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

Protein Folding01:22

Protein Folding

130.5K
Overview
130.5K
Protein Folding01:25

Protein Folding

12.5K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
12.5K
Protein Folding01:22

Protein Folding

36.5K
36.5K
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

20.8K
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
20.8K
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

15.5K
15.5K
Protein Organization01:13

Protein Organization

161.6K
Overview
161.6K

You might also read

Related Articles

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

Sort by
Same author

Thermodynamic Activation Parameters for Chemical Reactions in Enzymes and Solution from Computer Simulations at a Single Temperature.

Journal of chemical theory and computation·2026
Same author

Discovery of a cryptic aminoacidic triad involved in the temperature adaptation of GH1 enzymes.

The FEBS journal·2026
Same author

Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site.

Journal of chemical information and modeling·2026
Same author

Gaps in tropical science from unrepresentative distribution of sampling and citation across natural terrestrial environments.

Nature communications·2025
Same author

l-DOPA-Containing Protein Autoxidation: An Empirical Valence Bond Simulation of the Rate-Limiting Step.

The journal of physical chemistry. B·2025
Same author

Accurate predictions of protein mutational effects accelerated with a hybrid-topology free energy protocol.

Communications chemistry·2025

Related Experiment Video

Updated: Mar 29, 2026

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

15.7K

Folding-Reaction Coupling in a Self-Cleaving Protein.

Göran Wallin1, Torleif Härd2, Johan Åqvist1

  • 1Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.

Journal of Chemical Theory and Computation
|November 24, 2015
PubMed
Summary

Protein strain energy aids autoprocessing proteins like SEA in catalysis. Simulations reveal ~8 kcal/mol strain energy, crucial for cleavage reactions and coupled folding-reaction mechanisms.

More Related Videos

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
08:34

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Published on: February 5, 2020

7.2K
Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
09:34

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

Published on: February 6, 2020

8.1K

Related Experiment Videos

Last Updated: Mar 29, 2026

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

15.7K
OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
08:34

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Published on: February 5, 2020

7.2K
Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
09:34

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

Published on: February 6, 2020

8.1K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Autoprocessing proteins utilize backbone torsional strain for rate enhancement.
  • The SEA (Splicing-Esterase-Activity) protein domain exhibits coupled folding and proteolytic activity.
  • Experimental data suggests ~7 kcal/mol of folding free energy is available for catalysis in SEA.

Purpose of the Study:

  • To investigate the catalytic strategy of the SEA protein domain.
  • To quantitatively estimate the free energy stored as protein strain available for catalysis.
  • To elucidate the coupling between protein folding and the reaction coordinate.

Main Methods:

  • Molecular dynamics (MD) simulations.
  • Potential of Mean Force (PMF) free energy profiles.
  • B3LYP/6-311G(d,p) density functional calculations.

Main Results:

  • A quantitative estimate of ~8 kcal/mol of free energy stored as protein strain was obtained.
  • This strain energy is available for catalyzing the cleavage reaction, agreeing with experimental data.
  • Strong coupling between folding and reaction coordinates was observed, destabilizing the reactant state and stabilizing the transition state.

Conclusions:

  • The SEA domain employs protein strain energy as a significant catalytic strategy.
  • Coupling of folding and reaction coordinates actively contributes to catalysis by destabilizing reactants and stabilizing transition states.
  • The catalytic mechanism differs from preorganized active site models, with the stabilizing structure forming post-barrier.