Solvent Structure and Hammerhead Ribozyme Catalysis

Chemistry and Biology

Volumn 15, Issue 4, 2008, Pages 332-342

  Martick, Monika ^a   Lee, Tai Sung ^b   York, Darrin M ^b   Scott, William G ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

CHEMBIO; RNA

Indexed keywords

HAMMERHEAD RIBOZYME; MANGANESE; RIBOZYME; SOLVENT;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; METABOLISM; X RAY CRYSTALLOGRAPHY;

CATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; MANGANESE; MODELS, MOLECULAR; RNA, CATALYTIC; SOLVENTS;

EID: 41949138497     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2008.03.010     Document Type: Article

References (61)

1. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1987), Oxford University Press, Oxford
2. Auffinger P., and Westhof E. RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin. J. Mol. Biol. 269 (1997) 326-341
3. Auffinger P., and Westhof E. Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol. 300 (2000) 1113-1131
4. Bayly C.I., Cieplak P., Cornell W., and Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97 (1993) 10269-10280
5. Blount K.F., and Uhlenbeck O.C. The structure-function dilemma of the hammerhead ribozyme. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 415-440
6. Bourdeau V., Ferbeyre G., Pageau M., Paquin B., and Cedergren R. The distribution of RNA motifs in natural sequences. Nucleic Acids Res. 27 (1999) 4457-4467
7. Brunger 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., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
8. Canny M.D., Jucker F.M., Kellogg E., Khvorova A., Jayasena S.D., and Pardi A. Fast cleavage kinetics of a natural hammerhead ribozyme. J. Am. Chem. Soc. 126 (2004) 10848-10849
9. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Onufriev A., Simmerling C., Wang B., and Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
10. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D. Biol. Crystallogr. 50 (1994) 760-763
11. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
12. Dahm S.C., and Uhlenbeck O.C. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30 (1991) 9464-9469
13. Dahm S.C., Derrick W.B., and Uhlenbeck O.C. Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry 32 (1993) 13040-13045
14. De la Pena M., Gago S., and Flores R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22 (2003) 5561-5570
15. DeLano, W.L. (2003). The PyMOL Molecular Graphics System (http://pymol.sourceforge.net/).
16. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2126-2132
17. Essmann U., Perera L., Berkowitz M.L., Darden T., Hsing L., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
18. Ferbeyre G., Smith J.M., and Cedergren R. Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell. Biol. 18 (1998) 3880-3888
19. Forster A.C., and Symons R.H. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50 (1987) 9-16
20. Forster A.C., Davies C., Sheldon C.C., Jeffries A.C., and Symons R.H. Self-cleaving viroid and newt RNAs may only be active as dimers. Nature 334 (1988) 265-267
21. Giese T.J., Gregersen B.A., Liu Y., Nam K., Mayaan E., Moser A., Range K., Faza O.N., Lopez C.S., de Lera A.R., et al. QCRNA 1.0: a database of quantum calculations of RNA catalysis. J. Mol. Graph. Model. 25 (2006) 423-433
22. Han J., and Burke J.M. Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site. Biochemistry 44 (2005) 7864-7870
23. Haseloff J., and Gerlach W.L. Sequences required for self-catalysed cleavage of the satellite RNA of tobacco ringspot virus. Gene 82 (1989) 43-52
24. Hermann T., Auffinger P., Scott W.G., and Westhof E. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme. Nucleic Acids Res. 25 (1997) 3421-3427
25. Hertel K.J., Pardi A., Uhlenbeck O.C., Koizumi M., Ohtsuka E., Uesugi S., Cedergren R., Eckstein F., Gerlach W.L., Hodgson R., et al. Numbering system for the hammerhead. Nucleic Acids Res. 20 (1992) 3252
26. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
27. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
28. Kanyo Z.F., Scolnick L.R., Ash D.E., and Christianson D.W. Structure of a unique binuclear manganese cluster in arginase. Nature 383 (1996) 554-557
29. Khvorova A., Lescoute A., Westhof E., and Jayasena S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10 (2003) 708-712
30. Kim N.K., Murali A., and DeRose V.J. Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme. J. Am. Chem. Soc. 127 (2005) 14134-14135
31. Kisseleva N., Khvorova A., Westhof E., and Schiemann O. Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy. RNA 11 (2005) 1-6
32. Leclerc F., and Karplus M. Two-metal-ion mechanism for hammerhead-ribozyme catalysis. J. Phys. Chem. B 110 (2006) 3395-3409
33. 2+ in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation. J. Chem. Theory Comput. 3 (2007) 325-327
34. 2+ in hammerhead ribozyme catalysis from molecular simulation. J. Am. Chem. Soc. 130 (2008) 3053-3064
35. Lilley D.M.J. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 15 (2005) 313-323
36. Martick M., and Scott W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126 (2006) 309-320
37. Mayaan E., Range K., and York D.M. Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes. J. Biol. Inorg. Chem. 9 (2004) 807-817
38. Mayaan E., Moser A., Mackerell Jr. A.D., and York D.M. CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J. Comput. Chem. 28 (2007) 495-507
39. Murray J.B., Seyhan A.A., Walter N.G., Burke J.M., and Scott W.G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5 (1998) 587-595
40. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr 53 (1997) 240-255
41. Nelson J.A., and Uhlenbeck O.C. When to believe what you see. Mol. Cell 23 (2006) 447-450
42. Nelson J.A., and Uhlenbeck O.C. Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis. RNA 14 (2007) 43-54
43. Osborne E.M., Schaak J.E., and Derose V.J. Characterization of a native hammerhead ribozyme derived from schistosomes. RNA 11 (2005) 187-196
44. Penedo J.C., Wilson T.J., Jayasena S.D., Khvorova A., and Lilley D.M.J. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10 (2004) 880-888
45. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kalé L., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
46. Pley H.W., Flaherty K.M., and McKay D.B. Three-dimensional structure of a hammerhead ribozyme. Nature 372 (1994) 68-74
47. Prody G.A., Bakos J.T., Buzayan J.M., Schneider I.R., and Breuning G. Autolytic processing of dimeric plant virus satellite RNA. Science 231 (1986) 1577-1580
48. Przybilski R., and Hammann C. The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements. RNA 13 (2007) 1625-1630
49. Pyle A.M. Ribozymes: a distinct class of metalloenzymes. Science 261 (1993) 709-714
50. Rhodes M.M., Reblova K., Sponer J., and Walter N.G. Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc. Natl. Acad. Sci. USA 103 (2006) 13380-13385
51. Roychowdhury-Saha M., and Burke D.H. Extraordinary rates of transition metal ion-mediated ribozyme catalysis. RNA 12 (2006) 1846-1852
52. Ruffner D.E., Stormo G.D., and Uhlenbeck O.C. Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29 (1990) 10695-10702
53. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Physiol. 23 (1977) 327-341
54. Schiemann O., Fritscher J., Kisseleva N., Sigurdsson S.T., and Prisner T.F. Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding. ChemBioChem 4 (2003) 1057-1065
55. Scott W.G. RNA structure, metal ions, and catalysis. Curr. Opin. Chem. Biol. 3 (1999) 705-709
56. Scott W.G., Murray J.B., Arnold J.R., Stoddard B.L., and Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274 (1996) 2065-2069
57. Uhlenbeck O.C. A small catalytic oligoribonucleotide. Nature 328 (1987) 596-600
58. Wang S., Karbstein K., Peracchi A., Beigelman L., and Herschlag D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry 38 (1999) 14363-14378
59. Wedekind J.E., and McKay D.B. Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis. Annu. Rev. Biophys. Biomol. Struct. 27 (1998) 475-502
60. Winn M.D. An overview of the CCP4 project in protein crystallography: an example of a collaborative project. J. Synchrotron Radiat. 10 (2003) 23-25
61. Zhou J.M., Zhou D.M., Takagi Y., Kasai Y., Inoue A., Baba T., and Taira K. Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme. Nucleic Acids Res. 30 (2002) 2374-2382