantitative Analysis of Dynamic Allostery.
Qiaojing Huang1, Luhua Lai1,2,3, Zhirong Liu1
1Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
Journal of Chemical Information and Modeling
|May 5, 2022
Summary
Dynamic allostery, a regulatory mechanism without major shape changes, was quantified. Its contribution is small but consistently activates biological processes, decaying with distance.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Dynamic allostery regulates proteins without significant conformational changes.
- Quantifying pure dynamic allostery is crucial due to coupled enthalpic and entropic contributions.
Purpose of the Study:
- To quantitatively estimate the contribution of pure dynamic allostery in proteins.
- To identify key factors influencing dynamic allostery.
Main Methods:
- Developed a unified anisotropic elastic network model (uANM) incorporating side-chain and ligand information.
- Applied uANM to a dataset of allosteric proteins, excluding conformational changes.
- Constructed toy models for monomeric and oligomeric proteins.
Main Results:
- Pure dynamic allostery's contribution is generally small and consistently shows an allosteric activation effect.
- This effect decays exponentially with the distance between substrate and allosteric ligand.
- Short ligand-protein distances, specific ligand angles, strong protein-ligand, and weak protein internal interactions enhance dynamic allostery.
Conclusions:
- Provides a quantitative measure of pure dynamic allostery.
- Enhances understanding of dynamic allostery in biological regulation.
- Informs the design of allosteric drugs and proteins.
Related Concept Videos
01:58Cooperative Allosteric Transitions
2.4K
2.4K
01:08Allosteric Regulation
59.4K
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...
59.4K
01:19Allosteric Proteins-ATCase
5.9K
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...
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...
5.9K
01:19Protein Dynamics in Living Cells
2.3K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.3K
00:49Ligand Binding and Linkage
5.0K
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...
5.0K