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Cryo-electron Microscopy

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Related Experiment Video

Updated: Aug 11, 2025

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Conformational space exploration of cryo-EM structures by variability refinement.

Pavel V Afonine¹, Alexia Gobet², Loïck Moissonnier²

¹Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

Biochimica Et Biophysica Acta. Biomembranes

|February 4, 2023

Summary

This summary is machine-generated.

This study introduces a new tool for analyzing continuous heterogeneity in cryo-electron microscopy (cryo-EM) data. The method refines structural ensembles to visualize protein motion and identify variable regions within biological samples.

Keywords:

Cryo-EM Phenix.varref Structure modelling Variability analysis

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Last Updated: Aug 11, 2025

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Published on: January 31, 2022

Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Cryo-electron microscopy (cryo-EM) reveals sample heterogeneity, including continuous variations from local protein motion.
Analyzing this continuous heterogeneity is challenging for pinpointing specific structural details.
Variability analysis generates map series but lacks direct structural interpretation.

Purpose of the Study:

To develop a computational tool for refining structural ensembles against cryo-EM variability analysis maps.
To bridge the gap between observed structural heterogeneity and its molecular explanation.
To enable detailed investigation of protein dynamics and ligand interactions.

Main Methods:

Designed a novel tool to refine an ensemble of structures into variability analysis maps.
Integrated the tool into the Phenix software suite as phenix.varref.
Compared refined structural movements with molecular dynamics simulations.

Main Results:

The tool successfully refines structural ensembles, clearly highlighting variable and stable regions.
Refined movements align directionally with molecular dynamics simulations, differing mainly in amplitude.
The method is applicable to investigating ligand behavior within dynamic protein structures.

Conclusions:

Variability refinement provides a powerful approach to interpret continuous heterogeneity in cryo-EM data.
This method enhances the understanding of protein dynamics and structural variations.
The tool facilitates detailed structural analysis of biological samples, including ligand interactions.