ArticleNature communications2022
Effects of cryo-EM cooling on structural ensembles.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors.Biophysical journal · 2026Article
- New paradigm of q-CAR drug development targeting disease-specific protein conformations.npj drug discovery · 2026Review
- Direct Measurement of Protein Corona Thickness on Nanomaterials Using Dual-Color Stochastic Optical Reconstruction Microscopy (STORM).Small methods · 2026Article
- Digital twin of biomacromolecular thermodynamics in cryo-EM data.Communications chemistry · 2026Article
- Direct evidence of acid-driven protein desolvation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Comparing Multislice Projections of MD Simulations with CryoEM Exposes Structural Prediction Errors.bioRxiv : the preprint server for biology · 2026Article
- Unfreezing structural biology for drug discovery.Nature chemical biology · 2026Review
- Designing Rigid Protein Fiducials to Visualize GPCR Conformational States.bioRxiv : the preprint server for biology · 2026Article
- Atypical β-strand insertion mediates the noncovalent cross-linking in amyloid aggregates.Nature communications · 2026Article
- Article
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Spitrobot-2 advances time-resolved cryo-trapping crystallography to under 25 ms.Communications chemistry · 2025Article
- A cascade of structural rearrangements positions peptide release factor 2 for polypeptide hydrolysis on the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.bioRxiv : the preprint server for biology · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Gephyrin filaments represent the molecular basis of inhibitory postsynaptic densities.Nature communications · 2025Article
- Measuring multisubunit mechanics of geometrically programmed colloidal assemblies via cryo-EM multi-body refinement.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Economical and Versatile Subunit Design Principles for Self-Assembled DNA Origami Structures.ACS nano · 2025Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.
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