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Related Concept Videos

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...
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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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,...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jul 15, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Multiple graph alignment for the structural analysis of protein active sites.

Nils Weskamp1, Eyke Hüllermeier, Daniel Kuhn

  • 1Department of Mathematics and Computer Science and The Institute of Phamaceutical Chemistry, University of Marburg, Hans-Meerwein-Strasse, Marburg, Germany. weskamp@mathematik.uni-marburg.de

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|May 3, 2007
PubMed
Summary

This study introduces graph alignment for analyzing protein binding pockets. This method identifies conserved and different structural features, enabling functional protein family characterization and differentiation without sequence or fold homology.

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Area of Science:

  • Structural bioinformatics
  • Computational chemistry
  • Protein structure analysis

Background:

  • Protein active sites are often described using graphs representing geometry and physicochemical properties.
  • Identifying conserved and variable regions in binding pockets is crucial for understanding protein function and evolution.

Purpose of the Study:

  • To present graph alignment as a novel method for structural analysis of protein binding pockets.
  • To enable characterization and differentiation of protein families based on binding pocket structures, independent of sequence or fold homology.

Main Methods:

  • Utilizing inexact graph-matching techniques for structural analysis.
  • Developing optimized algorithms for efficient calculation of multiple graph alignments.
  • Analyzing physicochemical descriptors of protein binding pockets.

Main Results:

  • Graph alignment successfully identifies conserved and differing areas within and among binding pockets.
  • The method effectively characterizes and classifies 10 protein families using a PDB subset.
  • Structural differences between related serine protease families were automatically detected.

Conclusions:

  • Graph alignment provides a powerful tool for characterizing protein families and distinguishing related families based on binding pocket structure.
  • This approach facilitates the identification of characteristic and discriminative structural features.
  • The method offers an efficient and automated way to analyze protein binding pocket structures.