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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.
 
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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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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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Related Experiment Video

Updated: Aug 6, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design.

Sergi Roda1, Henrik Terholsen2, Jule Ruth Heike Meyer2

  • 1Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain.

The Journal of Physical Chemistry. B
|March 21, 2023
PubMed
Summary
This summary is machine-generated.

AsiteDesign, a new computational method, engineers enzyme active sites for industrial biocatalysis. This structure-based approach successfully created novel catalytic functions and improved substrate hydrolysis and enantioselectivity in an esterase enzyme.

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Area of Science:

  • Computational biology
  • Enzyme engineering
  • Biocatalysis

Background:

  • Advances in protein structure prediction increase the availability of high-quality structural data.
  • Structure-based enzyme engineering is crucial for optimizing biocatalysts in industrial applications.

Purpose of the Study:

  • To present AsiteDesign, a Monte Carlo-based protocol for structure-based engineering of enzyme active sites.
  • To introduce new catalytic residues into binding pockets to create or alter enzymatic activity.
  • To enhance enzyme performance for industrial processes.

Main Methods:

  • AsiteDesign protocol utilizes Monte Carlo simulations and pyRosetta implementation.
  • Incorporates enhanced sampling techniques for efficient exploration of the protein design space.
  • Tested on *Pseudomonas fluorescens* esterase (PFE) for active site redesign.

Main Results:

  • Successfully designed an alternative catalytic triad in PFE, experimentally verified for activity.
  • Mutations F158L/F198A and F125A/F158L significantly enhanced hydrolysis of a bulky chiral substrate (1-phenyl-2-pentyl acetate) by PFE.
  • Achieved a reversal of enantioselectivity from (R) to (S)-enantiopreference with 32% and 55% enantiomeric excess (ee), respectively.

Conclusions:

  • AsiteDesign is effective in designing alternative catalytic triads and modifying enzyme activity.
  • The protocol demonstrates potential for optimizing biocatalysts for specific industrial applications.
  • Successful experimental validation confirms the utility of AsiteDesign in protein engineering.