Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

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Authors

HERREROS David LEDERMAN Roy R. KRIEGER James M. JIMÉNEZ-MORENO Amaya MARTÍNEZ Marta MYŠKA David STŘELÁK David FILIPOVIČ Jiří SORZANO Carlos O. S. CARAZO José M.

Year of publication 2023
Type Article in Periodical
Magazine / Source Nature Communications
MU Faculty or unit

Institute of Computer Science

Citation
Web https://www.nature.com/articles/s41467-023-35791-y
Doi http://dx.doi.org/10.1038/s41467-023-35791-y
Keywords 3D reconstruction and image processing; single-particle cryo-EM; spherical harmonics; Zernike polynomials; conformations
Description 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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