Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms

MOTIVATION Cryo-electron tomography allows the imaging of macromolecular complexes in near living conditions. To enhance the nominal resolution of a structure it is necessary to align and average individual subtomograms each containing identical complexes. However, if the sample of complexes is heterogeneous, it is necessary to first classify subtomograms into groups of identical complexes. This task becomes challenging when tomograms contain mixtures of unknown complexes extracted from a crowded environment. Two main challenges must be overcomed: First, classification of subtomograms must be performed without knowledge of template structures. However, most alignment methods are too slow to perform reference-free classification of a large number of (e.g. tens of thousands) of subtomograms. Second, subtomograms extracted from crowded cellular environments, contain often fragments of other structures besides the target complex. However, alignment methods generally assume that each subtomogram only contains one complex. Automatic methods are needed to identify the target complexes in a subtomogram even when its shape is unknown. RESULTS In this article, we propose an automatic and systematic method for the isolation and masking of target complexes in subtomograms extracted from crowded environments. Moreover, we also propose a fast alignment method using fast rotational matching in real space. Our experiments show that, compared with our previously proposed fast alignment method in reciprocal space, our new method significantly improves the alignment accuracy for highly distorted and especially crowded subtomograms. Such improvements are important for achieving successful and unbiased high-throughput reference-free structural classification of complexes inside whole-cell tomograms. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.