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Related Concept Videos

Enzymes02:34

Enzymes

82.1K
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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Catalytically Perfect Enzymes01:07

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The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
 
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Structural Protein Function01:56

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Enzyme Kinetics01:19

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Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
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Ligand Binding and Linkage00:49

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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...
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Introduction to Mechanisms of Enzyme Catalysis01:13

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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...
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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

Karel J van der Weg1, Holger Gohlke1,2

  • 1John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.

Bioinformatics (Oxford, England)
|March 8, 2023
PubMed
Summary

TopEnzyme offers structural enzyme models, providing access to 60% of known enzyme functions. This database facilitates rapid retrieval of representative structural models, enhancing enzyme research.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Enzyme structure-function relationships are critical for biological understanding.
  • Comprehensive databases of structural enzyme models are essential for research.
  • Bridging the gap between known enzyme functions and available structural data is a key challenge.

Purpose of the Study:

  • To present TopEnzyme, a novel database of structural enzyme models.
  • To provide extensive structural coverage of the functional enzyme space.
  • To facilitate quick access to representative structural models for enzymes.

Main Methods:

  • Generation of structural enzyme models using TopModel.
  • Integration with SWISS-MODEL and AlphaFold Protein Structure Database.
  • Assessment of model quality using TopScore.

Main Results:

  • TopEnzyme contains over 200,000 enzyme models, covering 60% of known enzyme functions.
  • 9039 good-quality and 1297 high-quality structures were contributed.
  • TopModel and AlphaFold2 produced qualitatively similar structures for unseen targets.

Conclusions:

  • TopEnzyme significantly enhances structural coverage of the functional enzyme space.
  • The database provides a valuable resource for researchers lacking experimental structures.
  • TopEnzyme facilitates rapid access to reliable structural models for a vast number of enzymes.