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Related Concept Videos

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...
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,...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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Related Experiment Video

Updated: Jun 6, 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 geometry-based generic predictor for catalytic and allosteric sites.

Simon Mitternacht1, Igor N Berezovsky

  • 1Computational Biology Unit, Bergen Center for Computational Science, Bergen, Norway.

Protein Engineering, Design & Selection : PEDS
|December 17, 2010
PubMed
Summary
This summary is machine-generated.

We developed a new structure-based method to precisely identify binding sites in allosteric enzymes. This approach aids in understanding protein allostery and designing novel drugs targeting these crucial sites.

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

Related Experiment Videos

Last Updated: Jun 6, 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

Area of Science:

  • Biochemistry and structural biology
  • Computational biology and bioinformatics
  • Drug discovery and medicinal chemistry

Background:

  • Understanding protein allostery is key for designing artificial effectors.
  • Allosteric enzymes, often oligomeric, possess allosteric sites at domain interfaces.
  • Identifying substrate- and effector-binding sites is crucial for this understanding.

Purpose of the Study:

  • To devise a novel, structure-based method for predicting binding sites in allosteric enzymes.
  • To develop a computational approach applicable to both monomeric and multimeric proteins.
  • To identify non-catalytic effector sites as potential drug targets.

Main Methods:

  • Development of a local centrality measure for residue interaction graphs.
  • Application of the measure to protein structure analysis.
  • Validation of the method's performance on various protein types.

Main Results:

  • The local centrality measure accurately identifies binding sites in both small and large proteins.
  • The method is purely structure-based with clear geometrical interpretation and no free parameters.
  • The measure is unbiased towards catalytic residues, effectively finding non-catalytic effector sites.

Conclusions:

  • The developed local centrality measure is a robust tool for characterizing and predicting binding sites in allosteric enzymes.
  • This method facilitates the understanding of protein allostery and the design of artificial effectors.
  • The approach holds significant potential for drug discovery by identifying novel allosteric drug targets.