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

Bag, Sukantadev and Prentice, Michael B and Liang, Mingzhi and Warren, Martin J. and Roy Choudhury, Kingshuk (2016) Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions. BMC Bioinformatics, 17 (1). pp. 234-247. ISSN 1471-2105. (doi:https://doi.org/10.1186/s12859-016-1107-5) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided. (Contact us about this Publication)
Official URL
http://doi.org/10.1186/s12859-016-1107-5

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.

Item Type: Article
Uncontrolled keywords: Polyhedron graph ; Incomplete polyhedra ; Classification from incomplete data ; Cryo electron tomography ; Bacterial microcompartment
Subjects: Q Science
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Sue Davies
Date Deposited: 16 Jun 2016 10:27 UTC
Last Modified: 08 Jun 2017 10:56 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/55956 (The current URI for this page, for reference purposes)
  • Depositors only (login required):