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2DHybrid Analysis

  • Atsushi Matsumoto
  • Kenji Iwasaki
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1105)

Abstract

We have developed an approach termed ‘2D hybrid analysis’ for building three-dimensional (3D) structures from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by the approach in which 3DEM maps are reconstructed. In the proposed approach, a large number of atomic models with different conformations are first built by computer simulation. Then, simulated EM images are produced from each atomic model. Finally, these images are compared with an experimental EM image to identify the best-fitting atomic model. Two kinds of models are used to simulate the EM images: the negative-stain model and the simple projection model. Although the former is more realistic, the latter permits faster computation. We applied this approach to the averaged EM images of integrin. Although many of these were reproduced well by the best-fitting atomic models, others did not closely resemble any of the simulated EM images. However, the latter group were well reproduced by averaging multiple simulated EM images originating from atomic models with rather different conformations or orientations. This indicated that our approach is capable of detecting mixtures of conformations in the averaged EM images, which should assist in their correct interpretation.

Keywords

Simulated EM image Negative stain Averaging Modeling Protein structure 

Notes

Acknowledgments

Molecular graphics were performed using the UCSF Chimera package (Pettersen et al. 2004). This work was supported by the Platform Project for Supporting Drug Discovery and Life Science Research(Platform for Drug Discovery, Informatics, and Structural Life Science) from the Japan Agency for Medical Research and Development (AMED).

References

  1. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2(3):173–181CrossRefGoogle Scholar
  2. Burgess SA, Walker ML, White HD, Trinick J (1997) Flexibility within myosin heads revealed by negative stain and single-particle analysis. J Cell Biol 139(3):675–681CrossRefGoogle Scholar
  3. Chang HC, Bao Z, Yao Y, Tse AG, Goyarts EC, Madsen M, Kawasaki E, Brauer PP, Sacchettini JC, Nathenson SG, Reinherz EL (1994) A general method for facilitating heterodimeric pairing between two proteins: application to expression of α and β T-cell receptor extracellular segments. Proc Natl Acad Sci U S A 91(24):11408–11412CrossRefGoogle Scholar
  4. Henderson R (2013) Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise. ProcNatlAcad Sci U S A 110(45):18037–18041CrossRefGoogle Scholar
  5. Ludtke SJ, Baldwin PR, Chiu W (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128(1):82–97CrossRefGoogle Scholar
  6. Marabini R, Carazo JM (1994) Pattern recognition and classification of images of biological macromolecules using artificial neural networks. Biophys J 66(6):1804–1814CrossRefGoogle Scholar
  7. Matsumoto A, Ishida H (2009) Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures. Structure 17(12):1605–1613CrossRefGoogle Scholar
  8. Matsumoto A, Kamata T, Takagi J, Iwasaki K, Yura K (2008) Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis. Biophys J 95(6):2895–2908CrossRefGoogle Scholar
  9. Matsumoto A, Miyazaki N, Takagi J, Iwasaki K (2017) 2D hybrid analysis: approach for building three-dimensional atomic model by electron microscopy image matching. SciRep 7(1):377Google Scholar
  10. Miyashita O, Onuchic JN, Wolynes PG (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A 100(22):12570–12575CrossRefGoogle Scholar
  11. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612CrossRefGoogle Scholar
  12. Sadourny R, Arakawa A, Mintz Y (1968) Integration of the nondivergent barotropic vorticity equation with an icosahedral-hexagonal grid for the sphere. Mon Weather Rev 96(6):351–356CrossRefGoogle Scholar
  13. Schroder GF (2015) Hybrid methods for macromolecular structure determination: experiment with expectations. Curr Opin Struct Biol 31:20–27CrossRefGoogle Scholar
  14. Takagi J, Erickson HP, Springer TA (2001) C-terminal opening mimics ‘inside-out’ activation of integrin α5β1. Nat Struct Mol Biol 8(5):412–416CrossRefGoogle Scholar
  15. Takagi J, Petre BM, Walz T, Springer TA (2002) Global conformational rearrangements in integrin extracellular domains in outside-in and inside-out signaling. Cell 110(5):599–511CrossRefGoogle Scholar
  16. Tama F, Brooks CL 3rd (2005) Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol 345(2):299–314CrossRefGoogle Scholar
  17. Tirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77(9):1905–1908CrossRefGoogle Scholar
  18. Tsukasaki Y, Miyazaki N, Matsumoto A, Nagae S, Yonemura S, Tanoue T, Iwasaki K, Takeichi M (2014) Giant cadherins fat and Dachsous self-bend to organize properly spaced intercellular junctions. Proc Natl Acad Sci U S A 111(45):16011–16016CrossRefGoogle Scholar
  19. van Heel M (2013) Finding trimeric HIV-1 envelope glycoproteins in random noise. ProcNatlAcad Sci U S A 110(45):E4175–E4177CrossRefGoogle Scholar
  20. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. J Struct Biol 116(1):17–24CrossRefGoogle Scholar
  21. Villa E, Lasker K (2014) Finding the right fit: chiseling structures out of cryo-electron microscopy maps. Curr Opin Struct Biol 25:118–125CrossRefGoogle Scholar
  22. Xiong J-P, Stehle T, Diefenbach B, Zhang R, Dunker R, Scott DL, Joachimiak A, Goodman SL, Arnaout MA (2001) Crystal structure of the extracellular segment of integrin αVβ3. Science 294(5541):339–345CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Molecular Simulation and Modeling GroupNational Institutes for Quantum and Radiological Science and TechnologyKizugawaJapan
  2. 2.Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA)University of TsukubaTsukubaJapan

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