Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

4.0K
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...
4.0K
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

8.1K
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...
8.1K
Enzymes02:34

Enzymes

81.5K
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...
81.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis.

Protein engineering, design & selection : PEDS·2026
Same author

Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.

Nature chemical biology·2026
Same author

Conformational flexibility of soybean lipoxygenase is coupled to crystal solvent content in serial crystallography.

bioRxiv : the preprint server for biology·2026
Same author

Introducing Mikhail Kudryashev, Clorice R. Reinhardt, Alec H. Follmer, and Michael C. Thompson.

Structure (London, England : 1993)·2026
Same author

Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release.

Nature communications·2025
Same author

Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step.

Journal of the American Chemical Society·2025

Related Experiment Video

Updated: Jun 29, 2025

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

8.3K

Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling.

Rojo V Rakotoharisoa1,2, Behnoush Seifinoferest3, Niayesh Zarifi1,2

  • 1Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.

Journal of the American Chemical Society
|March 27, 2024
PubMed
Summary

Computational design significantly enhances artificial enzyme efficiency. This method uses structural ensembles to create highly active enzymes, outperforming traditional directed evolution without extensive screening.

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K

Related Experiment Videos

Last Updated: Jun 29, 2025

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

8.3K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.8K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Enzyme Engineering

Background:

  • Developing artificial enzymes with high catalytic efficiency is crucial for various chemical applications.
  • Traditional methods like directed evolution are time-consuming and require extensive screening.
  • De novo enzyme design aims to create novel catalysts from scratch.

Purpose of the Study:

  • To present a computational design method for significantly improving the catalytic efficiency of de novo enzymes.
  • To demonstrate this method's effectiveness without relying on directed evolution or high-throughput screening.
  • To validate the designed enzymes through structural and activity analysis.

Main Methods:

  • Utilized structural ensembles from dynamics-based refinement against X-ray diffraction data of Kemp eliminases HG3 and KE70.
  • Designed a small number of sequences (≤10 per enzyme) predicted to have enhanced catalytic activity.
  • Employed ensemble-based computational design to optimize active sites for improved catalysis.

Main Results:

  • Achieved 100-250-fold increases in catalytic efficiency (kcat/KM) for the designed enzymes.
  • The performance of the designed enzymes is comparable to those obtained through multiple rounds of directed evolution.
  • Crystal structures confirmed excellent agreement with computational models, showing designed catalytic contacts and low transition-state deviations (≤0.65 Å).

Conclusions:

  • Ensemble-based computational design is a powerful strategy for generating highly efficient artificial enzymes.
  • This approach effectively exploits the conformational flexibility of enzymes for active site optimization.
  • The method offers a rapid and efficient alternative to directed evolution for enzyme engineering.