A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps

Björn O. Forsberg (), Pranav N. M. Shah and Alister Burt
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Björn O. Forsberg: Karolinska Institute
Pranav N. M. Shah: University of Oxford
Alister Burt: MRC Laboratory of Molecular Biology

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction.

Date: 2023
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DOI: 10.1038/s41467-023-41478-1

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