Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification

Abstract

Cryogenic electron tomography (cryo-ET) allows studying biological macromolecular complexes in cells by three-dimensional (3D) data analysis. The complexes continuously change their shapes (conformations) to achieve biological functions. The shape heterogeneity in the samples imaged in the cryo electron microscope is a bottleneck for comprehending biological mechanisms and developing drugs. Low signal-to-noise ratio and spatial anisotropy (missing wedge artefacts) make cryo-ET data particularly challenging for resolving the shape variability. Other shape variability analysis techniques simplify the problem by considering discrete rather than continuous conformational changes of complexes. Recently, HEMNMA-3D was introduced for cryo-ET continuous shape variability analysis, based on elastic and rigid-body 3D registration between simulated shapes and cryo-ET data. The simulated motions are obtained by normal mode analysis of a high- or low-resolution 3D reference model of the complex under study. The rigid-body alignment is achieved via fast rotational matching with missing wedge compensation. HEMNMA-3D provides a visual insight into molecular dynamics by grouping and averaging subtomograms of similar shapes and by animating movies of registered motions. This article reviews the method and compares it with existing literature on a simulated dataset for nucleosome shape variability.