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 Organization01:24

Protein Organization

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.

You might also read

Related Articles

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

Sort by
Same author

Feature Frequency Profile (FFP) Method: A Language Model for Whole-Genome ("Organism") Phylogeny.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Whole-genome demography of COVID-19 virus during its pandemic period and on "panvalent" vaccine design.

Scientific reports·2024
Same author

On whole-genome demography of world's ethnic groups and individual genomic identity.

Scientific reports·2023
Same author

Cryo-EM structure of ABCG5/G8 in complex with modulating antibodies.

Communications biology·2021
Same author

Reply to Li et al.: Organism tree of life: Gene phylogeny vs. whole-proteome phylogeny.

Proceedings of the National Academy of Sciences of the United States of America·2020
Same author

Whole-proteome tree of life suggests a deep burst of organism diversity.

Proceedings of the National Academy of Sciences of the United States of America·2020
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Jun 22, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Water polygons in high-resolution protein crystal structures.

Jonas Lee1, Sung-Hou Kim

  • 1Department of Chemistry, University of California, Berkeley, California 94720-5230, USA.

Protein Science : a Publication of the Protein Society
|June 25, 2009
PubMed
Summary
This summary is machine-generated.

Researchers analyzed interstitial water (ISW) structures in protein crystals, revealing polygonal water arrangements. These findings offer insights into liquid water properties and stable water oligomers.

More Related Videos

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
08:58

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

Published on: July 5, 2018

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Related Experiment Videos

Last Updated: Jun 22, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques
08:58

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

Published on: July 5, 2018

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
07:11

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Area of Science:

  • Structural biology
  • Biophysics
  • Physical chemistry

Background:

  • Interstitial water (ISW) plays a crucial role in protein structure and function.
  • Understanding the organization of water molecules within protein crystals can provide insights into the properties of bulk liquid water.
  • Previous studies have suggested the existence of ordered water structures, but experimental evidence for specific oligomeric arrangements has been limited.

Purpose of the Study:

  • To investigate the structural arrangements of interstitial water molecules within protein crystal structures.
  • To identify and characterize recurring polygonal water structures (oligomers) in the interstitial spaces of proteins.
  • To explore the potential relationship between observed water structures and the physical properties of liquid water.

Main Methods:

  • Analysis of 1500 protein crystal structures from the Protein Data Bank (PDB).
  • Selection criteria included resolution >1.5 Å and <90% sequence similarity to ensure structural diversity.
  • Identification and classification of polygonal water clusters (3-8 water molecules) within the interstitial spaces of proteins.

Main Results:

  • Observed various polygonal water structures (trigons, tetragons, pentagons, hexagons, etc.) composed of 3 to 8 water molecules.
  • Approximately 13% of interstitial water molecules were localized enough for X-ray visibility, with 78% in the first hydration layer.
  • Beyond the first layer, nearly half of localized water molecules formed polygonal structures, with trigons being the most frequent. Octagons and nanogons often resulted from smaller polygon fusion.

Conclusions:

  • The study provides experimental evidence for the existence of stable, polygonal water oligomers in protein interstitial spaces.
  • These observed water polygons may represent time- and space-averaged structures of water oligomers in liquid water.
  • The findings suggest that incorporating these water polygon structures could improve correlations and predictions of liquid water properties.