Three dimensional electron microscopy and in silico tools for macromolecular structure determination

EXCLI Journal

Volumn 12, Issue , 2013, Pages 335-346

  Borkotoky, Subhomoi ^a   Meena, Chetan Kumar ^a   Khan, Mohammad Wahab ^a   Murali, Ayaluru ^a  

^a PONDICHERRY UNIVERSITY   (India)

Author keywords

cryo EM; CTF correction; Segmentation; Single particle analysis

Indexed keywords

LOW DENSITY LIPOPROTEIN; PROTEASOME;

ANALYTIC METHOD; COMPUTER ANALYSIS; COMPUTER PROGRAM; CRYO NEGATIVE STAINING; CRYOELECTRON MICROSCOPY; MACROMOLECULE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PLANT VIRUS; PROTEIN STRUCTURE; REVIEW; SINGLE PARTICLE ANALYSIS; STAINING; STRUCTURE ANALYSIS; THREE DIMENSIONAL TRANSMISSION ELECTRON MICROSCOPY; TRANSMISSION ELECTRON MICROSCOPY; TURNIP CRINKLE VIRUS; VIRUS MORPHOLOGY; X RAY CRYSTALLOGRAPHY;

EID: 84876727011     PISSN: None     EISSN: 16112156     Source Type: Journal    
DOI: None     Document Type: Review

References (78)

1. Abeysinghe SS, Baker M, Chiu W, Ju T. Segmentation-free skeletonization of grayscale volumes for shape understanding. IEEE International Conference on Shape Modeling and Applications 2008;63-71.
2. Adrian M, Dubochet J, Lepault J, McDowall AW. Cryo-electron microscopy of viruses. Nature 1984;308:32-36.
3. Adrian M, Dubochet J, Fuller SD, Harris JR. Cryo-negative staining. Micron 1998; 29:145-160.
4. Baker ML, Yu Z, Chiu W, Bajaj C. Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol 2006;156:432-441.
5. Baker ML, Ju T, Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure 2007;15:7-19.
6. Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP et al. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol 2011;174:360-373.
7. Bakker SE, Ford RJ, Barker AM, Robottom J, Saunders K, Pearson AR et al. Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus. J Mol Biol 2012; 417:65-78.
8. Beck F, Unverdorben P, Bohn S, Schweitzer A, Pfeifer G, Sakata E et al. Near-atomic resolution structural model of the yeast 26S proteasome. Proc Natl Acad Sci USA 2012;109:14870-5.
9. Berman HM, Kleywegt GJ, Nakamura H, Markley JL. The future of the protein data bank. Biopolymers 2013;99:218-222
10. Beucher S, Lantuejoul C. Use of watersheds in contour detection. In: Proceedings of the International Workshop on Image Processing, Real-Time Edge and Motion Detection/Estimation (pp 17-21). Rennes, France, 1979.
11. Booth CR, Jiang W, Baker ML, Zhou ZH, Ludtke SJ, Chiu W. A 9 angstrom single particle reconstruction from CCD captured images on a 200 kV electron cryo-microscope. J Struct Biol 2004;147:116-127.
12. Bremer A, Henn C, Engel A, Baumeister W, Aebi U. Has negative staining still a place in biomacromolecular electron microscopy? Ultramicroscopy 1992;46:85-111.
13. Brenner S, Horne RW. A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta 1959;34:103-110.
14. Cong Y, Ludtke SJ. Single particle analysis at high resolution. Methods Enzymol 2010; 482:211-235.
15. Daniel MC, Tsvetkova IB, Quinkert ZT, Murali A, De M, Rotello VM et al. Role of surface charge density in nanoparticle-templated assembly of bromovirus protein cages. ACS Nano 2010;4:3853-860.
16. De Carlo S, Harris JR. Negative staining and cryo-negative staining of macro-molecules and viruses for TEM. Micron 2011;42:117-131.
17. De Carlo S, El-Bez C, Alvarez-Rúa C, Borge J, Dubochet J. Cryo-negative staining reduces electron-beam sensitivity of vitrified biologi-cal particles. J Struct Biol 2002;138:216-226.
18. Dubochet J, Lepault J, Freeman R, Berri-man JA, Homo J-C. Electron microscopy of frozen water and aqueous solutions. J Mi-crosc 1982;128:219-237. doi: 10.1111/j.1365-2818.1982.tb04625.x (electronically published in 2011).
19. Fernandez JJ, Luque D, Caston JR, Carrascosa JL. Sharpening high resolution information in single particle electron cryo-microscopy. J Struct Biol 2008;164:170-175.
20. Frank J. Single-particle imaging of macro-molecules by cryo-electron microscopy. Annu Rev Biophys Biomol Stuct 2002;31: 303-319.
21. Frank J. Single-particle reconstruction of biological macromolecules in electron microscopy - 30 years. Quart Rev Biophys 2009;42:139-158.
22. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 1996;116:190-199.
23. Garzon JI, Kovacs J, Abagyan R, Chacon P. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 2007;23:427-433.
24. Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. J Struct Biol 2007;157:281-287.
25. Grigorieff N. FREALIGN: high-resolution refinement of single particle structures. J Struct Biol 2007;157:117-125.
26. Hainfeld JF, Safer D, Wall JS, Simon M, Lin B, Powell RD. Methylamine vanadate (NanoVan) negative stain. In: Proceedings of the 52nd Annual Meeting, Microscopy Society of America (pp 132-2). San Francisco, CA: San Francisco Press, 1994.
27. Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA et al. SPARX, a new environment for Cryo-EM image processing. J Struct Biol 2007; 157:47-55.
28. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-8, 27-28.
29. Jaffe JS, Glaeser RM. Preparation of frozen-hydrated specimens for high resolution electron microscopy. Ultramicroscopy 1984;13:373-377.
30. Jawhari A, Uhring M, De Carlo S, Crucifix C, Tocchini-Valentini G, Moras D et al. Structure and oligomeric state of human transcription factor TFIIE. EMBO Rep 2006;7:500-505.
31. Jiang W, Ludtke SJ. Electron cryo-micro-scopy of single particles at sub-nanometer resolution. Curr Opin Struct Biol 2005;15: 571-577.
32. Jiang W, Baker ML, Ludtke SJ, Chiu W. Bridging the information gap: Computational tools for intermediate resolution structure interpretation. J Mol Biol 2001; 308:1033-44.
33. Jonic S, Sorzano CO, Boisset N. Comparison of single-particle analysis and electron tomography approaches: an overview. J Microsc 2008;232:562-579.
34. Kassube SA, Fang J, Grob P, Yakovchuk P, Goodrich JA, Nogales E. Structural insights into Transcriptional Repression by non-coding RNAs that bind to Human Pol II. J Mol Biol 2012, Sep 4. pii: S0022-2836(12)00701-2. doi: 10.1016/j.jmb.2012.08.024 [Epub ahead of print].
35. Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol 1996;116:71-76.
36. Kumar V, Butcher SJ, Öörni K, Engelhardt P, Heikkonen J, Kaski K et al. Three-dimensional cryoEM reconstruction of native LDL particles to 16Å resolution at physiological body temperature. PLoS One 2011;6(5):e18841.
37. Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, Pulokas J et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol 2009;166:95-102.
38. Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P et al. Molecular architecture of the 26S proteasome holo-complex determined by an integrative approach. Proc Natl Acad Sci USA 2012; 109:1380-1387.
39. Llorca O. Introduction to 3D reconstruction of macromolecules using single particle electron microscopy. Acta Pharmacol Sin 2005;26:1153-1164.
40. Ludtke SJ, Chiu W. Focal pair merging for contrast enhancement of single particles. J Struct Biol 2003;144:73-78.
41. Ludtke SJ, Baldwin PR, Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 1999;128:82-97.
42. Ludtke SJ, Baker ML, Chen D-H, Song J-L, Chuang DT, Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 2008;16:441-448.
43. Ludwig K, Yan S, Fan H, Reutter W, Bottcher C. The 3D structure of rat DPPIV/ CD26 as obtained by cryo-TEM and single particle analysis. Biochem Biophys Res Commun 2003;304:73-77.
44. Mallick SP, Carragher B, Potter CS, Kriegman DJ. ACE: automated CTF estimation. Ultramicroscopy 2005;104:8-29.
45. Mindell JA, Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 2003;142:334-347.
46. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC et al. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605-1612.
47. Pintilie G, Chiu W. Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in Cryo-EM density maps. Bio-polymers 2012;97:742-760.
48. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol 2010;170:427-438.
49. Pruggnaller S, Mayr M, Frangakis AS. A visualization and segmentation toolbox for electron microscopy. J Struct Biol 2008; 164:161-165.
50. Roseman AM. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr D Biol Crystallogr 2000;56: 1332-1340.
51. Roseman AM. FindEM - a fast, efficient program for automatic selection of particles from electron micrographs. J Struct Biol 2004;145:91-99.
52. Rosenthal PB, Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 2003; 333:721-745.
53. Rossmann MG, Bernal R, Pletnev SV. Combining electron microscopic with X-ray crystallographic structures. J Struct Biol 2001;136:190-200.
54. Rouiller I, DeLaBarre B, May AP, Weis WI, Brunger AT, Milligan RA et al. Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle. Nat Struct Biol 2002;9: 950-957.
55. Ruprecht J, Nield J. Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction. Prog Biophys Mol Biol 2001;75:121-164.
56. Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, Schneidman-Duhovny D et al. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 2012;10:e1001244.
57. Saha M, Levitt M, Chiu W. MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. Bioinformatics 2010;26:i301-i309.
58. Schroeter JP, Bretaudiere JP. SUPRIM: easily modified image processing software. J Struct Biol 1996;116:131-137.
59. Shrive AK, Burns I, Chou HT, Stahlberg H, Armstrong PB, Greenhough TJ. Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations. J Mol Biol 2009;386:1240-1254.
60. Sorzano CO, Marabini R, Velazquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM et al. XMIPP: a new genera-tion of an open-source image processing package for electron microscopy. J Struct Biol 2004;148:194-204.
61. Sousa D, Grigorieff N. Ab initio resolution measurement for single particle structures. J Struct Biol 2007;157:201-210.
62. Spagnolo L, Rivera-Calzada A, Pearl LH, Llorca O. Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. Mol Cell 2006;22:511-519.
63. Sun J, DuFort C, Daniel MC, Murali A, Chen C, Gopinath K et al. Core-controlled polymorphism in virus-like particles. Proc Natl Acad Sci USA 2007;104:1354-1359.
64. Talmon Y, Davis HT, Scriven LE, Thomas EL. Cold-stage microscopy system for fast-frozen liquids. Rev Sci Instrum 1979;50: 698.
65. Taylor KA, Glaeser RM. Hydrophilic support films of controlled thickness and com-position. Rev Sci Instrum 1973;44: 1546-1547.
66. Thuman-Commike PA. Single particle macromolecular structure determination via electron microscopy. FEBS Lett 2001;505: 199-205.
67. Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res 2011;39:W167-70.
68. Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 2005;149:191-203.
69. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 2008;16:295-307.
70. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M. A new generation of the IMAGIC image processing system. J Struct Biol 1996;116:17-24.
71. Velazquez-Muriel JA, Sorzano CO, Scheres SH, Carazo JM. SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps. J Mol Biol 2005;345:759-771.
72. Vincent L, Soille P. Watersheds in digital spaces: an efficient algorithm based on immersion simulations. IEEE Trans Patt Anal Machine Intell 1991;13:583-98.
73. Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J Struct Biol 2002;138:123-129.
74. Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron micros-copy. J Struct Biol 2009;166:205-213.
75. Westenberger P. Avizo-3d visualization framework. Geoinformatics Conference 2008;1-11.
76. Winkler H. 3D reconstruction and processing of volumetric data in cryo-electron tomography. J Struct Biol 2007;157:126-137.
77. Wriggers W, Milligan RA, McCammon JA. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 1999; 125:185-195.
78. Yi W, Wah C, Zhou ZH. Full contrast transfer function correction in 3D cryo-EM reconstruction. IEEE Proc. of International Conference on Communications, Circuits and Systems (ICCCAS) 2004;2:960-964.