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Related Concept Videos

Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

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Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
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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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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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Enzymes02:34

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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.
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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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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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Updated: Aug 24, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database.

Bailu Yan1,2, Xinchun Ran1, Anvita Gollu1

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.

Journal of Chemical Information and Modeling
|October 26, 2022
PubMed
Summary

A new database, IntEnzyDB, integrates enzyme structure and kinetics data for biocatalyst design. It reveals mutations globally encode enhancements and close mutations are more likely to be deleterious.

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Area of Science:

  • Biocatalysis and enzyme engineering
  • Computational biology and bioinformatics
  • Structural biology and enzymology

Background:

  • Data-driven modeling is revolutionizing biocatalyst design and discovery.
  • Integrated databases linking enzyme structure and function are crucial for advancing this field.
  • Existing resources often lack comprehensive structure-kinetics data necessary for advanced modeling.

Purpose of the Study:

  • To introduce IntEnzyDB, an integrated database for enzyme structure and kinetics data.
  • To facilitate statistical modeling and machine learning applications in biocatalysis.
  • To provide a publicly accessible platform for enzymology data exploration.

Main Methods:

  • Developed IntEnzyDB using a relational database architecture with a flattened data structure for efficient data operations.
  • Integrated enzyme kinetics and structure data from six Enzyme Commission classes.
  • Analyzed 1050 enzyme structure-kinetics pairs to investigate mutation effects on enzyme efficiency.

Main Results:

  • Mutations that enhance enzyme efficiency are globally encoded across the enzyme structure.
  • Deleterious mutations are significantly more probable in residues close to the active site compared to distal residues.
  • The database architecture supports the incorporation of diverse enzyme function data.

Conclusions:

  • IntEnzyDB provides a valuable computational resource for data-driven biocatalyst design and discovery.
  • The findings highlight the distinct roles of proximal and distal mutations in enzyme function modulation.
  • Public access to IntEnzyDB will accelerate research in biocatalysis and molecular evolution.