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Related Concept Videos

Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
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,...
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...
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...

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Related Experiment Video

Updated: Jun 8, 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

Metric learning for enzyme active-site search.

Tsuyoshi Kato1, Nozomi Nagano

  • 1GSFS, University of Tokyo, 5-1-5 Kashiwahoha, Kashiwa, Chiba, Japan. kato-tsuyoshi@k.u-tokyo.ac.jp

Bioinformatics (Oxford, England)
|September 28, 2010
PubMed
Summary

This study introduces an algorithm for automatically selecting atoms to identify functionally analogous enzymes. This method improves template accuracy over manual selection, aiding in enzyme discovery.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying enzymes with similar functions based on active site structure is crucial.
  • Current methods rely on manual template creation, which is limited by atom selection.
  • This limitation hinders the accurate search for analogous enzyme active sites.

Purpose of the Study:

  • To develop an automated method for selecting atoms to define enzyme active site templates.
  • To improve the accuracy of identifying functionally analogous enzymes.
  • To gain insights into the importance of specific atoms in enzyme active site recognition.

Main Methods:

  • Developed a novel algorithm for automatic atom selection in active site template generation.
  • Employed metric learning techniques to optimize template effectiveness.

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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Last Updated: Jun 8, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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  • Validated the algorithm through experimental results and comparisons with manual methods.

    • Main Results:

    • The algorithm successfully automates atom selection for discriminating between matching and non-matching enzyme active sites.
    • It provides insights into the critical atoms influencing functional analogy predictions.
    • Experimental results demonstrate that automatically generated templates are more effective than manually curated ones.

    Conclusions:

    • Automated atom selection using metric learning enhances the identification of functionally analogous enzymes.
    • This approach offers a more robust and efficient alternative to traditional template-based methods.
    • The developed software is publicly available for broader research application.