Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes
Single-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed i...
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MDPI AG
2024-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/6/3371 |
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| author | Sepideh Valimehr Rémi Vuillemot Mohsen Kazemi Slavica Jonic Isabelle Rouiller |
| author_facet | Sepideh Valimehr Rémi Vuillemot Mohsen Kazemi Slavica Jonic Isabelle Rouiller |
| author_sort | Sepideh Valimehr |
| collection | DOAJ |
| description | Single-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed in solution, enabling the recording of images of the protein in multiple conformations. Various methods exist for capturing the conformational variability through analysis of cryo-EM data. Here, we analyzed the conformational variability in the hexameric AAA + ATPase p97, a complex with a six-fold rotational symmetric core surrounded by six flexible N-domains. We compared the performance of discrete classification methods with our recently developed method, MDSPACE, which uses 3D-to-2D flexible fitting of an atomic structure to images based on molecular dynamics (MD) simulations. Our analysis detected a novel conformation adopted by approximately 2% of the particles in the dataset and determined that the N-domains of p97 sway by up to 60° around a central position. This study demonstrates the application of MDSPACE in analyzing the continuous conformational changes in partially symmetrical protein complexes, systems notoriously difficult to analyze due to the alignment errors caused by their partial symmetry. |
| first_indexed | 2024-04-24T18:11:08Z |
| format | Article |
| id | doaj.art-34ca1b21fbd3416c896ff1fd7dc4a085 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-04-24T18:11:08Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-34ca1b21fbd3416c896ff1fd7dc4a0852024-03-27T13:45:53ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-03-01256337110.3390/ijms25063371Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical ComplexesSepideh Valimehr0Rémi Vuillemot1Mohsen Kazemi2Slavica Jonic3Isabelle Rouiller4Department of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, AustraliaDepartment of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, AustraliaDepartment of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, AustraliaIMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, 75005 Paris, FranceDepartment of Biochemistry & Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, AustraliaSingle-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed in solution, enabling the recording of images of the protein in multiple conformations. Various methods exist for capturing the conformational variability through analysis of cryo-EM data. Here, we analyzed the conformational variability in the hexameric AAA + ATPase p97, a complex with a six-fold rotational symmetric core surrounded by six flexible N-domains. We compared the performance of discrete classification methods with our recently developed method, MDSPACE, which uses 3D-to-2D flexible fitting of an atomic structure to images based on molecular dynamics (MD) simulations. Our analysis detected a novel conformation adopted by approximately 2% of the particles in the dataset and determined that the N-domains of p97 sway by up to 60° around a central position. This study demonstrates the application of MDSPACE in analyzing the continuous conformational changes in partially symmetrical protein complexes, systems notoriously difficult to analyze due to the alignment errors caused by their partial symmetry.https://www.mdpi.com/1422-0067/25/6/3371AAA+ ATPase p97continuous conformational variabilitysingle-particle cryo-electron microscopyMDSPACEpartially symmetrical protein complexes |
| spellingShingle | Sepideh Valimehr Rémi Vuillemot Mohsen Kazemi Slavica Jonic Isabelle Rouiller Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes International Journal of Molecular Sciences AAA+ ATPase p97 continuous conformational variability single-particle cryo-electron microscopy MDSPACE partially symmetrical protein complexes |
| title | Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes |
| title_full | Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes |
| title_fullStr | Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes |
| title_full_unstemmed | Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes |
| title_short | Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes |
| title_sort | analysis of the conformational landscape of the n domains of the aaa atpase p97 disentangling the continuous conformational variability in partially symmetrical complexes |
| topic | AAA+ ATPase p97 continuous conformational variability single-particle cryo-electron microscopy MDSPACE partially symmetrical protein complexes |
| url | https://www.mdpi.com/1422-0067/25/6/3371 |
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