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Related Concept Videos

Enzymes02:34

Enzymes

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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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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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Induced-fit Model01:13

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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...
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Introduction to Enzymes01:22

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The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an enzyme-catalyzed reaction. Wilhelm Kuhne coined the term 'enzyme' in 1877 from the Greek words ‘en’ meaning ‘in’ or ‘within’ and ‘zyme’ meaning ‘yeast.’
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Allosteric Proteins-ATCase01:19

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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...
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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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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Normal Modes Expose Active Sites in Enzymes.

Yitav Glantz-Gashai1, Tomer Meirson1, Abraham O Samson1

  • 1Faculty of Medicine in the Galilee, Bar Ilan University, Safed, Israel.

Plos Computational Biology
|December 22, 2016
PubMed
Summary

This study introduces EXPOSITE, a novel structure-based method for predicting enzyme active sites. EXPOSITE accurately identifies active sites by analyzing changes in solvent accessibility during normal mode dynamics, outperforming existing techniques.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Accurate prediction of enzyme active sites is crucial for understanding protein function and drug discovery.
  • Existing structure-based methods for active site prediction have limitations in accuracy and scope.

Purpose of the Study:

  • To develop and validate an improved structure-based technique for predicting active sites in enzymes.
  • To assess the performance of the new method against existing techniques and in a protein-ligand binding context.

Main Methods:

  • The study presents EXPOSITE (EXPOsure of active SITes through normal modEs), a novel method leveraging normal mode dynamics to detect large changes in solvent accessibility.
  • EXPOSITE was trained on a dataset of 133 enzymes and validated on a larger dataset of 845 enzymes with known active sites.
  • The method was further tested on the protein-ligand dataset (PLD) comprising 48 proteins.

Main Results:

  • EXPOSITE successfully located active sites in most tested enzymes, demonstrating high precision.
  • The method proved more accurate than other existing structure-based prediction techniques.
  • In several cases, EXPOSITE identified active sites that did not correspond to the largest pockets within the protein structure.

Conclusions:

  • EXPOSITE offers a significant advancement in structure-based active site prediction for enzymes.
  • The method's high precision and ability to identify non-obvious active sites pave the way for improved enzyme function analysis and drug design.