A Pattern Recognition Tool for Medium-Resolution Cryo-EM Density Maps and Low-Resolution Cryo-ET Density Maps
Cryo-electron microscopy (Cryo-EM) and cryo-electron tomography (cryo-ET) produce 3-D density maps of biological molecules at a range of resolution levels. Pattern recognition tools are important in distinguishing biological components from volumetric maps with the available resolutions. One of the most distinct characters in density maps at medium (5–10 Å) resolution is the visibility of protein secondary structures. Although computational methods have been developed, the accurate detection of helices and β-strands from cryo-EM density maps is still an active research area. We have developed a tool for protein secondary structure detection and evaluation of medium resolution 3-D cryo-EM density maps that combines three computational methods (SSETracer, StrandTwister, and AxisComparison). The program was integrated in UCSF Chimera, a popular visualization software in the cryo-EM community. In related work, we have developed BundleTrac, a computational method to trace filaments in a bundle from lower resolution cryo-ET density maps. It has been applied to actin filament tracing in stereocilia with good accuracy and can be potentially added as a tool in Chimera.
KeywordsPattern recognition Cryo-electron microscopy Density map Helix Beta-strands Filament Stereocilia
Acknowledgements and Author Contributions
The work in this article was supported, in part, by NSF DBI-1356621 (to J.H), NIH R01-GM062968 (to W.W.) and NIH P01-GM051487 (to M.A.). D.H. and J.H. designed the plugin of Chimera; D.H. implemented it. We would like to thank Taylor Gerpheide and Stephanie Zeil for initial work in the tool development when they worked as undergraduate research assistants. S.S., J.S., J.K., W.W., M.A. and J.H. worked together in the development of BundleTrac. J.H.. W.W. and M.A. wrote the paper. We thank Peter Barr-Gillespie for sample preparation and imaging of stereocilia.
- 1.Nobelprize.org: The Nobel Prize in Chemistry 2017: Nobel Media AB 2014. https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2017/. Accessed 11 Apr 2018
- 3.Europe PDBi: EMDB statistics release (2018). http://www.ebi.ac.uk/pdbe/emdb/statistics_releases.html/
- 5.Si, D., He, J.: Beta-sheet detection and representation from medium resolution Cryo-EM density maps. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington DC, USA, pp. 764–770. ACM (2013). https://doi.org/10.1145/2506583.2506707
- 9.Dal Palu, A., He, J., Pontelli, E., Lu, Y.: Identification of Alpha-Helices from low resolution protein density maps. In: Proceeding of Computational Systems Bioinformatics Conference, CSB, pp. 89–98 (2006)Google Scholar