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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

14.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.7K
Self-Evaluation: Self-Enhancement and Self-Verification03:00

Self-Evaluation: Self-Enhancement and Self-Verification

5.8K
Social psychologists have documented that feeling good about ourselves and maintaining positive self-esteem is a powerful motivator of human behavior (Tavris & Aronson, 2008). In the United States, members of the predominant culture typically think very highly of themselves and view themselves as good people who are above average on many desirable traits (Ehrlinger, Gilovich, & Ross, 2005). Often, our behavior, attitudes, and beliefs are affected when we experience a threat to our...
5.8K
Peptide Bonds02:43

Peptide Bonds

83.5K
A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
83.5K
Three Developmental Domains01:29

Three Developmental Domains

1.2K
Human development is typically examined across three main domains: physical, cognitive, and socio-emotional. These domains represent the significant areas of change and continuity throughout the lifespan, from infancy to late adulthood.
Physical Development
Physical processes, also known as maturation, encompass the biological changes that occur across an individual's life. These changes begin with genetic inheritance and continue through various stages, including growth in height and weight,...
1.2K
Membrane Domains01:18

Membrane Domains

7.2K
The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the...
7.2K
Three-Domain System of Life01:21

Three-Domain System of Life

1.4K
Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
1.4K

You might also read

Related Articles

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

Sort by
Same author

pH Sensitivity of the SERF1a Conformational Ensemble.

ACS omega·2026
Same author

Protein-membrane interactions with a twist.

Soft matter·2025
Same author

Influence of Stereochemistry in a Local Approach for Calculating Protein Conformations.

Journal of chemical information and modeling·2024
Same author

Conformational Space of the Translocation Domain of Botulinum Toxin: Atomistic Modeling and Mesoscopic Description of the Coiled-Coil Helix Bundle.

International journal of molecular sciences·2024
Same author

New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand.

Molecules (Basel, Switzerland)·2023
Same author

Secondary structure assignment of proteins in the absence of sequence information.

Bioinformatics advances·2023

Related Experiment Video

Updated: Feb 12, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.6K

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling.

Gilles Lamothe1,2, Thérèse E Malliavin3

  • 1Unité de Bioinformatique Structurale, UMR CNRS 3528 and Institut Pasteur, Paris, France.

BMC Structural Biology
|April 5, 2018
PubMed
Summary

Researchers adapted the TAMD method to create re-TAMD, allowing ligands to explore protein surfaces. This technique revealed how histone H3 peptide regions influence binding to the YEATS domain, aiding in understanding protein-ligand interactions.

Keywords:
Enhanced samplingProtein/peptide interactionTAMD

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K
Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry
08:37

Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry

Published on: August 7, 2012

11.9K

Related Experiment Videos

Last Updated: Feb 12, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.6K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K
Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry
08:37

Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry

Published on: August 7, 2012

11.9K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Understanding protein-ligand interactions is crucial for drug discovery and molecular design.
  • Identifying preferred binding regions helps detect cryptic pockets and enhance ligand selectivity.

Purpose of the Study:

  • To adapt enhanced sampling methods for exploring protein surface interactions.
  • To investigate the binding dynamics between the N-terminal peptide of histone H3 and the YEATS domain.

Main Methods:

  • Utilized the targeted molecular dynamics (TAMD) approach, adapted into a re-TAMD procedure.
  • Simulated ligand unbinding from its native site to explore the protein surface.
  • Analyzed peptide conformations and their diffusion around the protein.

Main Results:

  • The re-TAMD procedure successfully allowed exploration of the protein surface by the ligand.
  • Different regions of the histone H3 N-terminal peptide showed varying influences on binding to the YEATS domain.
  • Sampled peptide conformations reflected free diffusion dynamics around the protein surface.

Conclusions:

  • The re-TAMD approach provides insights into the relative contributions of different peptide regions to protein interactions.
  • This method can reveal key residues or regions involved in modulating protein-ligand binding affinity and specificity.