Computational Methods for Electron Tomography of Influenza Virus
Influenza is a rapidly changing virus that appears seasonally in the human population. Every year a new strain of the influenza virus appears with the potential to cause a serious global pandemic. Knowledge of the structure and density of the surface proteins is of critical importance in a vaccine candidate. Reconstruction techniques from a series of tilted electron-tomographic projection images provide quantification of surface proteins. Two major categories of reconstruction techniques are transform methods such as weighted backprojection (WBP) and series expansion methods such as the algebraic reconstruction techniques (ART) and the simultaneous iterative reconstruction technique (SIRT). Series expansion methods aim at estimating the object to be reconstructed by a linear combination of some fixed basis functions and they typically estimate the coefficients in such an expansion by an iterative algorithm. The choice of the set of basis functions greatly influences the result of a series expansion method. It has been demonstrated repeatedly that using spherically symmetric basis functions (blobs), instead of the more traditional voxels, results in reconstructions of superior quality, provided that the free parameters that occur in the definition of the family of blobs are appropriately tuned. In this chapter, it is demonstrated that, with the recommended data-processing steps performed on the projection images prior to reconstruction, series expansion methods such as ART (with its free parameters appropriately tuned) will provide 3D reconstructions of viruses from tomographic tilt series that allow reliable quantification of the surface proteins and that the same is not achieved using WBP.
KeywordsManifold Carbohydrate Influenza Expense Macromolecule
The work presented here is currently supported by the National Science Foundation award number DMS-1114901. The authors are grateful to Joachim Frank, Carlos Óscar Sanchez Sorzano, José-María Carazo, and especially Hstau Liao for their advice and help with producing filtered WBP reconstructions.
- 2.Bucher DJ, Kharitonenkov IG, Zakomirdin J, Grigoriev VB, Klimenko SM, Davis JF(1980) Incorporation of influenza virus M-protein into liposomes. J Virol 36:586–590Google Scholar
- 3.Burmeister WP, Ruigrok RW, Cusack S (1992) The 2.2 Å resolution crystal structure of influenza B neuraminidase and its complex with sialic acid. EMBO J 11:49–56Google Scholar
- 5.Carazo JM, Herman GT, Sorzano COS, Marabini R (2006) Algorithms for thee-dimensional reconstruction from the imperfect projection data provided by electron microscopy. In: Frank J (ed) Electron tomography: Methods for three-dimensional visualization of structures in the cell, 2nd edn. Springer, New York, pp 217–244CrossRefGoogle Scholar
- 7.DuBois RM, Zaraket H, Reddivari M, Heath RJ, White SW, Russell CJ (2011) Acid stability of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity. PLoS Pathog 7:e1002,398Google Scholar
- 9.Fidler DP (2010) Negotiating equitable access to influenza vaccines: Global health diplomacy and the controversies surrounding avian influenza H5N1 and pandemic influenza H1N1. PLoS Med 7:e1000,247Google Scholar
- 17.Harris A, Cardone G, Winkler DC, Heymann JB, Brecher M, White JM, Steven AC (2006) Influenza virus pleiomorphy characterized by cryoelectron tomography. Proc Natl Acad Sci 103:19,123–19,127Google Scholar
- 23.Marabini R, Rietzel E, Schroder R, Herman GT, Carazo JM (1997) Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: Application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection. J Struct Biol 120:363–371CrossRefGoogle Scholar
- 33.Wan X, Zhang F, Chu Q, Zhang K, FSun, Yuan B, Liu Z (2011) Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. J Struct Biol 175:277–287Google Scholar
- 34.Wang Q, Tao YJ (2010) Influenza: Molecular virology. Caister Academic Press, NorfolkGoogle Scholar