Exploring ribozyme conformational changes with X-ray crystallography

Methods

Volumn 49, Issue 2, 2009, Pages 87-100

  Spitale, Robert C ^b   Wedekind, Joseph E ^a,b  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^b Department of Chemistry   (United States)

Author keywords

Alternate conformation; Crystallization; Crystallographic ensembles; Difference Fourier; Fold and function; Long range motion; Non protein coding RNA; Ribozyme; RNA crystallography; RNA structure

Indexed keywords

RIBOZYME; RNA; URACIL;

CATALYST; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE; RNA SYNTHESIS; SOLID PHASE SYNTHESIS; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; FOURIER ANALYSIS; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; RNA, UNTRANSLATED; TRANSCRIPTION, GENETIC;

EID: 70349301373     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.06.003     Document Type: Review

References (121)

1. Amaral P.P., Dinger M.E., Mercer T.R., and Mattick J.S. Science 319 (2008) 1787-1789
2. L.H. Sullivan, Lippincott's Magazine, vol. 57, 1896, pp. 403-409.
3. Burley S.K. Nat. Struct. Biol. 7 Suppl. (2000) 932-934
4. Peracchi A., Beigelman L., Usman N., and Herschlag D. Proc. Natl. Acad. Sci. USA 93 (1996) 11522-11527
5. Holbrook S.R. Annu. Rev. Biophys. 37 (2008) 445-464
6. Cech T.R. Biochem. Soc. Trans. 30 (2002) 1162-1166
7. McKay D.B., and Wedekind J.E. In: Cech T. (Ed). The RNA World (1999), Cold Spring Harbor Laboratory Press, Cold Spring Harbor 265-286
8. Butcher S.E. Curr. Opin. Struct. Biol. 11 (2001) 315-320
9. Bevilacqua P.C., and Yajima R. Curr. Opin. Chem. Biol. 10 (2006) 455-464
10. Fedor M.J. Biochem. Soc. Trans. 30 (2002) 1109-1115
11. Chowrira B.M., and Burke J.M. Biochemistry 30 (1991) 8518-8522
12. Hampel A., and Tritz R. Biochemistry 28 (1989) 4929-4933
13. Hampel A., and Cowan J.A. Chem. Biol. 4 (1997) 513-517
14. Nesbitt S., Hegg L.A., and Fedor M.J. Chem. Biol. 4 (1997) 619-630
15. Young K.J., Gill F., and Grasby J.A. Nucleic Acids Res. 25 (1997) 3760-3766
16. Strobel S.A., and Cochrane J.C. Curr. Opin. Chem. Biol. 11 (2007) 636-643
17. Cochrane J.C., and Strobel S.A. Acc. Chem. Res. 41 (2008) 1027-1035
18. Kuzmin Y.I., Da Costa C.P., and Fedor M.J. J. Mol. Biol. 340 (2004) 233-251
19. Cottrell J.W., Kuzmin Y.I., and Fedor M.J. J. Biol. Chem. 282 (2007) 13498-13507
20. Rueda D., Bokinsky G., Rhodes M.M., Rust M.J., Zhuang X., and Walter N.G. Proc. Natl. Acad. Sci. USA 101 (2004) 10066-10071
21. Monzingo A.F., and Matthews B.W. Biochemistry 23 (1984) 5724-5729
22. Reed G.H., Poyner R.R., Larsen T.M., Wedekind J.E., and Rayment I. Curr. Opin. Struct. Biol. 6 (1996) 736-743
23. Wedekind J.E., Frey P.A., and Rayment I. Biochemistry 35 (1996) 11560-11569
24. Davies D.R., and Hol W.G. FEBS Lett. 577 (2004) 315-321
25. Schmeing T.M., Huang K.S., Strobel S.A., and Steitz T.A. Nature 438 (2005) 520-524
26. Doudna J.A., and Cech T.R. Nature 418 (2002) 222-228
27. Krasovska M.V., Sefcikova J., Spackova N., Sponer J., and Walter N.G. J. Mol. Biol. 351 (2005) 731-748
28. McDowell S.E., Spackova N., Sponer J., and Walter N.G. Biopolymers 85 (2007) 169-184
29. Martick M., Lee T.S., York D.M., and Scott W.G. Chem. Biol. 15 (2008) 332-342
30. Lee T.S., and York D.M. J. Am. Chem. Soc. 130 (2008) 7168-7169
31. Ditzler M.A., Sponer J., and Walter N.G. RNA 15 (2009) 560-575
32. Nam K., Gao J., and York D.M. J. Am. Chem. Soc. 130 (2008) 4680-4691
33. Nam K., Gao J., and York D.M. RNA 14 (2008) 1501-1507
34. Wedekind J.E., and McKay D.B. Nat. Struct. Biol. 6 (1999) 261-268
35. Wedekind J.E., and McKay D.B. Biochemistry 42 (2003) 9554-9563
36. Grum-Tokars V., Milovanovic M., and Wedekind J.E. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 142-145
37. MacElrevey C., and Wedekind J.E. Acta Cryst. F 61 (2005) 1049-1053
38. Spitale R.C., Torelli A.T., Krucinska J., Bandarian V., and Wedekind J.E. J. Biol. Chem. 284 (2009) 11012-11016
39. Kolatkar A.R., Clarage J.B., and Phillips Jr. G.N. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 210-218
40. Ke A., and Doudna J.A. Methods 34 (2004) 408-414
41. Ferre-D'Amare A.R., and Doudna J.A. J. Mol. Biol. 295 (2000) 541-556
42. Rupert P.B., and Ferre-D'Amare A.R. Methods Mol. Biol. 252 (2004) 303-311
43. Milligan J.F., and Uhlenbeck O.C. Methods Enzymol. 180 (1989) 51-62
44. Milligan J.F., Groebe D.R., Witherell G.W., and Uhlenbeck O.C. Nucleic Acids Res. 15 (1987) 8783-8798
45. Pleiss J.A., Derrick M.L., and Uhlenbeck O.C. RNA 4 (1998) 1313-1317
46. Sherlin L.D., Bullock T.L., Nissan T.A., Perona J.J., Lariviere F.J., Uhlenbeck O.C., and Scaringe S.A. RNA 7 (2001) 1671-1678
47. Batey R.T., and Kieft J.S. RNA 13 (2007) 1384-1389
48. Kieft J.S., and Batey R.T. RNA 10 (2004) 988-995
49. Wincott F., DiRenzo A., Shaffer C., Grimm S., Tracz D., Workman C., Sweedler D., Gonzalez C., Scaringe S., and Usman N. Nucleic Acids Res. 23 (1995) 2677-2684
50. Zon G., and Thompson J.A. Biochromatography 1 (1986) 22-32
51. Esteban J.A., Banerjee A.R., and Burke J.M. J. Biol. Chem. 272 (1997) 13629-13639
52. Hohng S., Wilson T.J., Tan E., Clegg R.M., Lilley D.M., and Ha T. J. Mol. Biol. 336 (2004) 69-79
53. Walter N.G., Burke J.M., and Millar D.P. Nat. Struct. Biol. 6 (1999) 544-549
54. Fedor M.J. Biochemistry 38 (1999) 11040-11050
55. Murchie A.I., Thomson J.B., Walter F., and Lilley D.M. Mol. Cell 1 (1998) 873-881
56. Walter F., Murchie A.I., and Lilley D.M. Biochemistry 37 (1998) 17629-17636
57. Walter F., Murchie A.I., Thomson J.B., and Lilley D.M. Biochemistry 37 (1998) 14195-14203
58. Zhuang X., Kim H., Pereira M.J., Babcock H.P., Walter N.G., and Chu S. Science 296 (2002) 1473-1476
59. Bokinsky G., Rueda D., Misra V.K., Rhodes M.M., Gordus A., Babcock H.P., Walter N.G., and Zhuang X. Proc. Natl. Acad. Sci. USA 100 (2003) 9302-9307
60. Nahas M.K., Wilson T.J., Hohng S., Jarvie K., Lilley D.M., and Ha T. Nat. Struct. Mol. Biol. 11 (2004) 1107-1113
61. Rupert P.B., and Ferre-D'Amare A.R. Nature 410 (2001) 780-786
62. Rupert P.B., Massey A.P., Sigurdsson S.T., and Ferre-D'Amare A.R. Science 298 (2002) 1421-1424
63. Fedor M.J. J. Mol. Biol. 297 (2000) 269-291
64. Butcher S.E., Heckman J.E., and Burke J.M. J. Biol. Chem. 270 (1995) 29648-29651
65. Alam S., Grum-Tokars V., Krucinska J., Kundracik M.L., and Wedekind J.E. Biochemistry 44 (2005) 14396-14408
66. Salter J., Krucinska J., Alam S., Grum-Tokars V., and Wedekind J.E. Biochemistry 45 (2006) 686-700
67. Esteban J.A., Walter N.G., Kotzorek G., Heckman J.E., and Burke J.M. Proc. Natl. Acad. Sci. USA 95 (1998) 6091-6096
68. MacElrevey C., Spitale R.C., Krucinska J., and Wedekind J.E. Acta Crystallogr. D Biol. Crystallogr. 63 (2007) 812-825
69. Collaborative Computational Project, Acta Crystallogr. D50 (1994) 760-763.
70. Blundell T., and Johnson L. Protein Crystallography (1976), Academic Press Inc., San Diego, CA, USA
71. MacElrevey C., Salter J.D., Krucinska J., and Wedekind J.E. RNA 14 (2008) 1600-1616
72. Wedekind J.E., and McKay D.B. Methods Enzymol. 317 (2000) 149-168
73. Saenger W. Principles of Nucleic Acid Structure (1984), Springer-Verlag, New York
74. Sugimoto N., Kierzek R., and Turner D.H. Biochemistry 26 (1987) 4554-4558
75. Walter A.E., Turner D.H., Kim J., Lyttle M.H., Muller P., Mathews D.H., and Zuker M. Proc. Natl. Acad. Sci. USA 91 (1994) 9218-9222
76. Walter A.E., Wu M., and Turner D.H. Biochemistry 33 (1994) 11349-11354
77. Kierzek R., Burkard M.E., and Turner D.H. Biochemistry 38 (1999) 14214-14223
78. Lu Z.J., Turner D.H., and Mathews D.H. Nucleic Acids Res. 34 (2006) 4912-4924
79. Nagaswamy U., Larios-Sanz M., Hury J., Collins S., Zhang Z., Zhao Q., and Fox G.E. Nucleic Acids Res. 30 (2002) 395-397
80. Selmer M., Dunham C.M., Murphy F.V.t., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Science 313 (2006) 1935-1942
81. Golden B.L., and Kundrot C.E. J. Struct. Biol. 142 (2003) 98-107
82. Golden B.L. Methods Mol. Biol. 363 (2007) 239-257
83. Kantardjieff K.A., and Rupp B. Protein Sci. 12 (2003) 1865-1871
84. Correll C.C., Wool I.G., and Munishkin A. J. Mol. Biol. 292 (1999) 275-287
85. Cate J.H., and Doudna J.A. Methods Enzymol. 317 (2000) 169-180
86. Keel A.Y., Rambo R.P., Batey R.T., and Kieft J.S. Structure 15 (2007) 761-772
87. Robertson M.P., and Scott W.G. Acta Crystallogr. D Biol. Crystallogr. D 64 (2008) 738-744
88. Golden B.L. Methods Enzymol. 317 (2000) 124-132
89. Golden B.L., Gooding A.R., Podell E.R., and Cech T.R. RNA 2 (1996) 1295-1305
90. Adams P.D., Gopal K., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., Pai R.K., Read R.J., Romo T.D., Sacchettin J.C., Sauter N.K., Storoni L.C., and Terwilliger T.C. J. Sync. Rad. 11 (2004) 53-55
91. Murshudov G.N., Vagin A.A., Lebedev A., Wilson K.S., and Dodson E.J. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 247-255
92. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G.L. Acta Crystallogr. D 54 (1998) 905-921
93. Brunger A.T. Nat. Protocol. 2 (2007) 2728-2733
94. Brunger A.T. Nature 355 (1992) 472-475
95. Adams P.D., Pannu N.S., Read R.J., and Brunger A.T. Proc. Natl. Acad. Sci. USA 94 (1997) 5018-5023
96. Brunger A.T. Methods Enzymol. 277 (1997) 366-396
97. Pannu N.S., and Read R.J. Acta Crystallogr. A 52 (1996) 659-668
98. Otwinowski Z., Borek D., Majewski W., and Minor W. Acta Crystallogr. A 59 (2003) 228-234
99. Otwinowski Z., and Minor W. Methods Enzymol. 276 (1997) 307-326
100. Pflugrath J.W. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 1718-1725
101. Kleywegt G.J., and Brunger A.T. Structure 4 (1996) 897-904
102. Jiang J.S., and Brunger A.T. J. Mol. Biol. 243 (1994) 100-115
103. Read R.J. Acta Crystallogr. A 42 (1986) 140-149
104. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Acta Crystallogr. A 47 Pt. 2 (1991) 110-119
105. Emsley P., and Cowtan K. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2126-2132
106. Branden C.I., and Jones T.A. Nature 343 (1990) 687
107. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., Murray L.W., Arendall III W.B., Snoeyink J., Richardson J.S., and Richardson D.C. Nucleic Acids Res. 35 (2007) W375-W383
108. Berzal-Herranz A., Joseph S., and Burke J.M. Genes Dev. 6 (1992) 129-134
109. Berzal-Herranz A., Joseph S., Chowrira B.M., Butcher S.E., and Burke J.M. EMBO J. 12 (1993) 2567-2573
110. Joseph S., and Burke J.M. J. Biol. Chem. 268 (1993) 24515-24518
111. Adams P.D., Pannu N.S., Read R.J., and Brunger A.T. Acta Crystallogr. D Biol. Crystallogr. 55 Pt. 1 (1999) 181-190
112. Kabsch W. Acta Crystallogr. A 34 (1978) 827-828
113. Kleywegt G.J., and Jones T.A. Methods Enzymol. 277 (1997) 525-545
114. Soukup G.A., and Breaker R.R. RNA 5 (1999) 1308-1325
115. Pinard R., Hampel K.J., Heckman J.E., Lambert D., Chan P.A., Major F., and Burke J.M. EMBO J. 20 (2001) 6434-6442
116. Torelli A.T., Krucinska J., and Wedekind J.E. RNA 13 (2007) 1052-1070
117. Torelli A.T., Spitale R.C., Krucinska J., and Wedekind J.E. Biochem. Biophys. Res. Commun. 371 (2008) 154-158
118. A.T. Torelli, Structural Studies of Transition-State Stabilization by a Small Catalytic RNA, Metabolite Binding by a Regulatory RNA Sequence and the Mechanism of Action of Activation Induced Deaminase, Doctoral Dissertation in Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York, 2008, p. 262.
119. Kuzmin Y.I., Da Costa C.P., Cottrell J.W., and Fedor M.J. J. Mol. Biol. 349 (2005) 989-1010
120. Spitale R.C., Volpini R., Heller M.G., Krucinska J., Cristalli G., and Wedekind J.E. J. Am. Chem. Soc. 131 (2009) 6093-6095
121. Zhao Z.Y., Wilson T.J., Maxwell K., and Lilley D.M. RNA 6 (2000) 1833-1846