Image processing of 2D crystal images

Methods in Molecular Biology

Volumn 955, Issue , 2013, Pages 171-194

  Arheit, Marcel ^a   Castaño Díez, Daniel ^a   Thierry, Raphaël ^a   Gipson, Bryant R ^a   Zeng, Xiangyan ^a   Stahlberg, Henning ^a  

^a NONE

Author keywords

3D structure determination; Electron crystallography; Electron microscopy; Image processing; Membrane proteins

Indexed keywords

ALGORITHM; CALCULATION; CRYSTAL; CRYSTAL STRUCTURE; FOURIER TRANSFORMATION; IMAGE ANALYSIS; IMAGE PROCESSING; TWO-DIMENSIONAL IMAGING; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; CRYSTALLOGRAPHY; FOURIER ANALYSIS; METHODOLOGY;

MEMBRANE PROTEIN;

ALGORITHMS; CRYSTALLOGRAPHY; FOURIER ANALYSIS; IMAGE PROCESSING, COMPUTER-ASSISTED; MEMBRANE PROTEINS; SOFTWARE;

EID: 84876041117     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-176-9_10     Document Type: Chapter

References (38)

1. Henderson R, Unwin PN (1975) Threedimensional model of purple membrane obtained by electron microscopy. Nature 257:28–32
2. Unwin PN, Henderson R (1975) Molecular structure determination by electron microscopy of unstained crystalline specimens. J Mol Biol 94:425–440
3. Amos LA, Henderson R, Unwin PN (1982) Three-dimensional structure determination by electron microscopy of two-dimensional crystals. Prog Biophys Mol Biol 39:183–231
4. Henderson R, Baldwin JM, Downing KH, Lepault J, Zemlin F (1986) Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 Å resolution. Ultramicroscopy 19:147–178
5. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213:899–929
6. Crowther RA, Henderson R, Smith JM (1996) MRC image processing programs. J Struct Biol 116:9–16
7. Kühlbrandt W, Wang DN, Fujiyoshi Y (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature 367: 614–621
8. Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407:599–605
9. Ren G, Reddy VS, Cheng A, Melnyk P, Mitra AK (2001) Visualization of a water-selective pore by electron crystallography in vitreous ice. Proc Natl Acad Sci USA 98:1398–1403
10. Miyazawa A, Fujiyoshi Y, Unwin N (2003) Structure and gating mechanism of the acetylcholine receptor pore. Nature 424:949–955
11. Gonen T, Sliz P, Kistler J, Cheng Y, Walz T (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193–197
12. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (2005) Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438:633–638
13. Hiroaki Y, Tani K, Kamegawa A, Gyobu N, Nishikawa K, Suzuki H, Walz T, Sasaki S, Mitsuoka K, Kimura K et al (2006) Implications of the aquaporin-4 structure on array formation and cell adhesion. J Mol Biol 355: 628–639
14. Tani K, Mitsuma T, Hiroaki Y, Kamegawa A, Nishikawa K, Tanimura Y, Fujiyoshi Y (2009) Mechanism of aquaporin-4’s fast and highly selective water conduction and proton exclusion. J Mol Biol 389:694–706
15. Holm PJ, Bhakat P, Jegerschold C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, Hebert H (2006) Structural basis for detoxification and oxidative stress protection in membranes. J Mol Biol 360:934–945
16. Nogales E, Wolf SG, Downing KH (1998) Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391:199–203
17. Smith JM (1999) Ximdisp – a visualization tool to aid structure determination from electron microscope images. J Struct Biol 125: 223–228
18. Schmid MF, Dargahi R, Tam MW (1993) SPECTRA: a system for processing electron images of crystals. Ultramicroscopy 48: 251–264
19. Hardt S, Wang B, Schmid MF (1996) A brief description of I.C.E.: the integrated crystallographic environment. J Struct Biol 116:68–70
20. Philippsen A, Schenk AD, Signorell GA, Mariani V, Berneche S, Engel A (2007) Collaborative EM image processing with the IPLT image processing library and toolbox. J Struct Biol 157:28–37
21. Philippsen A, Schenk AD, Stahlberg H, Engel A (2003) Iplt – image processing library and toolkit for the electron microscopy community. J Struct Biol 144:4–12
22. Sorzano CO, Marabini R, Velazquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A (2004) XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol 148:194–204
23. Marabini R, Masegosa IM, San Martin MC, Marco S, Fernandez JJ, de la Fraga LG, Vaquerizo C, Carazo JM (1996) Xmipp an image processing package for electron microscopy. J Struct Biol 116:237–240
24. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 116:190–199
25. Heymann JB (2001) Bsoft: image and molecular processing in electron microscopy. J Struct Biol 133:156–169
26. Gipson B, Zeng X, Zhang Z, Stahlberg H (2007) 2dx – user-friendly image processing for 2D crystals. J Struct Biol 157:64–72
27. Gipson B, Zeng X, Stahlberg H (2007) 2dx_ merge: data management and merging for 2D crystal images. J Struct Biol 160:375–384
28. Scherzer O (1948) The theoretical resolution limit of the electron microscope. J Appl Phys 20:20–29
29. Smith DJ, Saxton WO, O’Keefe MA, Wood GJ, Stobbs WM (1983) The importance of beam alignment and crystal tilt in high-resolution electron microscopy. Ultramicroscopy 11: 263–281
30. Glaeser R, Downing K, DeRosier D, Chiu W, Frank J (2007) Electron crystallography of biological macromolecules. Oxford University Press, New York
31. Glaeser RM, Typke D, Tiemeijer PC, Pulokas J, Cheng A (2011) Precise beam-tilt alignment and collimation are required to minimize the phase error associated with coma in high-resolution cryo-EM. J Struct Biol 174: 1–10
32. Thon F (1971) Phase contrast electron microscopy. Academic, London
33. Philippsen A, Engel HA, Engel A (2007) The contrast-imaging function for tilted specimens. Ultramicroscopy 107:202–212
34. Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142: 334–347
35. Zeng X, Gipson B, Zheng ZY, Renault L, Stahlberg H (2007) Automatic lattice determination for two-dimensional crystal images. J Struct Biol 160:353–361
36. Kunji ER, von Gronau S, Oesterhelt D, Henderson R (2000) The three-dimensional structure of halorhodopsin to 5 Å by electron crystallography: a new unbending procedure for two-dimensional crystals by using a global reference structure. Proc Natl Acad Sci USA 97:4637–4642
37. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760–763
38. Zeng X, Stahlberg H, Grigorieff N (2007) A maximum-likelihood approach to two-dimensional crystals. J Struct Biol 160:362–374