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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.
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
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...
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...

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Related Experiment Video

Updated: Jun 1, 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

De novo enzyme design using Rosetta3.

Florian Richter1, Andrew Leaver-Fay, Sagar D Khare

  • 1Department of Biochemistry, University of Washington, Seattle, Washington, United States of America. floric@u.washington.edu

Plos One
|May 24, 2011
PubMed
Summary
This summary is machine-generated.

The Rosetta de novo enzyme design protocol enables custom enzyme catalyst creation. This study details the complete four-stage process, using the triosephosphate isomerase reaction as an example.

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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
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Last Updated: Jun 1, 2026

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

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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
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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

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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
09:16

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Area of Science:

  • Computational biology
  • Biochemistry
  • Protein engineering

Background:

  • The Rosetta de novo enzyme design protocol is a powerful computational tool.
  • It has been successfully applied to design enzyme catalysts for diverse chemical reactions.
  • The protocol's flexibility allows for application to virtually any reaction of interest.

Purpose of the Study:

  • To provide a comprehensive, start-to-end demonstration of the Rosetta de novo enzyme design protocol.
  • To illustrate the practical application of the protocol using the triosephosphate isomerase reaction as a case study.
  • To guide researchers in implementing the full enzyme design workflow.

Main Methods:

  • The study outlines a four-stage enzyme design process: defining the catalytic mechanism and active site, identifying suitable protein scaffolds, optimizing residue interactions, and evaluating designed sequences.
  • Stages two through four are performed using the Rosetta software package.
  • Stage one, involving the selection of the catalytic mechanism and minimal active site, is conducted externally.

Main Results:

  • The Rosetta protocol was successfully applied to design enzyme catalysts.
  • The detailed illustration using the triosephosphate isomerase reaction demonstrates the protocol's feasibility and utility.
  • The study provides a practical workflow for de novo enzyme design.

Conclusions:

  • The Rosetta de novo enzyme design protocol offers a robust framework for creating novel enzyme catalysts.
  • This detailed guide facilitates the application of the protocol for various chemical transformations.
  • The methodology presented can accelerate the discovery of new biocatalysts.