Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps

Journal of Structural Biology - Tập 181 - Trang 195-206 - 2013
Qiu Wang1, Tsutomu Matsui2, Tatiana Domitrovic3, Yili Zheng4, Peter C. Doerschuk5, John E. Johnson3
1Electrical and Computer Engineering, Cornell University, NY, USA
2Department of Molecular Biology, The Scripps Research Institute and Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
3Department of Molecular Biology, The Scripps Research Institute, CA, USA
4Electrical and Computer Engineering, Purdue University, IN, USA
5Biomedical Engineering and Electrical and Computer Engineering, Cornell University, NY, USA

Tài liệu tham khảo

Baker, 2010, Cryo-EM of macromolecular assemblies at near-atomic resolution, Nat. Protoc., 5, 1697, 10.1038/nprot.2010.126 Bothner, 2005, Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex, Virology, 334, 17, 10.1016/j.virol.2005.01.017 Doerschuk, 2000, Ab initio reconstruction and experimental design for cryo electron microscopy, IEEE Trans. Info. Theory, 46, 1714, 10.1109/18.857786 Domitrovic, Tatiana, Matsui, Tsutomu, Johnson, John E., 2012. Dissecting quasi-equivalence in non-enveloped viruses: membrane disruption is promoted by lytic peptides released from subunit pentamers, not hexamers. J. Virol. (VI Accepts, published online ahead of print on 3 July 2012). http://dx.doi.org/10.1128/JVI.01089-12. EM Data Bank. Available at: <http://www.emdatabank.org/>. Erickson, 1973, The Fourier transform of an electron micrograph—first order and second order theory of image formation, vol. 5, 163 Fuller, 1996, Three-dimensional reconstruction of icosahedral particles – the uncommon line, J. Struct. Biol., 116, 48, 10.1006/jsbi.1996.0009 Helgstrand, 2004, The refined structure of Nudaurelia capensis ω Virus reveals control elements for a T=4 capsid maturation, Virology, 318, 192, 10.1016/j.virol.2003.08.045 Jensen, Grant J. (Ed.), 2010a. Cryo-EM, Part A: Sample Preparation and Data Collection, Methods in Enzymology, vol. 481. Elsevier Inc. Jensen, Grant J. (Ed.), 2010b. Cryo-EM, Part B: 3-D Reconstruction, Methods in Enzymology, vol. 482. Elsevier Inc. Jensen, Grant J. (Ed.), 2010c. Cryo-EM, Part C: Analyses, Interpretation, and Case Studies, Methods in Enzymology, vol. 483. Elsevier Inc. Lee, 2007, Exact reduced-complexity maximum likelihood reconstruction of multiple 3-D objects from unlabeled unoriented 2-D projections and electron microscopy of viruses, IEEE Trans. Image Proc., 16, 2865, 10.1109/TIP.2007.908298 Lee, 2011, Multi-class maximum likelihood symmetry determination and motif reconstruction of 3-D helical objects from projection images for electron microscopy, IEEE Trans. Image Proc., 20, 1962, 10.1109/TIP.2011.2107329 Lehmann, 1998 Lepault, 1984, Projected structure of unstained, frozen-hydrated T-layer of Bacillus brevis, EMBO J., 3, 101, 10.1002/j.1460-2075.1984.tb01768.x Liu, 2010, Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks, Science, 329, 1038, 10.1126/science.1187433 Mathworks. Available at: <http://www.mathworks.com/>. Matsui, 2010, Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus, Proc. Natl. Acad. Sci. USA, 107, 14111, 10.1073/pnas.1004221107 Munshi, 1996, The 2.8Å structure of a T=4 animal virus and its implications for membrane translocation of RNA, J. Mol. Biol., 261, 1, 10.1006/jmbi.1996.0437 Octave. Available at: <http://www.gnu.org/software/octave/, http://octave.sourceforge.net/>. Penczek, 2006, Estimation of variance in single-particle reconstruction using the bootstrap technique, J. Struct. Biol., 154, 168, 10.1016/j.jsb.2006.01.003 Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Provencher, 1988, Three-dimensional reconstructions from electron micrographs of disordered specimens: I. Method, Ultramicroscopy, 25, 209, 10.1016/0304-3991(88)90016-2 Prust, 2009, J. Struct. Biol., 167, 185, 10.1016/j.jsb.2009.04.013 Redner, 1984, Mixture densities, maximum likelihood and the EM algorithm, SIAM Rev., 26, 195, 10.1137/1026034 Scheres, 2010, Classification of structural heterogeneity by maximum-likelihood methods, vol. 482, 295 Scheres, 2012, A Bayesian view on cryo-EM structure determination, J. Mol. Biol., 415, 406, 10.1016/j.jmb.2011.11.010 Scheres, 2007, Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization, Nat. Methods, 4, 27, 10.1038/nmeth992 Sigworth, 1998, A maximum-likelihood approach to single-particle image refinement, J. Struct. Biol., 122, 328, 10.1006/jsbi.1998.4014 Sigworth, 2010, An introduction to maximum-likelihood methods in cryo-EM, vol. 482, 263 Taylor, 2002, Large-scale, pH-dependent, quaternary structure changes in an RNA virus capsid are reversible in the absence of subunit autoproteolysis, J. Virol., 76, 9972, 10.1128/JVI.76.19.9972-9980.2002 Toyoshima, 1988, Contrast transfer for frozen-hydrated specimens: determination from pairs of defocused images, Ultramicroscopy, 25, 279, 10.1016/0304-3991(88)90003-4 VIPERdb. Available at: <http://viperdb.scripps.edu/>. Vogel, 1988, Three-dimensional reconstructions from electron micrographs of disordered specimens: II. Implementation and results, Ultramicroscopy, 25, 223, 10.1016/0304-3991(88)90017-4 Vogel, 1986, Envelope structure of Semliki Forest virus reconstructed from cryo-electron micrographs, Nature, 320, 533, 10.1038/320533a0 Yin, 2003, A statistical approach to computer processing of cryo electron microscope images: virion classification and 3-D reconstruction, J. Struct. Biol., 144, 24, 10.1016/j.jsb.2003.09.023 Zhang, 2008, Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction, Proc. Natl. Acad. Sci. USA, 105, 1867, 10.1073/pnas.0711623105 Zheng, 2000, Explicit computation of orthonormal symmetrized harmonics with application to the identity representation of the icosahedral group, SIAM J. Math. Anal., 32, 538, 10.1137/S0036141098341770