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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...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
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...
Enzymes02:34

Enzymes

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...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Rapid catalytic template searching as an enzyme function prediction procedure.

Jerome P Nilmeier1, Daniel A Kirshner, Sergio E Wong

  • 1Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America.

Plos One
|May 16, 2013
PubMed
Summary

We developed Catalytic Site Identification (CatSId), an efficient algorithm for identifying enzyme protein function by matching catalytic residues. It accurately predicts enzyme function across diverse protein libraries, showing high performance.

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Last Updated: May 11, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Rapid, Enzymatic Methods for Amplification of Minimal, Linear Templates for Protein Prototyping using Cell-Free Systems
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Published on: June 14, 2021

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Enzyme function prediction is crucial for understanding biological processes.
  • Identifying catalytic residues is key to determining enzyme function.
  • Existing methods may lack efficiency or accuracy across diverse protein families.

Purpose of the Study:

  • To present a novel algorithm, Catalytic Site Identification (CatSId), for accurate enzyme protein function identification.
  • To develop an efficient and scalable method for matching catalytic residues.
  • To validate the algorithm's performance against a manually annotated library.

Main Methods:

  • Developed CatSId algorithm based on matching 3D residue arrangements.
  • Utilized the Catalytic Site Atlas (CSA) library of annotated catalytic residues.
  • Employed a two-process approach: rapid protein-to-template matching followed by physical descriptor-based re-scoring.

Main Results:

  • Achieved a high Receiver-Operator Characteristic Area Under Curve (AUC) of 0.971 on the training set.
  • Demonstrated robust handling of cofactors, ions, nonstandard residues, and substitutions.
  • Showed excellent performance (AUC > 0.90) for sites with >2 catalytic residues on both training and test sets.

Conclusions:

  • CatSId is a highly accurate and efficient algorithm for enzyme function identification.
  • The method shows promise for large-scale proteomic searches.
  • Further refinement may improve performance on challenging cases with fewer catalytic residues.