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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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: May 31, 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

A matching algorithm for catalytic residue site selection in computational enzyme design.

Yulin Lei1, Wenjia Luo, Yushan Zhu

  • 1Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.

Protein Science : a Publication of the Protein Society
|June 30, 2011
PubMed
Summary

A novel algorithm, PRODA_MATCH, aids in silico enzyme design by matching catalytic residues to scaffolds. It successfully identified native catalytic sites for 70% of tested reactions, showing potential for industrial enzyme development.

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Area of Science:

  • Computational chemistry
  • Enzyme engineering
  • Biotechnology

Background:

  • Enzyme design requires accurate placement of catalytic residues.
  • Existing methods may lack flexibility in residue conformation or binding considerations.

Purpose of the Study:

  • To develop a novel algorithm for matching catalytic residues onto enzyme scaffolds.
  • To evaluate the algorithm's performance in identifying native catalytic sites.

Main Methods:

  • Developed PRODA_MATCH, a loop closure-based sequential matching algorithm.
  • Algorithm is independent of rotamer libraries and optimizes geometric parameters.
  • Incorporated pseudo-spheres to account for surrounding residues and binding interactions.

Main Results:

  • PRODA_MATCH successfully identified native catalytic residue sites in benchmark tests.
  • Native sites were ranked within the top 10 designs for 7 out of 10 chemical reactions.
  • The algorithm demonstrated polynomial computational complexity.

Conclusions:

  • PRODA_MATCH is a promising tool for in silico enzyme design.
  • The algorithm's ability to consider conformation and binding enhances its utility.
  • It holds potential for designing industrial enzymes for specific chemical reactions.