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

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...
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...
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...
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.
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...

You might also read

Related Articles

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

Sort by
Same author

Pharmacological profiling of intravenous MP-04: sustained NAD<sup>+</sup> augmentation, immune modulation, and renal protection in preclinical models.

Frontiers in pharmacology·2026
Same author

Comprehensive Metabolomic Analysis of Saliva Using SWATH-DIA Reveals Systemic Metabolic Adaptations to Exercise.

ACS omega·2026
Same author

Dose-Dependent Effects of Dihydronicotinamide Riboside on Human Engineered Skeletal Muscle Development.

ACS biomaterials science & engineering·2026
Same author

Mechanistic insights into the association and activation of the SARS-CoV-2 2'-O-Methyltransferase (NSP16).

bioRxiv : the preprint server for biology·2026
Same author

Computational microbiology: Where is artificial intelligence addressing the barriers to large-scale simulations of bacterial cell envelopes?

Current opinion in structural biology·2026
Same author

Analysis of Intracellular Fatty Acid Metabolism during Doxorubicin-Induced Senescence of MCF7 Cells Using Raman Imaging.

ACS omega·2026
Same journal

The cell cloud: Adopting systems biology concepts in the era of single-cell immunology.

PLoS biology·2026
Same journal

Disinhibitory signaling enables flexible coding of top-down information in cortical networks.

PLoS biology·2026
Same journal

Correction: Cdc42 interacts with chaperone Ydj1 to enhance its stability and partitioning during asymmetric cell division and aging in yeast.

PLoS biology·2026
Same journal

Towards globally equitable bioinformatics adoption.

PLoS biology·2026
Same journal

The human claustrum supports cognitive networks for externally and internally driven task demands.

PLoS biology·2026
Same journal

Unusual decay: Recombination loss leads to splicing errors in green algae.

PLoS biology·2026
See all related articles

Related Experiment Video

Updated: May 27, 2026

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

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.

Arvind Ramanathan1, Pratul K Agarwal

  • 1Joint CMU-Pitt Program in Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

Plos Biology
|November 17, 2011
PubMed
Summary
This summary is machine-generated.

Protein flexibility is crucial for enzyme function, with conserved motions across species and even non-homologous enzymes facilitating catalysis. This reaction-coupled flexibility impacts enzyme-substrate interactions and has implications for drug design.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Related Experiment Videos

Last Updated: May 27, 2026

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Proteins exhibit intrinsic flexibility, but the role of internal motions in protein function, particularly enzyme catalysis, remains debated.
  • While protein structure is vital for enzyme catalysis, recent proposals suggest protein function involves multiple conformations linked to flexibility.
  • Conservation of structural features offers clues to function, and this principle may extend to identifying protein flexibility linked to enzyme function.

Purpose of the Study:

  • To investigate if protein flexibility, specifically reaction-coupled motions, is a conserved feature in enzyme function across different species and enzyme classes.
  • To explore the connection between conserved protein motions, active-site residues, and distant surface loop regions in enzyme catalysis.
  • To determine if non-homologous enzymes catalyzing the same reaction exhibit similar reaction-coupled motions.

Main Methods:

  • Detailed computational modeling was employed to examine three enzyme classes: prolyl-peptidyl isomerase, oxidoreductase, and nuclease.
  • Internal protein motions coupled to the chemical step in enzyme mechanisms were identified and characterized across multiple species.
  • Reaction-coupled motions in homologous and non-homologous enzyme systems were analyzed to assess conservation and impact on enzyme-substrate interactions.

Main Results:

  • Identical enzyme conformational fluctuations and conserved motions in distant surface loop regions (>10 Å) were observed across species for homologous enzymes.
  • Networks of conserved interactions and residues connect flexible surface regions to active-site residues, influencing substrate interaction.
  • Non-homologous enzymes catalyzing the same biochemical reaction exhibited remarkably similar reaction-coupled motions, inducing comparable changes in enzyme-substrate interactions.

Conclusions:

  • Reaction-coupled flexibility is a conserved aspect of enzyme molecular architecture, essential for catalysis.
  • Protein motions in distal areas of enzymes mediate crucial changes in active-site enzyme-substrate interactions, impacting catalyzed chemistry.
  • These findings have significant implications for understanding allostery, protein engineering, and drug design strategies.