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

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

15.2K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
15.2K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

10.1K
10.1K
Conserved Binding Sites01:49

Conserved Binding Sites

5.2K
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...
5.2K
Conserved Binding Sites01:49

Conserved Binding Sites

2.0K
2.0K
Ligand Binding Sites02:40

Ligand Binding Sites

15.2K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.2K
Ligand Binding Sites02:40

Ligand Binding Sites

8.9K
8.9K

You might also read

Related Articles

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

Sort by
Same author

State- versus Reaction-Based Information Processing in Biochemical Networks.

Physical review letters·2026
Same author

Exact Computation of Transfer Entropy with Path Weight Sampling.

Physical review letters·2025
Same author

The Escherichia coli replication initiator DnaA is titrated on the chromosome.

Nature communications·2025
Same author

Quantifying the nuclear localization of fluorescently tagged proteins.

Bioinformatics advances·2025
Same author

Information Processing in Biochemical Networks.

Annual review of biophysics·2025
Same author

Quantifying the genetic origins of body plan scaling.

Proceedings of the National Academy of Sciences of the United States of America·2024

Related Experiment Video

Updated: Feb 12, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K

Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux

Adithya Vijaykumar1, Pieter Rein Ten Wolde1, Peter G Bolhuis2

  • 1FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.

The Journal of Chemical Physics
|April 2, 2018
PubMed
Summary

This study presents a generalized rate expression for calculating protein binding and dissociation rate constants in multi-site systems. The findings enhance modeling of enzyme-substrate interactions and patchy particle systems.

More Related Videos

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.2K
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
08:53

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

31.6K

Related Experiment Videos

Last Updated: Feb 12, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

54.2K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.2K
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
08:53

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Published on: October 2, 2017

31.6K

Area of Science:

  • Biochemistry
  • Chemical Kinetics
  • Computational Biology

Background:

  • Predicting biochemical system responses requires understanding protein rate constants.
  • Existing methods for calculating rate constants are limited to single-site substrates.
  • Multi-site substrates introduce complexities like protein hopping between binding sites.

Purpose of the Study:

  • To derive a generalized rate expression for calculating transition rate constants in multi-state systems.
  • To develop explicit expressions for intrinsic and effective rate constants in multi-site binding scenarios.
  • To model association reactions in enzyme-substrate and patchy particle systems.

Main Methods:

  • Developed a generalized rate expression using forward flux sampling.
  • Derived explicit expressions for association, dissociation, and hopping rate constants.
  • Applied the method to a patchy particle enzyme binding to a two-site substrate.

Main Results:

  • Rate constants increase with particle rotational diffusion.
  • Hopping rate constants decrease with increased distance between binding sites.
  • Blocking one binding site enhances both association and dissociation rate constants.

Conclusions:

  • The generalized rate expression accurately models multi-site binding kinetics.
  • The findings improve understanding of enzyme-substrate interactions.
  • The approach facilitates large-scale multiscale simulations of complex binding systems.