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

Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

9.3K
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...
9.3K
Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

4.4K
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...
4.4K
Induced-fit Model01:13

Induced-fit Model

85.6K
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...
85.6K
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

6.1K
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...
6.1K
Enzyme Kinetics01:19

Enzyme Kinetics

100.9K
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...
100.9K
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

25.9K
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
25.9K

You might also read

Related Articles

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

Sort by
Same author

Resolving Local and Global Conformational Heterogeneity of the Human Intrinsically Disordered Proteome.

Journal of chemical theory and computation·2026
Same author

Zwitterionic-to-cationic ruthenium carbazole complexes: structure and selective hydroboration of quinolines and pyridines.

Dalton transactions (Cambridge, England : 2003)·2026
Same author

Computational Investigation of GNMT-Catalyzed Methyl Transfer Reaction: Integrating MD, QM, and ML Approaches.

Journal of computational chemistry·2026
Same author

A readily accessible CH anion transfer reagent for the preparation of a molybdenum methylidyne complex.

Chemical science·2026
Same author

Correction: The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study.

Physical chemistry chemical physics : PCCP·2026
Same author

Augmenting Large Language Models for Automated Discovery of F-Element Extractants.

Journal of the American Chemical Society·2026

Related Experiment Video

Updated: Oct 25, 2025

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

10.5K

Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study.

Thomas J Summers1, Qianyi Cheng1, Manuel A Palma1

  • 1Department of Chemistry, The University of Memphis, Memphis, Tennessee.

Biophysical Journal
|August 6, 2021
PubMed
Summary

Automated enzyme active site simulation is improved with the Residue Interaction Network Residue Selector (RINRUS) toolkit. RINRUS efficiently generates quantum mechanics (QM) cluster models, enabling accurate enzyme mechanism studies with fewer atoms.

More Related Videos

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

9.2K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.4K

Related Experiment Videos

Last Updated: Oct 25, 2025

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

10.5K
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

9.2K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.4K

Area of Science:

  • Computational Chemistry
  • Enzymology
  • Biochemistry

Background:

  • Accurate quantum mechanics (QM) simulations of enzyme active sites require including reactive species and crucial microenvironment components like residues, solvent, and coenzymes.
  • Developing effective QM models for enzyme active sites is computationally demanding and requires precise selection of relevant atoms.

Purpose of the Study:

  • To introduce and validate the Residue Interaction Network Residue Selector (RINRUS) toolkit for automated and rational QM-cluster model generation for enzyme active sites.
  • To assess the convergence and accuracy of RINRUS-generated models for simulating enzymatic reactions.

Main Methods:

  • Development of the Residue Interaction Network Residue Selector (RINRUS) toolkit, utilizing interatomic contact network information for residue selection.
  • Application of RINRUS to an x-ray crystal structure of catechol-O-methyltransferase to generate QM-cluster models.
  • Computation of reactant, product, and transition state energies for the methyl transfer reaction across 550 models to evaluate convergence.

Main Results:

  • RINRUS successfully generated QM-cluster models for enzyme active site simulations.
  • Models designed by RINRUS, comprising only 200-300 atoms, demonstrated convergence for QM calculations.
  • The computed free energies of activation and reaction confirmed the reliability of the generated models.

Conclusions:

  • The RINRUS toolkit provides an automated and efficient method for generating accurate QM-cluster models of enzyme active sites.
  • RINRUS-designed models enable reliable simulation of enzyme mechanisms with reduced computational cost.
  • RINRUS is poised to become a fundamental tool for advancing cheminformatics-based enzyme model design.