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-protein Interfaces02:04

Protein-protein Interfaces

15.0K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
15.0K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.6K
4.6K
Protein Networks02:26

Protein Networks

4.7K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.7K
Protein Networks02:26

Protein Networks

2.9K
2.9K
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

6.2K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
6.2K
Protein Organization01:24

Protein Organization

10.0K
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....
10.0K

You might also read

Related Articles

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

Sort by
Same author

Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.

The FEBS journal·2025
Same author

A structural perspective on enzymes and their catalytic mechanisms.

Current opinion in structural biology·2025
Same author

Paradigms of convergent evolution in enzymes.

The FEBS journal·2024
Same author

In silico prediction of heme binding in proteins.

The Journal of biological chemistry·2024
Same author

Enzyme function and evolution through the lens of bioinformatics.

The Biochemical journal·2023
Same author

EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.

Nature methods·2023
Same journal

Towards light-coupled sample preparation for time-resolved cryoEM studies.

IUCrJ·2026
Same journal

Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer.

IUCrJ·2026
Same journal

Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles.

IUCrJ·2026
Same journal

How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.

IUCrJ·2026
Same journal

CryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes.

IUCrJ·2026
Same journal

Cryo-EM-guided subtractive optimization of a novel VCP/p97 inhibitor.

IUCrJ·2026
See all related articles

Related Experiment Video

Updated: Mar 29, 2026

Measuring Transcellular Interactions through Protein Aggregation in a Heterologous Cell System
04:47

Measuring Transcellular Interactions through Protein Aggregation in a Heterologous Cell System

Published on: May 22, 2020

4.1K

Proteins: interaction at a distance.

Roman A Laskowski1, Janet M Thornton1

  • 1European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Iucrj
|November 24, 2015
PubMed
Summary
This summary is machine-generated.

Protein surface side chains either crumple inwards or extend outwards to optimize interactions during protein-protein binding. This study investigates these conformational changes to understand binding mechanisms.

Keywords:
bound and unbound protein formsprotein flexibilityprotein–protein interactions

More Related Videos

In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells
08:58

In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells

Published on: September 2, 2019

7.6K
Designing Silk-silk Protein Alloy Materials for Biomedical Applications
11:14

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

19.0K

Related Experiment Videos

Last Updated: Mar 29, 2026

Measuring Transcellular Interactions through Protein Aggregation in a Heterologous Cell System
04:47

Measuring Transcellular Interactions through Protein Aggregation in a Heterologous Cell System

Published on: May 22, 2020

4.1K
In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells
08:58

In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells

Published on: September 2, 2019

7.6K
Designing Silk-silk Protein Alloy Materials for Biomedical Applications
11:14

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

19.0K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biophysics

Background:

  • Protein-protein interactions are fundamental to virtually all biological processes.
  • Understanding how proteins achieve specific and stable binding is a key challenge in molecular biology.
  • The conformational dynamics of surface residues during binding remain incompletely understood.

Purpose of the Study:

  • To investigate the conformational behavior of protein surface side chains upon complex formation.
  • To determine whether side chains primarily crumple inwards or extend outwards to mediate protein-protein interactions.
  • To elucidate the role of side chain dynamics in optimizing binding affinity and specificity.

Main Methods:

  • Utilized molecular dynamics simulations to model protein-protein binding events.
  • Employed advanced structural analysis techniques to track side chain movements.
  • Compared conformational changes in various protein complexes.

Main Results:

  • Observed that surface side chains exhibit distinct behaviors, with some crumpling inwards and others extending outwards.
  • Found that the specific mode of interaction is dependent on the protein pair and the nature of the binding interface.
  • Demonstrated that these movements are crucial for maximizing favorable contacts and minimizing unfavorable ones.

Conclusions:

  • Protein surface side chains dynamically adapt their conformations to optimize interactions during binding.
  • Both inward crumpling and outward extension are utilized strategies, selected based on the specific binding context.
  • These findings provide new insights into the principles governing protein complex formation and stability.