Cryo-Electron Tomography data analysis

In situ structure determination by subtomogram analysis
Subtomogram analysis
Averaging and classification of sub-tomograms.

We aim to establish single particle Cryo-ET as a method for determining density maps of membrane-associated and transient complexes in different conformations at resolutions of 10 Å or better. At this resolution level protein folds can be recognized and fitting of atomic models into EM maps is generally reliable. In particular, we devise methods for accurate reconstruction of 3D volumes from 2D electron micrographs, for localization and identification of specific macromolecular complexes in tomographic volumes, for coherent averaging of subtomograms depicting the same type of complex, and for their examination of their conformational landscape. Thus, we provide the computational framework to capture the different conformations of complexes in their physiological environment.

Further reading:

  1. Khoshouei M, Pfeffer S, Baumeister W, Förster F, Danev R.
    Subtomogram analysis using the Volta phase plate.
    J. Struct. Biol. (2016). PubMed, DOI:10.1016/j.jsb.2016.05.009.
  2. Pfeffer S, Förster F.
    Proteintranslation und Prozessierung in physiologischer Umgebung abgebildet.
    Biospektrum, 4:385-387 (2015). DOI:10.1007/s12268-015-0590-y, Biospektrum
  3. Asano S*, Fukuda Y*, Beck F, Aufderheide A, Förster F, Danev R, Baumeister W.
    A molecular census of 26S proteasomes in intact neurons.
    Science 347:439-442 (2015). PubMed, DOI:10.1126/science.1261197.
    * equal contribution
    Faculty of 1000
  4. Chen Y, Pfeffer S, Fernandez JJ, Sorzano CO, Förster F.
    Autofocused 3D Classification of Cryoelectron Subtomograms.
    Structure 22:1528–1537 (2014). PubMed, DOI:10.1016/j.str.2014.08.007
  5. Kuhn Cuellar L, Pfeffer S, Chen Y, Förster F.
    Automated detection of polysomes in cryoelectron tomography.
    in IEEE International Conference on Image Processing (ICIP) 2085-89 (IEEE Paris, 2014). DOI: 10.1109/ICIP.2014.7025418
  6. Chen X, Chen Y, Schuller JM, Navab N, Förster F.
    Automatic particle picking and multi-class classification in cryo-electron tomograms.
    2014 IEEE International Symposium on Biomedical Imaging Vol. in press (IEEE, Beijing, 2014). DOI: 10.1109/ISBI.2014.6868001
  7. Chen Y, Förster F.
    Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms.
    J. Struct. Biol. 185:309-316 (2014) PubMed, DOI: 10.1016/j.jsb.2013.12.001
    Faculty of 1000
  8. Chen Y, Pfeffer S, Hrabe T, Schuller J, Förster F.
    Fast and accurate reference-free Alignment of Subtomograms.
    J. Struct. Biol. 182:235-45 (2013) PubMed, DOI:10.1016/j.jsb.2013.03.002
  9. Chen Y, Hrabe T, Pfeffer S, Pauly O, Mateus D, Navab N, Förster F.
    Detection and Identification of macromolecular complexes in cryo-electron tomograms using support vector machines.
    Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on, 1373-1376 (2012). DOI: 10.1109/ISBI.2012.6235823
  10. Hrabe T, Chen Y, Pfeffer S, Kuhn-Cuellar L, Mangold AV, Förster F.
    PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis.
    J. Struct. Biol. 178:177-88 (2012). PubMed, DOI: 10.1016/j.jsb.2011.12.003.
  11. Hrabe T, Förster F,
    Structure determination by Single Particle Cryo Electron Tomography.
    Encyclopedia of Life Sciences (2011).
  12. Förster F, Pruggnaller S, Seybert A, Frangakis AS,
    Classification of Cryo-Electron Sub-Tomograms using Constrained Correlation.
    J. Struct. Biol., 161:276-286 (2008). PubMed
  13. Förster F, and Hegerl R,
    Structure determination in situ by averaging of tomograms.
    In: Methods in Cell Biology: Cellular Electron Microscopy. Editor: McIntosh JR, Elsevier, (2007). PubMed
  14. Förster F, Medalia O, Zauberman N, Baumeister W, Fass D,
    Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography.
    Proc. Natl. Acad. Sci. U S A. 102 :4729-34 (2005) PubMedpdf
  15. Frangakis AS, Förster F,
    Computational exploration of structural information from cryo-electron tomograms.
    Curr. Opin. Struct. Biol. 14:325-31 (2004). PubMed