Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation
In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter wit...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Current Research in Structural Biology |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2665928X23000089 |
| _version_ | 1797397562894843904 |
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| author | Vladimir Y. Lunin Natalia L. Lunina Alexandre G. Urzhumtsev |
| author_facet | Vladimir Y. Lunin Natalia L. Lunina Alexandre G. Urzhumtsev |
| author_sort | Vladimir Y. Lunin |
| collection | DOAJ |
| description | In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter with the resolution of the atomic image in the map. We propose a local real-space procedure to estimate the values of these heterogeneity parameters, assuming that a fragment of the density map and atomic positions are given. The procedure is based on an analytic representation of the atomic image, as a function of the inhomogeneity parameters and atomic coordinates. In this article, we report the results of the tests both with maps simulated and those derived from experimental data. For simulated maps containing regions with different resolutions, the method determines the local map resolution around the atomic centers and the values of the displacement parameter with reasonable accuracy. For experimental maps, obtained as a Fourier synthesis of a given global resolution, estimated values of the local resolution are close to the global one, and the values of the estimated displacement parameters are close to the respective values of the closest atoms in the refined model. Shown successful applications of the proposed method to experimental crystallographic and cryo-EM maps can be seen as a practical proof of method. |
| first_indexed | 2024-03-09T01:11:51Z |
| format | Article |
| id | doaj.art-9e3c19bfd0224dcb99b7ec79ed3c3419 |
| institution | Directory Open Access Journal |
| issn | 2665-928X |
| language | English |
| last_indexed | 2024-03-09T01:11:51Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Structural Biology |
| spelling | doaj.art-9e3c19bfd0224dcb99b7ec79ed3c34192023-12-11T04:17:02ZengElsevierCurrent Research in Structural Biology2665-928X2023-01-016100102Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximationVladimir Y. Lunin0Natalia L. Lunina1Alexandre G. Urzhumtsev2Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 1, Professor Vitkevich St., Pushchino, 142290, Russia; Corresponding author. Institute of Mathematical Problems of Biology RAS, 1, Professor Vitkevich St., Pushchino, 142290, Russia.Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 1, Professor Vitkevich St., Pushchino, 142290, RussiaCentre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 239, 54506, Vandoeuvre-les-Nancy, France; Corresponding author. Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter with the resolution of the atomic image in the map. We propose a local real-space procedure to estimate the values of these heterogeneity parameters, assuming that a fragment of the density map and atomic positions are given. The procedure is based on an analytic representation of the atomic image, as a function of the inhomogeneity parameters and atomic coordinates. In this article, we report the results of the tests both with maps simulated and those derived from experimental data. For simulated maps containing regions with different resolutions, the method determines the local map resolution around the atomic centers and the values of the displacement parameter with reasonable accuracy. For experimental maps, obtained as a Fourier synthesis of a given global resolution, estimated values of the local resolution are close to the global one, and the values of the estimated displacement parameters are close to the respective values of the closest atoms in the refined model. Shown successful applications of the proposed method to experimental crystallographic and cryo-EM maps can be seen as a practical proof of method.http://www.sciencedirect.com/science/article/pii/S2665928X23000089Real-space refinementInhomogeneous resolutionAtomic imagesShell decomposition |
| spellingShingle | Vladimir Y. Lunin Natalia L. Lunina Alexandre G. Urzhumtsev Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation Current Research in Structural Biology Real-space refinement Inhomogeneous resolution Atomic images Shell decomposition |
| title | Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation |
| title_full | Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation |
| title_fullStr | Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation |
| title_full_unstemmed | Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation |
| title_short | Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation |
| title_sort | local heterogeneity analysis of crystallographic and cryo em maps using shell approximation |
| topic | Real-space refinement Inhomogeneous resolution Atomic images Shell decomposition |
| url | http://www.sciencedirect.com/science/article/pii/S2665928X23000089 |
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