ArticleCommunications chemistry2023
Measurement of charges and chemical bonding in a cryo-EM structure.
Article in Communications chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Self-stretching molecular monolayers with autonomous folding and mechanical adaptation.Science advances · 2026Article
- CryoEM in the fast lane of structural biology.IUCrJ · 2026Review
- Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential.Biophysical journal · 2026Article
- Atomic resolution cryo-EM at 200 keV.IUCrJ · 2026Article
- Measurement of atomic scattering factors by cryoelectron microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Direct from the seed: an atomic resolution protein structure by ab initio MicroED.Nature communications · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Advances in Crystallography and Cryo-Electron Microscopy for the Study of Membrane Proteins.Advances in experimental medicine and biology · 2026Review
- Article
- Limiting the effects of radiation damage in MicroED through dose selection during data processing.Acta crystallographica. Section D, Structural biology · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Article
- A realistic phantom dataset for benchmarking cryo-ET data annotation.Nature methods · 2025Article
- Low-Dose Elemental Mapping of Light Atoms in Liquid-phase Materials Using Cryo-EELS.Analytical chemistry · 2025Article
- Facile Control of a Tailed Virus Surrogate by Iron Conventional Coagulation and Electrocoagulation.Environmental science & technology · 2025Article
- Structural Insight Into a Human H Ferritin@Gold-Monocarbene Adduct: Aurophilicity Revealed in a Biological Context.Angewandte Chemie (International ed. in English) · 2025Article
- MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.Nature communications · 2025Article
- A large-scale curated and filterable dataset for cryo-EM foundation model pre-training.Scientific data · 2025Article
- De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential.bioRxiv : the preprint server for biology · 2025Article
- Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm.Biophysics and physicobiology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.
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