Measurement of charges and chemical bonding in a cryo-EM structure
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 pot...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Communications Chemistry |
| Online Access: | https://doi.org/10.1038/s42004-023-00900-x |
| _version_ | 1797811617173340160 |
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| author | Saori Maki-Yonekura Keisuke Kawakami Kiyofumi Takaba Tasuku Hamaguchi Koji Yonekura |
| author_facet | Saori Maki-Yonekura Keisuke Kawakami Kiyofumi Takaba Tasuku Hamaguchi Koji Yonekura |
| author_sort | Saori Maki-Yonekura |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T07:25:20Z |
| format | Article |
| id | doaj.art-631393fd03f1446bae1085e5c8423048 |
| institution | Directory Open Access Journal |
| issn | 2399-3669 |
| language | English |
| last_indexed | 2024-03-13T07:25:20Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Chemistry |
| spelling | doaj.art-631393fd03f1446bae1085e5c84230482023-06-04T11:23:15ZengNature PortfolioCommunications Chemistry2399-36692023-05-01611810.1038/s42004-023-00900-xMeasurement of charges and chemical bonding in a cryo-EM structureSaori Maki-Yonekura0Keisuke Kawakami1Kiyofumi Takaba2Tasuku Hamaguchi3Koji Yonekura4Biostructural Mechanism Laboratory, RIKEN SPring-8 CenterBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterAbstract 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.https://doi.org/10.1038/s42004-023-00900-x |
| spellingShingle | Saori Maki-Yonekura Keisuke Kawakami Kiyofumi Takaba Tasuku Hamaguchi Koji Yonekura Measurement of charges and chemical bonding in a cryo-EM structure Communications Chemistry |
| title | Measurement of charges and chemical bonding in a cryo-EM structure |
| title_full | Measurement of charges and chemical bonding in a cryo-EM structure |
| title_fullStr | Measurement of charges and chemical bonding in a cryo-EM structure |
| title_full_unstemmed | Measurement of charges and chemical bonding in a cryo-EM structure |
| title_short | Measurement of charges and chemical bonding in a cryo-EM structure |
| title_sort | measurement of charges and chemical bonding in a cryo em structure |
| url | https://doi.org/10.1038/s42004-023-00900-x |
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