MPicker: visualizing and picking membrane proteins for cryo-electron tomography
Abstract Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contra...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55767-w |
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| _version_ | 1841544507517042688 |
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| author | Xiaofeng Yan Shudong Li Weilin Huang Hao Wang Tianfang Zhao Mingtao Huang Niyun Zhou Yuan Shen Xueming Li |
| author_facet | Xiaofeng Yan Shudong Li Weilin Huang Hao Wang Tianfang Zhao Mingtao Huang Niyun Zhou Yuan Shen Xueming Li |
| author_sort | Xiaofeng Yan |
| collection | DOAJ |
| description | Abstract Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins. |
| format | Article |
| id | doaj-art-4dd9d26c8616476482e086dbf8bc7255 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-4dd9d26c8616476482e086dbf8bc72552025-01-12T12:29:49ZengNature PortfolioNature Communications2041-17232025-01-0116111310.1038/s41467-024-55767-wMPicker: visualizing and picking membrane proteins for cryo-electron tomographyXiaofeng Yan0Shudong Li1Weilin Huang2Hao Wang3Tianfang Zhao4Mingtao Huang5Niyun Zhou6Yuan Shen7Xueming Li8Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversitySchool of Life Sciences, Tsinghua UniversityKey Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversityKey Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversityKey Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversityKey Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversitySchool of Life Sciences, Tsinghua UniversityDepartment of Electronic Engineering, Tsinghua UniversityKey Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua UniversityAbstract Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins.https://doi.org/10.1038/s41467-024-55767-w |
| spellingShingle | Xiaofeng Yan Shudong Li Weilin Huang Hao Wang Tianfang Zhao Mingtao Huang Niyun Zhou Yuan Shen Xueming Li MPicker: visualizing and picking membrane proteins for cryo-electron tomography Nature Communications |
| title | MPicker: visualizing and picking membrane proteins for cryo-electron tomography |
| title_full | MPicker: visualizing and picking membrane proteins for cryo-electron tomography |
| title_fullStr | MPicker: visualizing and picking membrane proteins for cryo-electron tomography |
| title_full_unstemmed | MPicker: visualizing and picking membrane proteins for cryo-electron tomography |
| title_short | MPicker: visualizing and picking membrane proteins for cryo-electron tomography |
| title_sort | mpicker visualizing and picking membrane proteins for cryo electron tomography |
| url | https://doi.org/10.1038/s41467-024-55767-w |
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