Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials
| Autor: | Roy R. Lederman, Ivet Bahar, José María Carazo, David Myška, James Krieger, Marta Martínez, David Strelak, Jiri Filipovic, David Herreros, A. Jiménez-Moreno, Carlos Sierra Sánchez |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Zernike polynomials
Computer science Biochemistry single-particle cryo-EM 03 medical and health sciences symbols.namesake 0302 clinical medicine Normal mode General Materials Science 030304 developmental biology Variable (mathematics) Flexibility (engineering) 0303 health sciences multi-dimensional scaling (MDS) Crystallography Basis (linear algebra) Spherical harmonics spherical harmonics General Chemistry 3D reconstruction and image processing Condensed Matter Physics Research Papers Structural biology QD901-999 Principal component analysis symbols conformations Biological system 030217 neurology & neurosurgery |
| Zdroj: | IUCrJ IUCrJ, Vol 8, Iss 6, Pp 992-1005 (2021) |
| ISSN: | 2052-2525 |
| Popis: | A new tool based on 3D Zernike polynomials is presented that allows the study of the continuous heterogeneity of biological macromolecules, revealing the structural relationships present among different states by the approximation of deformation fields. Structural biology has evolved greatly due to the advances introduced in fields like electron microscopy. This image-capturing technique, combined with improved algorithms and current data processing software, allows the recovery of different conformational states of a macromolecule, opening new possibilities for the study of its flexibility and dynamic events. However, the ensemble analysis of these different conformations, and in particular their placement into a common variable space in which the differences and similarities can be easily recognized, is not an easy matter. To simplify the analysis of continuous heterogeneity data, this work proposes a new automatic algorithm that relies on a mathematical basis defined over the sphere to estimate the deformation fields describing conformational transitions among different structures. Thanks to the approximation of these deformation fields, it is possible to describe the forces acting on the molecules due to the presence of different motions. It is also possible to represent and compare several structures in a low-dimensional mapping, which summarizes the structural characteristics of different states. All these analyses are integrated into a common framework, providing the user with the ability to combine them seamlessly. In addition, this new approach is a significant step forward compared with principal component analysis and normal mode analysis of cryo-electron microscopy maps, avoiding the need to select components or modes and producing localized analysis. |
| Databáze: | OpenAIRE |
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