Taking X-ray diffraction to the limit: Macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation

Annual Review of Biophysics and Biomolecular Structure

Volumn 33, Issue , 2004, Pages 157-176

  Miao, Jianwei ^a   Chapman, Henry N ^b   Kirz, Janos ^c   Sayre, David ^c   Hodgson, Keith O ^a,d  

^a SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

Diffraction microscopy; Iterative algorithms; Oversampling phasing method; Single molecule imaging; X ray free electron lasers

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ANALYTIC METHOD; CELL ORGANELLE; CELL STRUCTURE; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; ESCHERICHIA COLI; IMAGE DISPLAY; LASER; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RADIATION INJURY; REVIEW; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS; SYNCHROTRON RADIATION; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ALGORITHMS; CELLS; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; PROTEINS; SIGNAL PROCESSING, COMPUTER-ASSISTED; X-RAY DIFFRACTION;

ESCHERICHIA COLI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 3042590313     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.33.110502.140405     Document Type: Review

References (79)

1. Argos P, Rossmann MG. 1980. Molecular replacement method. In Theory and Practice of Direct Methods in Crystallography, ed. MFC Ladd, RA Palmer, pp. 361-417. New York: Plenum
2. Barakat R, Newsam G. 1984. Necessary conditions for a unique solution to two-dimensional phase recover. J. Math. Phys. 25:3190-93
3. Barletta WA, Winick H. 2003. Introduction to special section on future light sources. Nucl. Instr. Methods A 500:1-10
4. Bates RHT. 1982. Fourier phase problems are uniquely soluble in more than one dimension. I. Underlying theory. Optik 61:247-62
5. Baumeister W, Grimm R, Walz J. 1999. Electron tomography of molecules and cells. Trends Cell Biol. 9:81-85
6. Beetz T, Jacobsen C. 2002. Soft X-ray radiation damage studies in PMMA using a cryo-STXM. J. Synchrotron Radiat. 10:280-83
7. Beetz T, Jacobsen C, Kao CC, Kirz J, Mentes O, et al. 2003. Development of novel apparatus for experiments in soft X-ray diffraction imaging and diffraction tomography. J. Phys. IV Fr. 104:27-30
8. Bonifacio R, Pellegrini C, Narducci LM. 1984. Collective instabilities and high gain regime in a free-electron laser. Opt. Commun. 50:373-78
9. Bottcher B, Wynne SA, Crowther RA. 1997. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386:88-91
10. Bricogne G. 1974. Geometric sources of redundancy in intensity data and their use for phase determination. Acta Crystallogr. A 30:395-405
11. Bruck YM, Sodin LG. 1979. On the ambiguity of the image reconstruction problem. Opt. Commun. 30:304-8
12. Cornacchia M, Arthur J, Bentson L, Carr R, Emma P, et al. 2001. Sub-picosecond photon pulse facility for SLAC. SLAC-PUB-8950
13. Crowther RA. 1969. The use of non-crystallographic symmetry for phase determination. Acta Crystallogr. B 25:2571-80
14. Crowther RA. 1971. Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos. Trans. R. Soc. London Ser. B. 261:221-30
15. Elser V. 2003. Phase retrieval by iterated projections. J. Opt. Soc. Am. A 20:40-55
16. Fienup JR. 1978. Reconstruction of an object from the modulus of its Fourier transform. Opt. Lett. 3:27-29
17. Fienup JR. 1987. Reconstruction of a complex-valued object from the modulus of its Fourier transform using a support constraint. J. Opt. Soc. Am. A 4:118-23
18. Frank J. 2002. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31:303-19
19. Gerchberg RW, Saxton WO. 1972. A practical algorithm for the determination of phase from image and diffraction plane pictures. Optik 35:237-46
20. Giacovazzo C. 1998. Direct Phasing in Crystallography. New York: Oxford Univ. Press
21. Green DW, Ingram VM, Perutz MF. 1954. The structure of haemoglobin. IV. Sign determination by the isomorphous replacement method. Proc. R. Soc. London Ser. A 255:287-307
22. Gruner SM, Tigner M. 2001. Study for a proposed Phase I energy recovery linac (ERL) synchrotron light source at Cornell University. CHESS Tech. MEMO 01-003 and JLAB-ACT-01-04
23. He H, Marchesini S, Howells M, Weierstall U, Chapman H, et al. 2003. Inversion of X-ray diffuse scattering to images using prepared objects. Phys. Rev. B 67:174114
24. Henderson R. 1990. Cryoprotection of protein crystals against radiation damage in electron and X-ray diffraction. Proc. R. Soc. London Sci. Ser. B 241:6-8
25. Henderson R. 1995. The potential and limitations for neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys. 28:171-93
26. Hendrickson WA, Smith JL, Sheriff S. 1985. Direct phase determination based on anomalous scattering. Methods Enzymol. 115:41-55
27. Henke BL, Gullikson EM, Davis JC. 1993. X-ray interactions: photoabsorption, scattering, transmission, and reflection at E = 50-30000 eV, Z = 1-92. At. Data Nucl. Data Tables 54:181-342
28. Huldt G, Szöke A, Hajdu J. 2003. Diffraction imaging of single particles and biomolecules. J. Struct. Biol. 144:219-27
29. Johnson LN, Blundell TL. 1999. Introductory overview. J. Synchrotron Radiat. 6:813-15
30. Jurek Z, Faigel G, Tegze M. 2003. Dynamics in a cluster under the influence of intense femtosecond hard X-ray pulses. http://arxiv.org/abs/ physics/0306102
31. Kirz J, Jacobsen C, Howells M. 1995. Soft X-ray microscopes and their biological applications. Q. Rev. Biophys. 28:33-130
32. Larsen JJ, Hald K, Bjerre N, Stapelfeldt H, Seideman T. 2000. Three-dimensional alignment of molecules using elliptically polarized laser fields. Phys. Rev. Lett. 85: 2470-73
33. Lima E, Shapiro D, Kirz J, Sayre D. 2003. Algorithmic image reconstruction using iterative phase retrieval schema. J. Phys. IV Fr. 104:631-34
34. London RA, Rosen MD, Trebes JE. 1989. Wavelength choice for soft X-ray laser holography of biological samples. Appl. Opt. 28:3397-404
35. Madey JM. 1971. Stimulated emission of Bremsstrahlung in a periodic magnetic field. J. Appl. Phys. 42:1906
36. Marchesini S, Chapman HN, Hau-Riege SP, London RA, Szöke A, et al. 2003. Coherent X-ray diffractive imaging: applications and limitations. Opt. Exp. 11:2344-53
37. Marchesini S, He H, Chapman HN, Hau-Riege SP, Noy A, et al. 2003. X-ray imaging without lenses. Phys. Rev. B. In press
38. Maser J, Osanna A, Wang Y, Jacobsen C, Kirz J, et al. 2000. Soft X-ray microscopy with a cryo STXM. I. Instrumentation, imaging, and spectroscopy J. Microsc. 197:68-79
39. McGuire EJ. 1969. K-shell Auger transition rates and fluorescence yields for elements Be-Ar. Phys. Rev. 185:1-6
40. McIntosh JR. 2001. Electron microscopy of cells: a new beginning for a new century. J. Cell Biol. 153:25-32
41. Miao J, Amonette JE, Nishino Y, Ishikawa T, Hodgson KO. 2003. Direct determination of the absolute electron density of nanostructured and disordered materials at sub-10-nm resolution. Phys. Rev. B 68:012201
42. Miao J, Charalambous P, Kirz J, Sayre D. 1999. Extending the methodology of X-ray crystallography to allow imaging of micrometer-sized non-crystalline specimens. Nature 400:342-44
43. Miao J, Hodgson KO, Ishikawa T, Larabell CA, LeGros MA, Nishino Y. 2003. Imaging whole Escherichia coli bacteria by using single-particle X-ray diffraction. Proc. Natl. Acad. Sci. USA 100:110-12
44. Miao J, Hodgson KO, Sayre D. 2001. An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images. Proc. Natl. Acad. Sci. USA 98:6641-45
45. Miao J, Ishikawa T, Anderson EH, Hodgson KO. 2003. Phase retrieval of diffraction patterns from non-crystalline samples by using the oversampling method. Phys. Rev. B 67:174104
46. Miao J, Ishikawa T, Johnson B, Anderson EH, Lai B, Hodgson KO. 2002. High resolution three-dimensional X-ray diffraction microscopy. Phys. Rev. Lett. 89:088303
47. Miao J, Kirz J, Sayre D. 2000. The oversampling phasing method. Acta Crystallogr. D 56:1312-15
48. Miao J, Sayre D. 2000. On possible extensions of X-ray crystallography through diffraction-pattern oversampling. Acta Crystallogr. A 56:596-605
49. Miao J, Sayre D, Chapman HN. 1998. Phase retrieval from the magnitude of the Fourier transforms of non-periodic objects. J. Opt. Soc. Am. A 15:1662-69
50. Millane RP. 1996. Multidimensional phase problems. J. Opt. Soc. Am. A 13:725-34
51. Mozumder A. 1969. Charged particle tracks and their structure. In Advances in Radiation Chemistry, ed. M Burton and JL Magee, pp. 1-102. New York: Wiley
52. Neutze R, Wouts R, Spoel D, Weckert E, Hajdu J. 2000. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406:752-57
53. Pellegrini C. 1992. A 4 to 0.1 FEL based on the SLAC Linac. In Proceedings of the Workshop on 4th Generation Light Sources, ed. M Cornacchia, H Winick, pp. 376-84. Stanford, CA: SLAC
54. Phillips JC, Wlodawer A, Goodfellow JM, Watenpaugh KD, Sieker LC, et al. 1977. Applications of synchrotron radiation to protein crystallography. II. Anomalous scattering, absolute intensity, and polarization. Acta Crystallogr. A 33:445-55
55. Phillips JC, Wlodawer A, Yevitz MM, Hodgson KO. 1976. Applications of synchrotron radiation to protein crystallography: preliminary results. Proc. Natl. Acad. Sci. USA 73:128-32
56. Robinson IK, Vartanyants IA, Williams GJ, Pfeifer MA, Pitney JA. 2001. Reconstruction of the shapes of gold nanocrystals using coherent X-ray diffraction. Phys. Rev. Lett. 87:195505
57. Rossmann MG, Blow DM. 1963. Determination of phases by the conditions of non-crystallographic symmetry. Acta Crystallogr. 16:39-45
58. Sayre D. 1952. Implications of a theorem due to Shannon. Acta Crystallogr. 5:843
59. Sayre D. 1980. Prospects for long-wavelength X-ray microscopy and diffraction. In Imaging Processes and Coherence in Physics. Springer Lecture Notes in Physics, Vol. 112, ed. M Schlenker, M Fink, JP Goedgebuer, C Malgrange, JC Vienot, RH Wade, pp. 229-35. Berlin: Springer
60. Sayre D. 1991. Note on "superlarge" structures and their phase problem. In Direct Methods of Solving Crystal Structures, ed. H Schenck, pp. 353-56. New York: Plenum
61. Sayre D, Chapman H. 1995. X-ray microscopy. Acta Crystallogr. A 51:237-52
62. Sayre D, Chapman HN, Miao J. 1998. On the extendibility of X-ray crystallography to noncrystals. Acta Crystallogr. A 54:233-39
63. Sayre D, Kirz J, Feder R, Kim DM, Spiller E. 1977. Transmission microscopy of unmodified biological materials: comparative radiation dosages with electrons and ultrasoft X-ray photons. Ultramicroscopy 2:337-41
64. Schneider G. 1998. Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast. Ultramicroscopy 75:85-104
65. Solem J, Baldwin GC. 1982. Microholography of living organisms. Science 218:229-35
66. Spence JCH, Howells M, Marks LD, Miao J. 2001. Lensless imaging: a workshop on new approaches to the phase problem for non-periodic objects. Ultramicroscopy 90:1-6
67. Spence JCH, Wu JS, Giacovazzo C, Carrozzini B, Cascarano GL, Padmore HA. 2003. Solving non-periodic structures using direct methods: phasing diffuse scattering. Acta Crystallogr. A 59:255-61
68. Stroud RM, Agard DA. 1979. Structure determination of asymmetric membrane profiles using an iterative Fourier method. Biophys. J. 25:495-512
69. Tigner M. 1965. A possible apparatus for electron clashing-beam experiments. Nuovo Cimento 37:1228-31
70. Vartanyants IA, Robinson IK. 2001. Partial coherence effects on the imaging of small crystals using coherent X-ray diffraction. J. Phys. Condens. Matter 13:10593-611
71. Wang BC. 1985. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115:90-112
72. Watenpaugh K, Smith J, eds. 1991. Report of the Biological Synchrotron Users Organization (Biosync). http://biosync.sdsc. edu/
73. Weierstall U, Chen Q, Spence JCH, Howells MR, Isaacson M, Panepucci RR. 2001. Image reconstruction from electron and X-ray diffraction patterns using iterative algorithms: experiment and simulation. Ultramicroscopy 90:171-95
74. Williams GJ, Pfeifer MA, Vartanyants IA, Robinson IK. 2003. Three-dimensional imaging of microstructure in Au nanocrystals. Phys. Rev. Lett. 90:175501
75. Woolfson M, Fan HF. 1995. Physical and Non-physical Methods of Solving Crystal Structures. Cambridge: Cambridge Univ. Press
76. Yun W, Kirz J, Sayre D. 1987. Observation of the soft X-ray diffraction pattern of a single diatom. Acta Crystallogr. A 43:131-33
77. Ziaja B, Szöke A, Hajdu J. 2002. Electron cascades produced by photoelectrons in diamond. http://arxiv.org/abs/cond-mat/ 0208515
78. Ziaja B, Szöke A, van der Spoel D, Hajdu J. 2002. Space-time evolution of electron cascades in diamond. Phys. Rev. B 66:024116
79. Ziaja B, van der Spoel D, Szöke A, Hajdu J. 2001. Auger-electron cascades in diamond and amorphous carbon. Phys. Rev. B 64:214104