Frealix: Model-based refinement of helical filament structures from electron micrographs

Journal of Structural Biology

Volumn 186, Issue 2, 2014, Pages 234-244

  Rohou, Alexis ^a,b   Grigorieff, Nikolaus ^a,b  

^a BRANDEIS UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Amyloid; A ; Cryo EM; Curvature; Filament; Helical; Structure; WLC

Indexed keywords

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN[1-40]; PROTEIN;

ALGORITHM; AQUEOUS SOLUTION; ARTICLE; COMPUTER PROGRAM; ELECTRON MICROGRAPHY; ELECTRON MICROSCOPY; FIBER; FILM; NONHUMAN; PRIORITY JOURNAL; PROTEIN FILAMENT; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THIN FILAMENT; TOBACCO MOSAIC VIRUS; CHEMISTRY; PROCEDURES; ULTRASTRUCTURE;

TOBACCO MOSAIC VIRUS;

ALGORITHMS; AMYLOID BETA-PEPTIDES; MICROSCOPY, ELECTRON; PROTEINS; SOFTWARE; TOBACCO MOSAIC VIRUS;

EID: 84899983054     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2014.03.012     Document Type: Article

References (50)

1. Alushin G.M., Ramey V.H., Pasqualato S., Ball D.a., Grigorieff N., Musacchio A., Nogales E. The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Nature 2010, 467:805-810.
2. Behrmann E., Tao G., Stokes D.L., Egelman E.H., Raunser S., Penczek P.A. Real-space processing of helical filaments in SPARX. J. Struct. Biol. 2012, 177:302-313.
3. Bicek A.D., Tüzel E., Demtchouk A., Uppalapati M., Hancock W.O., Kroll D.M., Odde D.J. Anterograde microtubule transport drives microtubule bending in LLC-PK1 epithelial cells. Mol. Biol. Cell 2009, 20:2943-2953.
4. Bluemke D.A., Carragher B., Josephs R. The reconstruction of helical particles with variable pitch. Ultramicroscopy 1988, 26:255-270.
5. Boal D.H. Mechanics of the Cell 2002, Cambridge University Press, Cambridge, New York.
6. Brest J., Greiner S., Boskovic B., Mernik M., Zumer V. Self-adapting control parameters in differential evolution: a comparative study on numerical benchmark problems. IEEE Trans. Evol. Comput. 2006, 10:646-657.
7. Brilot A.F., Chen J.Z., Cheng A., Pan J., Harrison S.C., Potter C.S., Carragher B., Henderson R., Grigorieff N. Beam-induced motion of vitrified specimen on holey carbon film. J. Struct. Biol. 2012, 177:630-637.
8. Chen J.Z., Settembre E.C., Aoki S.T., Zhang X., Bellamy aR., Dormitzer P.R., Harrison S.C., Grigorieff N. Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc. Natl. Acad. Sci. USA 2009, 106:10644-10648.
9. Craven P., Wahba G. Smoothing noisy data with spline functions. Numer. Math. 1978, 31:377-403.
10. De Rosier D., Klug A. Reconstruction of three dimensional structures from electron micrographs. Nature 1968, 217:130-134.
11. DeRosier D.J. Electron crystallography of helical structures. Electron Crystallography of Biological Macromolecules 2007, 304-342. Oxford University Press, USA, New York. R.M. Glaeser, K.H. Downing, D. DeRosier, W. Chiu, J. Frank (Eds.).
12. Desfosses A., Ciuffa R., Gutsche I., Sachse C. SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs. J. Struct. Biol. 2013.
13. Egelman E.H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 2000, 85:225-234.
14. Falvo M.R., Washburn S., Superfine R., Finch M., Brooks F.P., Chi V., Taylor R.M. Manipulation of individual viruses: friction and mechanical properties. Biophys. J. 1997, 72:1396-1403.
15. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies 2006, Oxford University Press, USA, New York. 2nd ed.
16. Frigo M., Johnson S.G. The design and implementation of FFTW3. Proc. IEEE 2005, 93:216-231.
17. Fujii T., Iwane A.H., Yanagida T., Namba K. Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature 2010, 467:724-728.
18. Galassi M., Davies J., Theiler J., Gough B., Jungman G., Booth M., Rossi F. GNU Scientific Library Reference Manual, Distribution 2003, Network Theory Ltd.
19. Galkin V.E., Orlova A., Egelman E.H. Actin filaments as tension sensors. Curr. Biol. 2012, 22:R96-R101.
20. Grigorieff N. FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 2007, 157:117-125.
21. Harwell Numerical Library, 1979.
22. Howard J. Mechanics of Motor Proteins & the Cytoskeleton 2001, Sinauer Associates.
23. Jackson J.I., Meyer C.H., Nishimura D.G., Macovski A. Selection of a convolution function for Fourier inversion using gridding. IEEE Trans. Med. Imaging 1991, 10:473-478.
24. Knott G.D. Interpolating cubic splines 2000, Springer.
25. Kornyshev A., Lee D., Leikin S., Wynveen A. Structure and interactions of biological helices. Rev. Mod. Phys. 2007, 79:943-996.
26. Kratky O., Porod G. Röntgenuntersuchung gelöster Fadenmoleküle. Recl. des Trav. Chim. des Pays-Bas 1949, 68:1106-1122.
27. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996, 116:71-76.
28. Kreyszig E. Differential Geometry 1959, Dover.
29. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
30. Meinhardt J., Sachse C., Hortschansky P., Grigorieff N., Fändrich M. Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils. J. Mol. Biol. 2009, 386:869-877.
31. Mindell J.A., Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 2003, 142:334-347.
32. Nelder J.A., Mead R. A simplex method for function minimization. Comput. J. 1964, 7:308-313.
33. Poelert S.L., Zadpoor A.A. Analytical and numerical methods for capturing the thermal fluctuations of semiflexible polymers. Macromol. Theory Simulations 2012, 21:357-371.
34. Rappaport, S.M., Medalion, S., Rabin, Y., 2008. Curvature Distribution of Worm-like Chains in Two and Three Dimensions. arXiv:08013183.
35. Roseman A.M. Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 2003, 94:225-236.
36. Sachse, C., 2007. High-resolution electron cryo-microscopy of amyloid fibrils. Friederich-Schiller-Universitat Jena.
37. Sachse C., Chen J.Z., Coureux P.-D., Stroupe M.E., Fändrich M., Grigorieff N. High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus. J. Mol. Biol. 2007, 371:812-835.
38. Sachse C., Fändrich M., Grigorieff N. Paired β-sheet structure of an Aβ(1-40) amyloid fibril revealed by electron microscopy. Proc. Natl. Acad. Sci. 2008, 105:7462-7466.
39. Sachse C., Grigorieff N., Fändrich M. Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy. Angew. Chem. Int. Ed. Engl. 2010, 49:1321-1323.
40. Schmatulla A., Maghelli N., Marti O. Micromechanical properties of tobacco mosaic viruses. J. Microsc. 2007, 225:264-268.
41. Schmidt M., Sachse C., Richter W., Xu C., Fändrich M., Grigorieff N. Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures. Proc. Natl. Acad. Sci. USA 2009, 106:19813-19818.
42. Sigworth F.J. A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 1998, 122:328-339.
43. Smith M.B., Li H., Shen T., Huang X., Yusuf E., Vavylonis D. Segmentation and tracking of cytoskeletal filaments using open active contours. Cytoskeleton (Hoboken) 2010, 67:693-705.
44. Stewart A., Grigorieff N. Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 2004, 102:67-84.
45. Storn R., Price K. Minimizing the real functions of the ICEC'96 contest by differential evolution. IEEE Conf. Evol. Comput. 1996, 842-844.
46. Turner M.S., Briehl R.W., Wang J.C., Ferrone F.A., Josephs R. Anisotropy in sickle hemoglobin fibers from variations in bending and twist. J. Mol. Biol. 2006, 357:1422-1427.
47. Vale R.D., Coppin C.M., Malik F., Kull F.J., Milligan R.A. Tubulin GTP hydrolysis influences the structure, mechanical properties, and kinesin-driven transport of microtubules. J. Biol. Chem. 1994, 269:23769-23775.
48. Williams, T., Kelley, C., 2012. gnuplot 4.6, An Interactive Plotting Program.
49. Yang Q., Karpikov A., Toomre D., Duncan J.S. 3-D reconstruction of microtubules from multi-angle total internal reflection fluorescence microscopy using Bayesian framework. IEEE Trans. Image Process. 2011, 20:2248-2259.
50. Zhao Y., Ge Z., Fang J. Elastic modulus of viral nanotubes. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 2008, 78:031914.