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

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...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...

You might also read

Related Articles

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

Sort by
Same author

Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor.

Journal of proteome research·2025
Same author

A comparative study of the cryo-EM structures of <i>Saccharomyces cerevisiae</i> and human anaphase-promoting complex/cyclosome (APC/C).

eLife·2024
Same author

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.

Nature methods·2024
Same author

Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis.

Journal of structural biology·2024
Same author

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.

Research square·2024
Same author

Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides.

Molecular & cellular proteomics : MCP·2023
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

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

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

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

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

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

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

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

Characterization of Bioactive Saponins from Sea Cucumbers.

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

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: May 10, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Studying protein-ligand interactions using X-ray crystallography.

Andrew P Turnbull1, Paul Emsley

  • 1CRT Discovery Laboratories, Department of Biological Sciences, Birkbeck, University of London, London, UK.

Methods in Molecular Biology (Clifton, N.J.)
|June 5, 2013
PubMed
Summary
This summary is machine-generated.

X-ray crystallography routinely determines protein-ligand complex structures. Advances enable easier structure determination and ligand fitting, even for challenging cases.

More Related Videos

Protein Crystallization for X-ray Crystallography
09:27

Protein Crystallization for X-ray Crystallography

Published on: January 16, 2011

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Related Experiment Videos

Last Updated: May 10, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Protein Crystallization for X-ray Crystallography
09:27

Protein Crystallization for X-ray Crystallography

Published on: January 16, 2011

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Structural Biology
  • Biochemistry
  • Crystallography

Background:

  • Protein-ligand interactions are crucial for biological processes.
  • X-ray crystallography is a key method for elucidating these interactions at atomic resolution.
  • Previous limitations in routine structure determination of complexes have been a bottleneck.

Purpose of the Study:

  • To highlight the advancements in X-ray crystallography for protein-ligand complex structure determination.
  • To emphasize the routine applicability of these techniques.
  • To showcase improved methods for data acquisition and analysis.

Main Methods:

  • Utilizing established protein structures and crystallization conditions.
  • Employing techniques such as ligand soaking or co-crystallization.
  • Leveraging molecular replacement for phase determination.
  • Applying advanced protein structure model building for automated ligand fitting into electron density maps.

Main Results:

  • Routine determination of protein-ligand complex structures is now achievable.
  • Ligand fitting into residual electron density is facilitated by automated model building.
  • The described methods provide comprehensive structural data for complexes.

Conclusions:

  • X-ray crystallography, with recent advancements, is a powerful and routine tool for studying protein-ligand interactions.
  • The integration of improved crystallization, data collection, and model building techniques enhances structural biology research.
  • These advancements facilitate a deeper understanding of molecular recognition and drug design.