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

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.

Automated summary

The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.