Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex
Abstract Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statist...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-41575-1 |
| _version_ | 1797558264599150592 |
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| author | Xu Han Dongliang Zhang Lu Hong Daqi Yu Zhaolong Wu Tian Yang Michael Rust Yuhai Tu Qi Ouyang |
| author_facet | Xu Han Dongliang Zhang Lu Hong Daqi Yu Zhaolong Wu Tian Yang Michael Rust Yuhai Tu Qi Ouyang |
| author_sort | Xu Han |
| collection | DOAJ |
| description | Abstract Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level. |
| first_indexed | 2024-03-10T17:28:51Z |
| format | Article |
| id | doaj.art-cd37a6687ca9499b982a7ec98d097bb6 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-10T17:28:51Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-cd37a6687ca9499b982a7ec98d097bb62023-11-20T10:06:13ZengNature PortfolioNature Communications2041-17232023-09-0114111110.1038/s41467-023-41575-1Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complexXu Han0Dongliang Zhang1Lu Hong2Daqi Yu3Zhaolong Wu4Tian Yang5Michael Rust6Yuhai Tu7Qi Ouyang8State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityGraduate Program in Biophysical Sciences, University of ChicagoState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityDepartments of Molecular Genetics and Cell Biology and of Physics, University of ChicagoIBM T. J. Watson Research CenterState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking UniversityAbstract Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level.https://doi.org/10.1038/s41467-023-41575-1 |
| spellingShingle | Xu Han Dongliang Zhang Lu Hong Daqi Yu Zhaolong Wu Tian Yang Michael Rust Yuhai Tu Qi Ouyang Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex Nature Communications |
| title | Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex |
| title_full | Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex |
| title_fullStr | Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex |
| title_full_unstemmed | Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex |
| title_short | Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex |
| title_sort | determining subunit subunit interaction from statistics of cryo em images observation of nearest neighbor coupling in a circadian clock protein complex |
| url | https://doi.org/10.1038/s41467-023-41575-1 |
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