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

8.4K
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...
8.4K
Enzyme Kinetics01:19

Enzyme Kinetics

97.8K
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...
97.8K
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

20.4K
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...
20.4K
Catalytically Perfect Enzymes01:07

Catalytically Perfect Enzymes

4.1K
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...
4.1K
Enzymes02:34

Enzymes

82.2K
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...
82.2K
Measuring Reaction Rates03:09

Measuring Reaction Rates

25.6K
Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical...
25.6K

You might also read

Related Articles

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

Sort by
Same author

Fast Motions in 5 Alpha Reductase and Its Impact on Enzyme Kinetics.

ACS catalysis·2026
Same author

The Shaping of Enzymatic Free Energy Barriers through the Creation of Rate-Promoting Vibrations via Inter-Residue Cross-Talk on Multiple Time Scales.

The journal of physical chemistry. B·2025
Same author

Unraveling Mutation-Induced Protein Communication Pathways in the Actomyosin Complex: Insights from Comprehensive Metadynamics Simulations.

The journal of physical chemistry. B·2025
Same author

Targeted TPS Shooting Using Computer Vision to Generate Ensemble of Trajectories.

Journal of chemical theory and computation·2025
Same author

Directed Evolution's Selective Use of Quantum Tunneling in Designed Enzymes─A Combined Theoretical and Experimental Study.

The journal of physical chemistry. B·2025
Same author

The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament.

Protein science : a publication of the Protein Society·2024
Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026
Same journal

Efficient Coupled-Cluster Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture.

Journal of chemical theory and computation·2026
Same journal

Extending the MARTINI 3 Coarse-Grained Force Field to Polypeptoids.

Journal of chemical theory and computation·2026
Same journal

Statistical Mechanics of Density- and Temperature-Dependent Potentials: Application to Condensed Phases within GenDPDE.

Journal of chemical theory and computation·2026
Same journal

BFEE-Docking: A User-Friendly and Customizable End-to-End Tool from High-Throughput Virtual Screening to Binding Free-Energy Calculations.

Journal of chemical theory and computation·2026
Same journal

On-the-Fly Trajectory Simulation of Two-Pulse, Three-Pulse, and Higher-Order Pump-Probe Signals.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Aug 23, 2025

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues
08:36

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues

Published on: May 26, 2018

11.9K

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.

Steven D Schwartz1

  • 1Department of Chemistry and Biochemistry University of Arizona Tucson, Arizona 85721, United States.

Journal of Chemical Theory and Computation
|October 28, 2022
PubMed
Summary
This summary is machine-generated.

Transition Path Sampling (TPS) reveals enzyme mechanisms by analyzing protein vibrations and electrostatic effects. This computational method is crucial for understanding enzyme function and designing novel artificial enzymes.

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

9.1K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.9K

Related Experiment Videos

Last Updated: Aug 23, 2025

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues
08:36

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues

Published on: May 26, 2018

11.9K
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

9.1K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.9K

Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Enzymatically catalyzed reactions are fundamental to biological processes.
  • Understanding enzyme mechanisms is key to biochemistry and drug development.
  • Traditional methods often struggle to capture the dynamic nature of enzyme catalysis.

Purpose of the Study:

  • To review the application of Transition Path Sampling (TPS) for studying enzyme mechanisms.
  • To highlight how TPS has advanced our understanding of enzymatic catalysis.
  • To discuss the role of TPS in the design of artificial enzymes.

Main Methods:

  • Transition Path Sampling (TPS) simulations.
  • Analysis of molecular dynamics and reaction pathways.
  • Integration of computational findings with experimental observations.

Main Results:

  • TPS has elucidated key principles of enzymatic catalysis, such as protein-promoted vibrations.
  • The method has reconciled concepts like electrostatic preorganization with dynamic enzyme function.
  • TPS is instrumental in identifying design principles for artificial enzymes.

Conclusions:

  • Transition Path Sampling is a powerful computational tool for dissecting enzyme mechanisms.
  • This method provides insights into both natural and artificial enzyme functions.
  • Continued application of TPS will drive innovation in enzyme engineering and design.