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Related Concept Videos

Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

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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.
 
Most enzymes...
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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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Introduction to Enzymes01:22

Introduction to Enzymes

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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.’
Most enzymes are proteins that speed up biochemical reactions without being consumed. Enzymes contain one or more active sites that...
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Updated: May 28, 2025

Multi-enzyme Screening Using a High-throughput Genetic Enzyme Screening System
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A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.

Aitor Vega1, Antoni Planas1,2, Xevi Biarnés1

  • 1Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain.

International Journal of Molecular Sciences
|February 13, 2025
PubMed
Summary
This summary is machine-generated.

Computational enzyme engineering accelerates discovery by guiding tool selection for improving enzyme properties like affinity, efficiency, and stability. This review categorizes available software to aid researchers in optimizing biocatalysts.

Keywords:
binding affinitycatalytic efficiencycomputational predictioncomputational protein engineeringenzyme designmolecular modelingmolecular recognitionprotein solubilityprotein stability

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Area of Science:

  • Biotechnology
  • Computational Biology
  • Enzyme Engineering

Background:

  • Growing demand for efficient, selective, and stable enzymes drives innovation in computational enzyme engineering.
  • Researchers face challenges selecting appropriate computational tools due to the plethora of available software.
  • This review focuses on enhancing existing enzymes, not de novo design.

Purpose of the Study:

  • To categorize computational tools for enzyme engineering.
  • To guide researchers in selecting software based on desired biocatalytic property enhancement.
  • To align computational tools with specific enzyme engineering goals.

Main Methods:

  • Categorization of computational tools based on their application.
  • Focus on tools enhancing protein-ligand affinity/selectivity, catalytic efficiency, thermostability, and solubility.
  • Alignment of tools with their respective scoring functions.

Main Results:

  • A structured overview of computational tools for enzyme engineering is provided.
  • Guidance is offered for selecting software to fine-tune specific enzymatic properties.
  • The review facilitates practical protein engineering campaigns.

Conclusions:

  • Computational enzyme engineering is a key complement to experimental methods.
  • Proper tool selection is crucial for successful enzyme optimization.
  • This review serves as a practical guide for researchers in enzyme engineering.