Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Determination of Crystal Structures

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

Mapping the avoid-ome: a systematic open-science approach to predictive ADMET.

Nature communications·2026

Same author

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.

Journal of chemical information and modeling·2026

Same author

Development of High-Affinity Ligands for Human UBR2.

Journal of medicinal chemistry·2026

Same author

Inhibiting the interaction between the mitochondrial receptor Tom70 and SARS CoV 2 Orf9b with small molecules.

bioRxiv : the preprint server for biology·2026

Same author

A PKA-selective inhibitor captures an open but more ordered conformation of the PKA catalytic subunit.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.

Journal of chemical information and modeling·2026

Same journal

Scotty: lattice coincidences in the Protein Data Bank.

Acta crystallographica. Section D, Structural biology·2026

Same journal

Scotty: lattice coincidences for macromolecular crystallographic phasing.

Acta crystallographica. Section D, Structural biology·2026

Same journal

Miroslav Z. Papiz (1955-2026).

Acta crystallographica. Section D, Structural biology·2026

Same journal

Structural basis of regioselective double halogenation of the β-carboline tryptoline by the single-component halogenase AetF.

Acta crystallographica. Section D, Structural biology·2026

Same journal

Simulating neutron protein crystallography experiments: applications to the development of the NMX instrument at ESS.

Acta crystallographica. Section D, Structural biology·2026

Same journal

Molecular architecture of the human citrate synthase-malate dehydrogenase 2 metabolon.

Acta crystallographica. Section D, Structural biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 12, 2026

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

Molecular-dynamics simulation methods for macromolecular crystallography.

David C Wych¹, Phillip C Aoto², Lily Vu²

¹Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Acta Crystallographica. Section D, Structural Biology

|January 5, 2023

Summary

This summary is machine-generated.

Molecular-dynamics (MD) simulations enhance macromolecular crystallography (MX) by improving protein structure modeling. This approach aids in interpreting ambiguous density, revealing multiple conformations and providing mechanistic insights into enzyme function.

Keywords:

conformational ensembles molecular-dynamics simulations protein kinases water structure

More Related Videos

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

Related Experiment Videos

Last Updated: Jun 12, 2026

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Published on: July 6, 2019

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

Area of Science:

Structural Biology
Computational Biology

Background:

Protein crystal structures are traditionally represented by single atomic coordinates.
Conformational flexibility is crucial for protein function, necessitating multi-structure models.
Current modeling methods struggle with ambiguous crystallographic density, particularly at protein-solvent interfaces.

Purpose of the Study:

To investigate the utility of molecular-dynamics (MD) simulations for enhancing macromolecular crystallography (MX) studies.
To develop and apply integrated MD-MX methods for improved protein structure modeling.
To gain mechanistic insights into enzyme function through refined structural models.

Main Methods:

Development of integrated MD-MX methods combining molecular dynamics simulations with conventional modeling and refinement.
Application of these methods to a cyclic adenosine monophosphate-dependent protein kinase crystal structure at room temperature.
Analysis of crystallographic density interpretation, water modeling, and protein conformational states.

Main Results:

Improved interpretation of ambiguous crystallographic density.
Generation of an alternative water model and a revised protein model incorporating multiple conformations.
Successful application to a specific enzyme, revealing mechanistic details.

Conclusions:

MD-MX methods offer a powerful approach to overcome limitations in conventional MX modeling.
The integration of MD simulations enhances the accuracy and detail of protein structural models.
This methodology can yield significant mechanistic insights for various protein crystallography studies.