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Related Concept Videos

Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

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.
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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 a mild...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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 a mild...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Turnover Number and Catalytic Efficiency01:19

Turnover Number and Catalytic Efficiency

The turnover number of an enzyme is the maximum number of substrate molecules it can transform per unit time. Turnover numbers for most enzymes range from 1 to 1000 molecules per second. Catalase has the known highest turnover number, capable of converting up to 2.8×106 molecules of hydrogen peroxide into water and oxygen per second. Lysozyme has the lowest known turnover number of half a molecule per second.
Chymotrypsin is a pancreatic enzyme that breaks down proteins during digestion. The...
Enzyme Kinetics01:19

Enzyme Kinetics

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.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...

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Related Experiment Video

Updated: May 13, 2026

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

Computational enzyme design.

Gert Kiss1, Nihan Çelebi-Ölçüm, Rocco Moretti

  • 1Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA.

Angewandte Chemie (International Ed. in English)
|March 26, 2013
PubMed
Summary
This summary is machine-generated.

Computational enzyme engineering, using an "inside-out" approach, designs novel proteins for new reactions. Combining computational design with directed evolution and simulations enhances protein performance beyond initial limitations.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • The
  • inside-out
  • approach integrates computational chemistry and biology for enzyme engineering.
  • Novel proteins are designed to catalyze reactions previously unobserved in nature.
  • Current success rates for engineered enzymes remain low.

Purpose of the Study:

  • To highlight the achievements and limitations of computational
  • inside-out
  • enzyme design.
  • To contrast this approach with other protein engineering techniques.
  • To explore methods for improving the performance of computationally designed enzymes.

Main Methods:

  • Computational
  • inside-out
  • protein design.
  • Directed evolution.
  • Molecular dynamics simulations.
  • Crowd-sourced structure prediction.

Main Results:

  • Computational design alone yields catalytically active and selective proteins.
  • However, kinetic performance is inferior to natural enzymes.
  • Integration with directed evolution and simulations improves binding, turnover, and thermal stability.

Conclusions:

  • The
  • inside-out
  • approach shows promise for novel enzyme catalysis.
  • Synergistic combination with experimental techniques is crucial for optimizing enzyme function.
  • Further research can enhance the kinetic and stability profiles of engineered enzymes.