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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,...
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...
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 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...
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...
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...

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Related Experiment Video

Updated: May 27, 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

Predicting binding sites by analyzing allosteric effects.

Dengming Ming1, Michael E Wall

  • 1Department of Physiology and Biophysics, School of Life Science, Fudan University, Shanghai, China.

Methods in Molecular Biology (Clifton, N.J.)
|November 5, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces Dynamics Perturbation Analysis (DPA), a method to analyze how molecular interactions affect protein shapes. DPA is valuable for understanding allosteric effects and predicting where molecules bind to proteins.

Related Experiment Videos

Last Updated: May 27, 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

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Allosteric regulation is crucial for protein function.
  • Understanding how molecular interactions alter protein conformations is key.
  • Existing methods may not fully capture dynamic allosteric effects.

Purpose of the Study:

  • To present Dynamics Perturbation Analysis (DPA), a novel method for analyzing allosteric effects.
  • To demonstrate DPA's utility in predicting ligand-binding sites on proteins.
  • To elucidate the hypothesis linking native binding site interactions to conformational changes.

Main Methods:

  • Dynamics Perturbation Analysis (DPA) is detailed, focusing on its mathematical underpinnings.
  • The method analyzes changes in protein conformational distributions.
  • A practical guide for applying DPA to predict binding sites is provided.

Main Results:

  • DPA provides insights into allosteric mechanisms.
  • The method effectively predicts ligand-binding sites based on conformational changes.
  • The study validates the hypothesis that native binding sites induce significant conformational shifts.

Conclusions:

  • Dynamics Perturbation Analysis (DPA) is a powerful tool for studying protein allostery.
  • DPA offers a computational approach to identify functional binding sites.
  • This method advances the understanding of protein dynamics and molecular recognition.