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Herreros D, Lederman RR, Krieger JM, Jiménez-Moreno A, Martínez M, Myška D, Strelak D, Filipovic J, Sorzano COS, Carazo JM. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nat Commun 2023; 14:154. [PMID: 36631472 PMCID: PMC9832421 DOI: 10.1038/s41467-023-35791-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
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Affiliation(s)
- D Herreros
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - R R Lederman
- The Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - J M Krieger
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - A Jiménez-Moreno
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - M Martínez
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - D Myška
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - D Strelak
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain.,Faculty of Informatics, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - J Filipovic
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - C O S Sorzano
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
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