Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Introduction to Mechanisms of Enzyme Catalysis

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...

Allosteric Proteins-ATCase

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...

Ligand Binding and Linkage

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...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Induced-fit Model

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...

Conserved Binding Sites

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...

You might also read

Related Articles

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

Sort by

Same author

Amidine isosteric modification tunes proteolytic stability and activity.

RSC chemical biology·2026

Same author

<sup>1</sup>H, <sup>15</sup>N, <sup>13</sup>C backbone resonance assignment of Escherichia coli AlkB in complex with Zn(II) and α-ketoglutarate.

Biomolecular NMR assignments·2026

Same author

A Molecular Grammar for Programmable Multiphase Protein-RNA Vesicles.

JACS Au·2026

Same author

<math><mrow><mi>β</mi></mrow></math> -motifs and molecular flux promote amyloid nucleation at condensate interfaces.

bioRxiv : the preprint server for biology·2026

Same author

A Versatile Strategy for Head-to-Tail Macrocyclization and Traceless Backbone Editing of Short Peptides.

Journal of the American Chemical Society·2026

Same author

A molecular grammar for programmable multiphase protein-RNA vesicles.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Aug 22, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Temperature-sensitive contacts in disordered loops tune enzyme I activity.

Daniel Burns¹, Aayushi Singh², Vincenzo Venditti^1,2

¹Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011.

Proceedings of the National Academy of Sciences of the United States of America

|November 14, 2022

Summary

Enzyme sequence determines activity at optimal temperatures. Molecular dynamics and mutagenesis reveal temperature-sensitive contacts in enzyme I (EIC) loops control activity, enabling rational enzyme design.

Keywords:

allostery enzyme catalysis molecular dynamics mutagenesis thermal adaptation

More Related Videos

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Related Experiment Videos

Last Updated: Aug 22, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

Area of Science:

Biophysics
Enzymology
Structural Biology

Background:

Homologous enzymes with similar structures can display varied thermal and kinetic properties.
Understanding sequence-based control of enzyme activity across temperatures is crucial.
Disordered loops in bacterial enzyme I C-terminal domain (EIC) variants influence thermophilic/mesophilic catalytic tuning.

Purpose of the Study:

To elucidate the mechanism of sequence-dependent activity tuning in EIC homologs.
To investigate how temperature affects enzyme structure-function relationships.
To develop computational methods for enzyme engineering.

Main Methods:

Utilized molecular dynamics simulations to analyze enzyme dynamics.
Employed mutagenesis experiments to test specific residue effects.
Assayed thermophilic EIC mutants and mesophilic mutations.

Main Results:

Identified a network of contacts in catalytic loops highly sensitive to temperature.
Observed distinct linear and nonlinear temperature-dependent trends in these contacts.
Correlated temperature sensitivity of positions with the impact of mutations on enzyme activity.
Distinguished regions prone to order or disorder at elevated temperatures.

Conclusions:

Provided a mechanistic explanation for sequence-dependent temperature tuning in enzymes.
Demonstrated that mutations at temperature-sensitive sites significantly impact enzyme activity.
Established a computational approach for rational enzyme modification and optimization.