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

Ligand Binding Sites02:40

Ligand Binding Sites

12.9K
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...
12.9K
Protein Folding01:22

Protein Folding

118.5K
Overview
118.5K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

52.0K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
52.0K
Protein Organization01:24

Protein Organization

6.6K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.6K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

17.9K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.9K

You might also read

Related Articles

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

Sort by
Same author

Phase Engineering of Iridium Oxides Enables Direct Coupling of Proton Exchange Membrane Water Electrolysis With Intermittent Electrical Energy.

Advanced materials (Deerfield Beach, Fla.)·2026
Same author

Corrigendum to "Xanthoxylin alleviates dextran sulfate sodium (DSS)-induced colitis by targeting macrophage infiltration via the tumor necrosis factor (TNF)/nuclear factor-kappa B (NF-κB) signaling pathway" [Phytomedicine 153:157971 (2026) PMID: 41720014].

Phytomedicine : international journal of phytotherapy and phytopharmacology·2026
Same author

AdaptCMVC++: Robust and Flexible Adaptation to Incremental Views in Continual Multi-view Clustering.

IEEE transactions on pattern analysis and machine intelligence·2026
Same author

Rapid and real-time detection of trace BPA based on solution-gated graphene field-effect transistor by cerium-doped ZIF-8 carbon material.

Talanta·2026
Same author

A Multi-Regional Single-nucleus Atlas of the Huntington's Disease Brain.

Scientific data·2026
Same author

Machine learning-aided 3D-AFM for identification of spatial heterogeneity in interfacial solvation structures.

Nanoscale·2026

Related Experiment Video

Updated: Jul 22, 2025

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

10.7K

Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding.

Lin Yang1,2, Shuai Guo1, Chenchen Liao3

  • 1National Key Laboratory of Science and Technology on Advanced Composites in Special Environments Center for Composite Materials and Structures Harbin Institute of Technology Harbin 150080 P. R. China.

Global Challenges (Hoboken, NJ)
|July 24, 2023
PubMed
Summary

Protein-protein binding is driven by low-entropy hydration shells. Shape matching between these shells at binding sites guides hydrophobic collapse, enabling accurate prediction of protein binding sites.

Keywords:
Gibbs free energybinding sitehydration shelllow entropyprotein–protein interactions

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.5K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.4K

Related Experiment Videos

Last Updated: Jul 22, 2025

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

10.7K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.5K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.4K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Protein-protein binding is crucial for biological self-organization.
  • It is driven by physical forces, including hydrophobic interactions.
  • Hydrophobic interactions are long-range attractions mediated by low-entropy hydration shells.

Purpose of the Study:

  • To develop a method for identifying low-entropy hydration shell regions.
  • To investigate the role of these regions in protein-protein binding.
  • To establish a universal law governing protein complex formation.

Main Methods:

  • Developed a novel method to identify low-entropy hydration shell regions by masking pseudohydrophilic groups.
  • Analyzed determined protein complex structures to identify shape matching between hydration shells.
  • Performed bioinformatics analyses on hundreds of protein complex structures.

Main Results:

  • Identified that low-entropy hydration shell regions typically cover protein binding sites.
  • Discovered shape matching between low-entropy hydration shells of binding partners as a universal law.
  • Verified that protein-protein binding is primarily driven by hydrophobic collapse between matched hydration shells.
  • Proposed a simple algorithm for accurate prediction of protein binding sites.

Conclusions:

  • Protein-protein binding is predominantly governed by hydrophobic collapse between shape-matched, low-entropy hydration shells.
  • This finding provides a new perspective on the fundamental mechanisms of protein complex formation.
  • The developed method and algorithm offer a powerful tool for predicting protein binding sites.