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 Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

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...
Protein Folding01:22

Protein Folding

Overview
Hydrogen Bonds01:04

Hydrogen Bonds

A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...

You might also read

Related Articles

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

Sort by
Same author

A damage accumulation model identifies distinct aging regimes across species.

Nature aging·2026
Same author

Disordered Tails Shape DNA Specificity of Myc:Max via Transient Competition.

Journal of molecular biology·2026
Same author

Foundations of Gerophysics.

Aging·2026
Same author

Dynamics of the end-of-life phase explained by the saturating removal model.

bioRxiv : the preprint server for biology·2026
Same author

Excitability as a design principle in the immune system.

Science advances·2026
Same author

Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs.

Nature communications·2026

Related Experiment Video

Updated: Jun 20, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Understanding hydrogen-bond patterns in proteins using network motifs.

Ofer Rahat1, Uri Alon, Yaakov Levy

  • 1Department of Biological Chemistry, Department of Molecular Cell Biology and Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Bioinformatics (Oxford, England)
|September 22, 2009
PubMed
Summary
This summary is machine-generated.

Protein structures were analyzed as networks of amino acid residues. Network motifs, or recurring sub-graphs, reveal structural differences between NMR, molecular dynamics, and X-ray crystallography methods.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

Related Experiment Videos

Last Updated: Jun 20, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Network science

Background:

  • Protein structures are represented as networks of amino acid residues and their contacts.
  • Network motifs are recurring sub-graphs within these protein networks.

Purpose of the Study:

  • To identify and characterize network motifs in protein structures.
  • To compare structural differences between NMR, molecular dynamics (MD) simulations, and X-ray crystallography using motif analysis.

Main Methods:

  • Dissecting protein structures into six-node sub-graphs (network motifs).
  • Analyzing backbone hydrogen bonds (H-bonds) and covalent interactions as edges.
  • Comparing motif composition across different experimental and simulation structures (NMR, MD, X-ray).

Main Results:

  • Identified 35 significantly frequent network motifs in a protein structure dataset.
  • Found that motifs correspond to known secondary structures (alpha-helices, beta-sheets) and novel sub-structures.
  • Observed consistent, albeit small, differences in motif composition between NMR/MD structures and X-ray structures for Lysozyme, SH3, and lambda repressor.

Conclusions:

  • Topological characterization of protein structures via network motifs provides a detailed difference map.
  • Discrepancies in motif composition suggest potential differences in structural representation or dynamics between NMR, MD, and X-ray methods.
  • Differences may arise from energy functions used in simulations or the inherent dynamic nature of proteins.