Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions

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Date
2016-06-13
Authors
Bag, Sukantadev
Prentice, Michael B.
Liang, Mingzhi
Warren, Martin J.
Roy Choudhury, Kingshuk
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Publisher
BioMed Central
Published Version
10.1186/s12859-016-1107-5
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Abstract
Background: Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most current approaches for structure determination improve cryo-ET resolution either by some form of sub-tomogram averaging or template matching, respectively precluding detection of shapes that vary across objects or are a priori unknown. Various macromolecular structures possess polyhedral structure. We propose a classification method for polyhedral shapes from incomplete individual cryo-ET reconstructions, based on topological features of an extracted polyhedral graph (PG). Results: We outline a pipeline for extracting PG from 3-D cryo-ET reconstructions. For classification, we construct a reference library of regular polyhedra. Using geometric simulation, we construct a non-parametric estimate of the distribution of possible incomplete PGs. In studies with simulated data, a Bayes classifier constructed using these distributions has an average test set misclassification error of?<?5 % with upto 30 % of the object missing, suggesting accurate polyhedral shape classification is possible from individual incomplete cryo-ET reconstructions. We also demonstrate how the method can be made robust to mis-specification of the PG using an SVM based classifier. The methodology is applied to cryo-ET reconstructions of 30 micro-compartments isolated from E. coli bacteria. Conclusions: The predicted shapes aren’t unique, but all belong to the non-symmetric Johnson solid family, illustrating the potential of this approach to study variation in polyhedral macromolecular structures.
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Keywords
Polyhedron graph , Incomplete polyhedral , Classification from incomplete data , Cryo electron tomography , Bacterial microcompartment
Citation
Bag, S., Prentice, M. B., Liang, M., Warren, M. J. and Roy Choudhury, K. (2016) 'Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions', BMC Bioinformatics, 17, 234 (14pp). doi: 10.1186/s12859-016-1107-5
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https://hdl.handle.net/10468/4127
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Microbiology - Journal Articles
Mathematical Sciences- Journal Articles
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© 2016, Bag et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.