Synchrotron radiation applications to macromolecular crystallography

Current Opinion in Structural Biology

Volumn 7, Issue 5, 1997, Pages 689-696

  Moffat, Keith ^a   Ren, Zhong ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; MACROMOLECULE; PRIORITY JOURNAL; REVIEW; SYNCHROTRON; TECHNIQUE; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

EID: 0030833143     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80079-6     Document Type: Article

References (97)

1. Helliwell JR: Macromolecular crystallography with synchrotron radiation. Cambridge, UK: Cambridge University Press; 1992.
2. Chayen NE, Boggon TJ, Cassetta A, Deacon A, Gleichmann T, Habash J, Harrop SJ, Helliwell JR, Nieh YP, Peterson MR, et al. Trends and challenges in experimental macromolecular crystallography. Quart Rev Biophys. 29:1996;227-278 A thorough review with a substantial section on synchrotron-related developments. of special interest.
3. Helliwell JR. Overview of synchrotron radiation and macromolecular crystallography. Methods Enzymol. 276A:1997;203-217.
4. Ealick S, Walter R. Synchrotron beamlines for macromolecular crystallography. Curr Opin Struct Biol. 3:1993;725-736.
5. Hendrickson WA. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science. 254:1991;51-58.
6. Dauter Z, Lamzin VS, Wilson KS. Proteins at atomic resolution. Curr Opin Struct Biol. 5:1995;784-790.
7. Dauter Z. Atomic resolution protein crystal structures. Synchrotron Rad News. 10:1997;22-25.
8. Zhou L, Luo M. Crystallization and preliminary X-ray analysis of two density populations of feline calcivirus particles. Acta Crystallogr D. 51:1995;850-852.
9. Burroughs JN, Grimes JM, Mertens PP, Stuart DI. Crystallization and preliminary X-ray analysis of the core particle of bluetongue virus. Virology. 210:1995;217-220.
10. Teng T-Y, Srajer V, Moffat K. Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K. Nat Struct Biol. 1:1994;701-705.
11. Gouet P, Jouve H-M, Williams PA, Andersson I, Andreoletti P, Nussaume L, Hajdu J. Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy. Nat Struct Biol. 3:1996;951-956 The state of the art in slower time-resolved crystallography, carefully linked to optical studies. of outstanding interest.
12. Genick UK, Borgstahl GE, Ng K, Ren Z, Pradervand C, Burke PM, Srajer V, Teng T-Y, Schildkamp W, McRee DE, et al. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science. 275:1997;1471-1475 Quite fast time-resolved studies can be conducted efficiently at second-generation sources, here, the National Synchrotron Light Source. The intrinsic light-sensitivity of photoactive yellow protein is exploited to generate a light-driven reaction in the crystal, which reveals later stages in the rather complex photocycle of this protein with 10 ms time resolution. The interpretation of results is complicated by unexpected structural heterogeneity in the photostationary state. of special interest.
13. Srajer V, Teng T-Y, Ursby T, Pradervand C, Ren Z, Adachi S-I, Schildkamp W, Bourgeois D, Wulff M, Moffat K. Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography. Science. 274:1996;1726-1729 The elaborate experimental techniques developed in [15] finally yield real structure results. of outstanding interest.
14. Szebenyi DME, Arvai A, Ealick S, Laiuppa JM, Nielsen C. A system for integrated collection and analysis of crystallographic diffraction data. J Synchrotron Rad. 4:1997;128-135.
15. Bourgeois D, Ursby T, Wulff M, Pradervand C, LeGrand A, Schildkamp W, Laboure S, Srajer V, Teng T-Y, Roth M, Moffat K. Feasibility and realization of single pulse Laue diffraction on macromolecular crystals at ESRF. J Synchrotron Rad. 3:1996;65-74 Ultrarapid time-resolved crystallography poses severe experimental demands; this paper explains how they have been met. of outstanding interest.
16. Hendrickson WA, Brändén CI. Editorial. Structure. 5:(1):1997.
17. Harding MM. Recording diffraction data for structure determination for very small crystals. J Synchrotron Rad. 3:1996;250-259.
18. Balaic DX, Barnea Z, Nugent KA, Garrett RF, Varghese JN, Wilkins SW. Protein crystal diffraction patterns using a capillary-focused synchrotron X-ray beam. J Synchrotron Rad. 3:1996;289-295.
19. Hendrickson WA, Ogata CM. Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276A:1997;494-523 A recent overview and survey of the MAD phasing technique. It contains an explicit deduction of MAD phasing theory and lists of commonly accessible absorption edges, MAD beamline parameters, and structures determined by MAD phasing. of outstanding interest.
20. Pappa HS, Stewart AE, McDonald NQ. Incorporating anomalous scattering centers into macromolecules. Curr Opin Struct Biol. 6:1996;611-616 A review on incorporation of heavy atoms into macromolecules using chemical modification, protein engineering and in vivo labeling. of special interest.
21. Guss JM, Merritt EA, Phizackerley, R.P, Freeman HC. The structure of a phytocyanin, the basic blue protein from cucumber, refined at 1.8 Å resolution. J Mol Biol. 262:1996;686-705.
22. Walter RL, Ealick SE, Friedman AM, Blake RC II, Proctor P, Shoham M. Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability. J Mol Biol. 263:1996;730-751.
23. 1 complex determined by MAD phasing at 1.5 Å resolution. Structure. 4:1996;567-579.
24. Concha NO, Rasmussen BA, Bush K, Herzberg O. Crystal structure of the wide-spectrum binuclear zinc β-lactamase from Bacteroides fragilis. Structure. 4:1996;823-836.
25. Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA. Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Biol. 4:1997;586-591.
26. Davies C, White SW, Ramakrishnan V. The structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus. Structure. 4:1996;55-66.
27. Lee Y-H, Ogata C, Pflugrath JW, Levitt DG, Sarma R, Banaszak LJ, Pilkis SJ. Crystal structure of the rat liver fructose-2,6-bisphosphatase based on selenomethionine multiwavelength anomalous dispersion phases. Biochemistry. 35:1996;6010-6019.
28. Reinemer P, Prade L, Hof P, Neuefeind T, Huber R, Zettl R, Palme K, Schell J, Koelln I, Bartunik HD, Bieseler B. Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2 Å resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases and a novel active site architecture. J Mol Biol. 255:1996;289-309.
29. Thorn KS, Christensen HEM, Shigeta R Jr, Huddler D Jr, Shalaby L, Lindberg U, Chua N-H, Schutt CE. The crystal structure of a major allergen from plants. Structure. 5:1997;19-32.
30. Peat TS, Frank EG, McDonald JP, Levine AS, Woodgate R, Hendrickson WA. Structure of the UmuD′ protein and its regulation in response to DNA damage. Nature. 380:1996;727-734.
31. Martinez-Hackert E, Stock AM. The DNA-binding domain of OmpR: crystal structure of a winged helix transcription factor. Structure. 5:1997;109-124.
32. Tong L, Pav S, White DM, Rogers S, Crane KM, Cywin CL, Brown ML, Pargellis CA. A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket. Nat Struct Biol. 4:1997;311-316.
33. 2+-induced conformational changes. Nat Struct Biol. 4:1997;532-538.
34. Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276A:1997;523-530.
35. Geiger JH, Hahn S, Lee S, Sigler PB. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science. 272:1996;830-836.
36. Peat TS, Frank EG, Woodgate R, Hendrickson WA. Production and crystallization of a selenomethionyl variant of UmuD′, an Escherichia coli SOS response protein. Proteins. 25:1996;506-509.
37. Sondek J, Bohm A, Lambright, D.G, Hamm HE, Sigler PB. Crystal structure of a GA protein βγ dimer at 2.1 Å resolution. Nature. 379:1996;369-374.
38. Boissy G, de La Fortelle E, Kahn R, Huet J-C, Bricogne G, Pernollet J-C, Brunie S. Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins. Structure. 4:1996;1429-1439.
39. Yamaguchi H, Hendrickson WA. Structure basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation. Nature. 384:1996;484-489.
40. Shapiro L, Fannon AM, Kwong PD, Thompson A, Lehmann MS, Grubel G, Legrand J-F, Als-Nielsen J, Colman DR, Hendrickson WA. Structure basis of cell - cell adhesion by cadherins. Nature. 374:1995;327-337.
41. McDonald NQ, Panayotatos N, Hendrickson WA. Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing. EMBO J. 14:1995;2689-2699.
42. Burling FT, Weis WI, Flaherty KM, Brunger AT. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science. 271:1996;72-77 The most accurate and complete experimental phase set obtained so far. of outstanding interest.
43. Thygesen J, Weinstein S, Franceschi F, Yonath A. The suitability of multi-metal clusters for phasing in crystallography of large macromolecular assemblies. Structure. 4:1996;513-518 This paper describes procedures for soaking, cocrystallizing, and specific covalent binding of heavy atom clusters to very large macromolecular assemblies, with the aim of introducing sufficient phasing power for structure determination. of special interest.
44. Read RJ. As MAD as can be. Structure. 4:1996;11-14 Comments on the observed phase set in [42]. of outstanding interest of special interest.
45. Athappilly FK, Hendrickson WA. Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure. 3:1995;1407-1419.
46. Terwilliger TC. Multiwavelength anomalous diffraction phasing of macromolecular structures: analysis of MAD data as single isomorphous replacement with anomalous scattering data using the MADMRG program. Methods Enzymol. 276A:1997;530-537.
47. Ramakrishnan V, Biou V. Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol. 276A:1997;538-557.
48. Otwinowski Z. Isomorphous replacement and anomalous scattering. Wolf W, Evans PR, Leslie AGW. Proceedings of the CCP4 Study Weekend. 1991;80-86 SERC Daresbury Laboratory, Warrington.
49. Furey W, Swaminathan S. PHASES: a program package for the processing and analysis of diffraction data from macromolecules. Methods Enzymol. 276B:1997;. in press.
50. Xu R-M, Koch C, Liu Y, Horton JR, Knapp D, Nasmyth K, Cheng X. Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis. Structure. 5:1997;349-358.
51. Yamamoto M, Fujisawa T, Nakasako M, Tanaka T, Uruga T, Kimura H, Yamaoka H, Inoue Y, Iwasaki H, Ishikawa T, et al. Conceptual design of SPring-8 contract beamline for structural biology. Rev Sci Instrum. 66:1995;1833-1835.
52. Lee PL, Ogata CM. Simultaneous multiwavelength anomalous diffraction (SMAD): an energy-dispersive synchrotron method for macromolecules. J Appl Crystallogr. 28:1995;661-665.
53. Munshi S, Liljas L, Cavarelli J, Bomu W, McKinney B, Reddy V, Johnson JE. The 2.8 Å structure of a T=4 animal virus and its implications for membrane translocation of RNA. J Mol Biol. 261:1996;1-10.
54. Zhao R, Pevear DC, Kremer MJ, Giranda VL, Kofron JA, Kuhn RJ, Rossmann MG. Human rhinovirus 3 at 3.0 Å resolution. Structure. 4:1996;1205-1210.
55. 4: induced structural changes in the presence of calcium ions and functional implications. J Mol Biol. 256:1996;736-750.
56. Hadfield AT, Lee W-M, Zhao R, Oliveira MA, Minor I, Rueckert RR, Rossmann MG. The refined structure of human rhinovirus 16 at 2.15 Å resolution: implications for the viral life cycle. Structure. 5:1997;427-441.
57. Golmohammadi R, Fridborg K, Bundule M, Valegard K, Liljas L. The crystal structure of bacteriophage Qβ at 3.5 Å resolution. Structure. 4:1996;543-554.
58. Luo M, Toth KS, Zhou L, Pritchard A, Lipton HL. The structure of a highly virulent Theiler's murine encephalomyelitis virus (GDVII) and implications for determinants of viral persistence. Virology. 220:1996;246-250.
59. Stehle T, Gamblin SJ, Yan Y, Harrison SC. The structure of simian virus 40 refined at 3.1 Å resolution. Structure. 4:1996;165-182.
60. Hadfield A, Hajdu J, Chapman MS, Rossmann MG. Laue diffraction studies of human rhinovirus 14 and canine parvovirus. Acta Crystallogr D. 51:1995;859-870.
61. Llamas-Saiz AL, Agbandje-McKenna M, Parker JSL, Wahid ATM, Parrish C, Rossmann MG. Structure analysis of a mutation in canine parvovirus which controls antigenicity and host range. Virology. 225:1996;65-71.
62. Dokland T, McKenna R, Ilag LL, Bowman BR, Incardona NL, Fane BA, Rossmann MG. Structure of a viral procapsid with molecular scaffolding. Nature. 1997;. in press.
63. Lowe J, Stock D, Jap B, Zwickl P, Baumeister W, Huber R. Crystal structure of the 20S proteasome from the archaeon T. Acidophilum at 3.4 Å resolution. Science. 268:1995;533-539.
64. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. Structure of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 Å Science. 269:1995;1069-1074.
65. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å Science. 272:1996;1136-1144 The cytochrome c oxidase structure [64,65] has been eagerly anticipated; it will provide the basis for interpretation of decades of results by bioenergeticists. All cell dimensions are around 200Å with two molecules per asymmetric unit. Structure determination at 2.6 Å resolution using isomorphous replacement, solvent flattening and phase extension benefited greatly from the high quality data collected with the Weissenberg camera [81,82] at the Photon Factory. of outstanding interest.
66. Krauss N, Schubert W-D, Klukas O, Fromme P, Witt HT, Saenger W. Photosystem I at 4 resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nat Struct Biol. 3:1996;965-973.
67. Koepke J, Hu X, Muenke C, Schulten K, Michel H. The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure. 4:1996;581-597.
68. Garman EF, Schneider TR. Macromolecular cryocrystallography. J Appl Crystallogr. 30:1997;211-237 A comprehensive review of the principles and practice of cryocrystallography, essential to the effective use of beamlines that impose a high heating rate on the crystal. of special interest.
69. Longhi S, Czjzek M, Lamzin V, Nicholas A, Cambillau C. Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis. J Mol Biol. 268:1997;779-799 If your crystals are terrific, then careful structure analysis at atomic resolution can supply new data on, for example, the planarity of the peptide bond. of special interest.
70. Moffat K, Henderson R. Freeze trapping of reaction intermediates. Curr Opin Struct Biol. 5:1995;656-663.
71. Teng T-Y, Moffat K. Cooling rates during flash cooling. J Appl Crystallogr. 1997;. in press.
72. Ealick SE. Now we're cooking: new successes for Shake-and-Bake. Structure. 5:1997;469-472.
73. Mozzarelli A, Rossi GL. Protein function in the crystal. Annu Rev Biophys Biomol Struct. 25:1996;343-365 Remarkably few macromolecular crystals have had their activity quantitatively examined in the crystalline state, yet we routinely seek to correlate the crystal structure with functional proteins derived from studies in dilute solution in the absence of precipitants and of lattice forces. This paper reviews activity in the crystal from an enzymological and spectroscopic perspective. of special interest.
74. Moffat K. Time-resolved macromolecular crystallography. Synchrotron Rad News. 9:1996;15-18.
75. Sawaya MR, Kraut J. Loop and subdomain movement in the mechanism of E. coli dihydrofolate reductase: crystallographic evidence. Biochemistry. 36:1997;586-603.
76. Stoddard BL. Caught in a chemical trap. Nat Struct Biol. 3:1996;907-909.
77. Stoddard BL, Koshland DE Jr. Structure of isocitrate dehydrogenase with α-ketoglutarate at 2.7-Å resolution: conformational changes induced by decarboxylation of isocitrate. Biochemistry. 32:1993;9317-9322.
78. Bolduc JM, Dyer DH, Scott WG, Singer P, Sweet RM, Koshland DE Jr, Stoddard BL. Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Science. 268:1995;1312-1318.
79. Stoddard BL, Dean A, Bash PA. Combining Laue diffraction and molecular dynamics to study enzyme intermediates. Nat Struct Biol. 3:1996;590-595 Transient structural states are often present at lower occupancy and may be characterized by higher temperature factors on key atoms, which provides an additional challenge to crystallographic methods. Computational molecular dynamics studies can complement the crystallography, particularly in mobile regions of the structure, and can provide more confident mechanistic insights. Conversely, the computational studies are heavily dependent on excellent stereochemical information from the crystallography. of outstanding interest.
80. Mesecar AD, Stoddard BL, Koshland DE Jr. Orbital steering in the catalytic power of enzymes: small structure changes with large catalytic consequences. Science. 277:1997;202-206 The relationship between structure, energetics, and the origins of rate acceleration in enzyme mechanisms is not always straightforward. Freeze trapping of active complexes of isocitrate dehydrogenase probes this relation and re-examines the role of orbital steering. of special interest.
81. Sakabe K, Sasaki K, Watanabe N, Susuki M, Wang ZG, Miyahara J, Sakabe N. Large-format imaging plate and Weissenberg camera for accurate protein crystallographic data collection using synchrotron radiation. J Synchrotron Rad. 4:1997;136-146.
82. Kamiya N, Sasaki K, Watanabe N, Sakabe N, Sakabe K. Time-resolved protein crystallography with large-angle oscillations: an application of a protein data-collection system using the Weissenberg technique and a large-format imaging plate. J Synchrotron Rad. 4:1997;14-16.
83. Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:1996;2065-2069 Freeze trapping of an intermediate in the divalent cation catalyzed self-cleavage of a ribozyme reveals structure changes that are largely restricted to the active site. On the basis of these and more conventional, static studies, the structure of a transition state can be inferred and the reaction mechanism can be pieced together. of outstanding interest.
84. Hartmann H, Zinser S, Komninos P, Schneider RT, Nienhaus GU, Parak F. X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation. Proc Natl Acad Sci USA. 93:1996;7013-7016.
85. Teng T-Y, Srajer V, Moffat K. The initial trajectory of carbon monoxide after photodissociation from myoglobin at cryogenic temperatures. Biochemistry. 1997;. in press.
86. Schlichting I, Berendzen J, Phillips GN Jr, Sweet RM. Crystal structure of photolysed carbonmonoxy-myoglobin. Nature. 371:1994;808-812.
87. Vitkup D, Petsko GA, Karplus M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nat Struct Biol. 4:1997;202-208.
88. Ng K, Getzoff ED, Moffat K. Optical studies of a bacterial photoreceptor protein, photoactive yellow protein, in single crystals. Biochemistry. 34:1995;879-890.
89. Ren Z, Ng K, Borgstahl GEO, Getzoff ED, Moffat K. Quantitative analysis of time-resolved Laue diffraction patterns. J Appl Crystallogr. 29:1996;246-260.
90. Ren Z, Moffat K. Quantitative analysis of synchrotron Laue diffraction patterns in macromolecular crystallography. J Appl Crystallogr. 28:1995;461-481.
91. Ren Z, Moffat K. Deconvolution of energy overlaps in Laue diffraction. J Appl Crystallogr. 28:1995;482-493.
92. Bourgeois D, Longhi S, Wulff M, Cambillau C. Accuracy of structural information obtained at the European Synchrotron Radiation Facility from very rapid Laue data collection on macromolecules. J Appl Crystallogr. 30:1997;153-163.
93. Szebenyi DME, Bilderback DH, LeGrand A, Moffat K, Schildkamp W, Smith Temple B, Teng T-Y. Quantitative analysis of Laue diffraction patterns recorded with a 120 ps exposure from an X-ray undulator. J Appl Crystallogr. 25:1992;414-423.
94. Eaton WA, Henry ER, Hofrichter J. Nanosecond crystallographic snapshots of protein structural changes. Science. 274:1996;1631-1632.
95. Moffat K. Time-resolved macromolecular crystallography. Annu Rev Biophys Biophys Chem. 18:1989;309-332.
96. Neutze R, Hajdu J. Femtosecond time resolution in X-ray diffraction experiments. Proc Natl Acad Sci USA. 94:1997;5651-5655 A thought-provoking new approach to structural kinetics on the subnanosecond timescale. of special interest.
97. Doniach S. Studies of the structure of matter with photons from a X-ray free-electron laser. J Synchrotron Rad. 3:1996;260-267.