Chemically engineered ribosomes: A new frontier in synthetic biology

Current Organic Chemistry

Volumn 14, Issue 2, 2010, Pages 148-161

  Chirkova, Anna ^a   Erlacher, Matthias ^a   Micura, Ronald ^b   Polacek, Norbert ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; HYDROGEN BONDS; NUCLEOTIDES; PEPTIDES; RNA;

AMIDE BOND; CHEMICALLY MODIFIED; FUNCTIONAL ASSAYS; IN-VITRO; PEPTIDYL TRANSFER; RIBOZYMES; RNA CATALYSIS; RNA FOLDING; SYNTHETIC BIOLOGY; TRANSFER REACTION;

SYNTHESIS (CHEMICAL);

EID: 77949407904     PISSN: 13852728     EISSN: None     Source Type: Journal    
DOI: 10.2174/138527210790069848     Document Type: Article

References (124)

1. Kruger, K.; Grabowski, P. J.; Zaug, A. J.; Sands, J.; Gottschling, D. E.; Cech, T. R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 1982, 31, 147-57.
2. Guerrier-Takada, C.; Gardiner, K.; Marsh, T.; Pace, N.; Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 1983, 35, 849-857.
3. Serganov, A.; Patel, D. J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genet., 2007, 8, 776-790.
4. Emilsson, G. M.; Nakamura, S.; Roth, A.; Breaker, R. R. Ribozyme speed limits. RNA, 2003, 9, 907-918.
5. Stage-Zimmermann, T. K.; Uhlenbeck, O. C. Hammerhead ribozyme kinetics. RNA, 1998, 4, 875-889.
6. Wilson, T. J.; Lilley, D. M. Biochemistry. The evolution of ribozyme chemistry. Science, 2009, 323, 1436-1438.
7. Walter, N. G. Ribozyme catalysis revisited: is water involved? Mol. Cell, 2007, 28, 923-929.
8. Fedor, M. J.; Williamson, J. R. The catalytic diversity of RNAs. Nat. Rev. Mol. Cell Biol., 2005, 6, 399-412.
9. Das, S. R.; Piccirilli, J. A. General acid catalysis by the hepatitis delta virus ribozyme. Nat. Chem. Biol., 2005, 1, 45-52.
10. Kuimelis, R. G.; McLaughlin, L. W. Application of a 5'-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage. Bioorg. Med. Chem., 1997, 5, 1051-1061.
11. Piccirilli, J. A.; Vyle, J. S.; Caruthers, M. H.; Cech, T. R. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature, 1993, 361, 85-88.
12. Liu, L.; Cottrell, J. W.; Scott, L. G.; Fedor, M. J. Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme. Nat. Chem. Biol., 2009, 5, 351-357.
13. Ryder, S. P.; Strobel, S. A. Nucleotide analog interference mapping. Methods, 1999, 18, 38-50.
14. Strobel, S. A.; Shetty, K. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci., 1997, 94, 2903-2908.
15. Kazantsev, A. V.; Pace, N. R. Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P. RNA, 1998, 4, 937-947.
16. Oyelere, A. K.; Kardon, J. R.; Strobel, S. A. pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry, 2002, 41, 3667-3675.
17. Gordon, P. M.; Fong, R.; Deb, S. K.; Li, N. S.; Schwans, J. P.; Ye, J. D.; Piccirilli, J. A. New strategies for exploring RNA's 2'-OH expose the impor-tance of solvent during group II intron catalysis. Chem. Biol. 2004, 11, 237246.
18. Mendel, D.; Cornish, V. W.; Schultz, P. G. Site-directed mutagenesis with an expanded genetic code. Annu. Rev. Biophys. Biomol. Struct., 1995, 24, 435-462.
19. Merryman, C.; Green, R. Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules. Chem. Biol. 2004, 11, 575-582.
20. Zhang, Z.; Gildersleeve, J.; Yang, Y. Y.; Xu, R.; Loo, J. A.; Uryu, S.; Wong, C. H.; Schultz, P. G. A new strategy for the synthesis of glycoproteins. Science, 2004, 303, 371-373.
21. Starck, S. R.; Qi, X.; Olsen, B. N.; Roberts, R. W. The puromycin route to assess stereoand regiochemical constraints on peptide bond formation in eukaryotic ribosomes. J. Am. Chem. Soc., 2003, 125, 8090-8091.
22. Josephson, K.; Hartman, M. C.; Szostak, J. W. Ribosomal synthesis of un-natural peptides. J. Am. Chem. Soc., 2005, 127, 11727-11735.
23. Li, S.; Roberts, R. W. A novel strategy for in vitro selection of peptide-drug conjugates. Chem. Biol., 2003, 10, 233-239.
24. Merryman, C.; Weinstein, E.; Wnuk, S. F.; Bartel, D. P. A bifunctional tRNA for in vitro selection. Chem. Biol., 2002, 9, 741-746.
25. Pavlov, M. Y.; Watts, R. E.; Tan, Z.; Cornish, V. W.; Ehrenberg, M.; Forster, A. C. Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc. Natl. Acad. Sci., 2009, 106, 50-54.
26. Dedkova, L. M.; Fahmi, N. E.; Golovine, S. Y.; Hecht, S. M. Enhanced Damino acid incorporation into protein by modified ribosomes. J. Am. Chem. Soc., 2003, 125, 6616-6617.
27. Phelps, S. S.; Jerinic, O.; Joseph, S. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol. Cell, 2002, 10, 799-807.
28. Phelps, S. S.; Joseph, S. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation. J. Mol. Biol., 2005, 349, 288-301.
29. Feinberg, J. S.; Joseph, S. Identification of molecular interactions between Psite tRNA and the ribosome essential for translocation. Proc. Natl. Acad. Sci., 2001, 98, 11120-11125.
30. Dorner, S.; Panuschka, C.; Schmid, W.; Barta, A. Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2'-OH to activity. Nucleic Acids Res., 2003, 31, 6536-6542.
31. Dorner, S.; Polacek, N.; Schulmeister, U.; Panuschka, C.; Barta, A. Molecular aspects of the ribosomal peptidyl transferase. Biochem. Soc. Trans., 2002, 30, 1131-1136.
32. Weinger, J. S.; Parnell, K. M.; Dorner, S.; Green, R.; Strobel, S. A. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat. Struct. Mol. Biol., 2004, 11, 1101-1106.
33. Schmeing, T. M.; Huang, K. S.; Strobel, S. A.; Steitz, T. A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature, 2005, 438, 520-524.
34. Höbartner, C.; Rieder, R.; Kreutz, C.; Puffer, B.; Lang, K. Polonskaia, A.; Serganov, A.; Micura, R., Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography. J. Am. Chem. Soc., 2005, 127, 12035-12045.
35. Erlacher, M. D.; Polacek, N. Ribosomal catalysis: the evolution of mechanistic concepts for peptide bond formation and peptidyl-tRNA hydrolysis. RNA Biol., 2008, 5, 5-12.
36. Bieling, P.; Beringer, M.; Adio, S.; Rodnina, M. V. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol., 2006, 13, 423-428.
37. Lovmar, M.; Ehrenberg, M. Rate, accuracy and cost of ribosomes in bacterial cells. Biochimie, 2006, 88, 951-961.
38. Krayevsky, A. A.; Kukhanova, M. K. The peptidyltransferase center of ribosomes. Prog. Nucleic Acid Res. Mol. Biol., 1979, 23, 1-51.
39. Nierhaus, K. H.; Schulze, H.; Cooperman, B. S. Molecular mechanisms of the ribosomal peptidyltransferase center. Biochem. Int., 1980, 1, 185-192.
40. Sievers, A.; Beringer, M.; Rodnina, M. V.; Wolfenden, R. The ribosome as an entropy trap. Proc. Natl. Acad. Sci., 2004, 101, 7897-7901.
41. Polacek, N.; Mankin, A. S. The ribosomal peptidyl transferase center: Structure, function, evolution, inhibition. Crit. Rev. Biochem. Mol., 2005, 40, 285-311.
42. Ban, N.; Nissen, P.; Hansen, J.; Moore, P. B.; Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 2000, 289, 905-920.
43. Harms, J.; Schluenzen, F.; Zarivach, R.; Bashan, A.; Gat, S.; Agmon, I.; Bartels, H.; Franceschi, F.; Yonath, A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell, 2001, 107, 679-688.
44. Nissen, P.; Hansen, J.; Ban, N.; Moore, P. B.; Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science, 2000, 289, 920-930.
45. Green, R.; Noller, H. F. Ribosomes and translation. Annu. Rev. Biochem., 1997, 66, 679-716.
46. Polacek, N. Peptidyl transferase directed drugs: inhibitors of an RNA-enzyme? In RNA-binidng antibiotics, Schroeder, R.; Wallis, M. G., Eds.; Eurekah.com/Landes Bioscience: Georgetown, Texas, 2001; pp 1-10.
47. Barta, A.; Kuechler, E. Part of the 23S RNA located in the 11S RNA fragment is a constituent of the ribosomal peptidyltransferase centre. FEBS Lett., 1983, 163, 319-323.
48. Barta, A.; Steiner, G.; Brosius, J.; Noller, H. F.; Kuechler, E. Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc. Natl. Acad. Sci.,1984, 81, 3607-3611.
49. Steiner, G.; Kuechler, E.; Barta, A. Photo-affinity labelling at the peptidyl transferase centre reveals two different positions for the Aand P-sites in domain V of 23S rRNA. EMBO J., 1988, 7, 3949-3955.
50. Barta, A.; Dorner, S.; Polacek, N. Mechanism of ribosomal peptide bond formation. Science, 2001, 291, 203.
51. Bayfield, M. A.; Dahlberg, A. E.; Schulmeister, U.; Dorner, S.; Barta, A. A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc. Natl. Acad. Sci., 2001, 98, 10096-10101.
52. Beringer, M.; Adio, S.; Wintermeyer, W.; Rodnina, M. The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA, 2003, 9, 919-922.
53. Xiong, L.; Polacek, N.; Sander, P.; Böttger, E. C.; Mankin, A. pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA, 2001, 7, 1365-1369.
54. Polacek, N.; Gaynor, M.; Yassin, A.; Mankin, A. S. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature, 2001, 411, 498-501.
55. Thompson, J.; Kim, D. F.; O'Connor, M.; Lieberman, K. R.; Bayfield, M. A.; Gregory, S. T.; Green, R.; Noller, H. F.; Dahlberg, A. E. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc. Natl. Acad. Sci., 2001, 98, 9002-9007.
56. Youngman, E. M.; Brunelle, J. L.; Kochaniak, A. B.; Green, R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell, 2004, 117, 589-599.
57. Beringer, M.; Bruell, C.; Xiong, L.; Pfister, P.; Bieling, P.; Katunin, V. I.; Mankin, A. S.; Bottger, E. C.; Rodnina, M. V. Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J. Biol. Chem., 2005, 280, 36065-36072.
58. Hansen, J. L.; Schmeing, T. M.; Moore, P. B.; Steitz, T. A. Structural insights into peptide bond formation. Proc. Natl. Acad. Sci., 2002, 99, 1167011675.
59. Meselson, M.; Nomura, M.; Brenner, S.; Davern, C.; Schlessinger, D. Conservation of ribosomes during bacterial growth. J. Mol. Biol., 1964, 9, 696-711.
60. Spirin, A. S.; Kiselev, N. A.; Shakulov, R. S.; Bogdanov, A. A. [Studies on the Structure of Ribosomes; Reversible Unfolding of Ribonucleoprotein Strands and Packing Models.]. Biokhimiia, 1963, 28, 920-930.
61. Nomura, M.; Erdmann, V. A. Reconstitution of 50S ribosomal subunits from dissociated molecular components. Nature, 1970, 228, 744-748.
62. Nomura, M.; Traub, P.; Bechmann, H. Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins. Nature, 1968, 219, 793-799.
63. Nierhaus, K. H.; Dohme, F. Total reconstitution of functionally active 50S ribosomal subunits from scherichia coli. Proc. Natl. Acad. Sci., 1974, 71, 4713-4717.
64. Nierhaus, K. H. The assembly of prokaryotic ribosomes. Biochimie, 1991, 73, 739-755.
65. Franceschi, F. J.; Nierhaus, K. H. Ribosomal proteins L15 and L16 are mere late assembly proteins of the large ribosomal subunit. Analysis of an Escherichia coli mutant lacking L15. J. Biol. Chem., 1990, 265, 16676-16682.
66. Schulze, H.; Nierhaus, K. H. Minimal set of ribosomal components for reconstitution of the peptidyltransferase activity. EMBO J., 1982, 1, 609-613.
67. Cunningham, P. R.; Richard, R. B.; Weitzmann, C. J.; Nurse, K.; Ofengand, J. The absence of modified nucleotides affects both in vitro assembly and in vitro function of the 30S ribosomal subunit of Escherichia coli. Biochimie, 1991, 73, 789-796.
68. Green, R.; Noller, H. F. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA, 1996, 2, 1011-1021.
69. Green, R.; Noller, H. F., Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23S rRNA. Biochemistry, 1999, 38, 1772-1779.
70. Khaitovich, P.; Tenson, T.; Kloss, P.; Mankin, A. S. Reconstitution of functionally active Thermus aquaticus large ribosomal subunits with in vitrotranscribed rRNA. Biochemistry, 1999, 38, 1780-1788.
71. Erlacher, M. D.; Lang, K.; Shankaran, N.; Wotzel, B.; Huttenhofer, A.; Micura, R.; Mankin, A. S.; Polacek, N. Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451. Nucleic Acids Res., 2005, 33, 1618-1627.
72. Erlacher, M. D.; Lang, K.; Wotzel, B.; Rieder, R.; Micura, R.; Polacek, N. Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA. J. Am. Chem. Soc., 2006, 128, 4453-4459.
73. Beaucage, S. L. Solid-phase synthesis of siRNA oligonucleotides. Curr. Opin. Drug. Discov. Dev., 2008, 11, 203-216.
74. Chow, C. S.; Mahto, S. K.; Lamichhane, T. N. Combined Approaches to Site-Specific Modification of RNA. ACS Chem. Biol., 2008, 3, 30-37.
75. Höbartner, C.; Wachowius, F. Chemical synthesis of modified RNA. In The Chemical Biology of Nucleic Acids, Mayer, G., Ed. Wiley VCH, 2009; in press.
76. Eritja, R., Solid-phase synthesis of modified oligonucleotides. Int. J. Pept. Therap., 2007, 13, 53-68.
77. Marshall, W. S.; Kaiser, R. J. Recent advances in the high-speed solid phase synthesis of RNA. Curr. Opin. Chem. Biol., 2004, 8, 222-229.
78. Micura, R. Small interfering RNAs and their chemical synthesis. Angew. Chem. Int. Ed. Engl., 2002, 41, 2265-2269.
79. Müller, S.; Wolf, J.; Ivanov, S. A. Current strategies for the synthesis of RNA. Curr. Org. Synth., 2004, 1, 293-307.
80. Reese, C. B. Oligoand poly-nucleotides: 50 years of chemical synthesis. Org. Biomol. Chem., 2005, 3, 3851-3868.
81. Pitsch, S.; Weiss, P. A. Chemical synthesis of RNA sequences with 2'-O-[(triisopropylsilyl)oxy]methyl-protected ribonucleoside phosphoramidites. Curr. Protoc. Nucleic Acid Chem., 2002, Chapter 3, Unit 38.
82. Pitsch, S.; Weiss, P. A. Preparation of 2'-O-[(Triisopropylsilyl)oxy]methyl-protected ribonucleosides. Curr. Protoc. Nucleic Acid Chem., 2002, Chapter 2, Unit 29.
83. Pitsch, S.; Weiss, P. A.; Jenny, L.; Stutz, A.; Wu, X. Reliable chemical synthesis of oligoribonucleotides (RNA) with 2'-O-[(triisopropylsilyl)oxy]methyl(2'-O-TOM)-protected phosphoramidites. Helv. Chim. Acta., 2001, 84, 3773-3795.
84. Pitsch, S.; Weiss, P. A.; Jenny, L. Ribonucleoside-derivative and method for preparing the same. US patent 5986084, 1999.
85. Höbartner, C.; Kreutz, C.; Flecker, E.; Ottenschläger, E.; Pils, W.; Grub mayr, K.; Micura, R. The synthesis of 2'-O-[(triisopropylsilyl)oxy]methyl (TOM) phosphoramidites of methylated ribonucleosides (m1G, m2G, m22G, m1I, m3U, m4C, m6A, m62A) for use in automated RNA solid-phase synthesis. Monatsh. Chem. Chem. Monthly, 2003, 134, 851-873.
86. Porcher, S.; Pitsch, S. Synthesis of 2'-O [(triisopropylsilyl)oxy]methyl(=tom)-protected ribonucleoside phosphoramidites containing various nucleobase analogs. Helv. Chim. Acta., 2005, 88, 2683-2704.
87. Micura, R., Cyclic oligoribonucleotides (RNA) by solid-phase synthesis. Chem. Eur. J., 1999, 5, 2077-2082.
88. Micura, R.; Pils, W.; Grubmayr, K. Bridged Cyclic Oligoribonucleotides as Model Compounds for Codon Anticodon Pairing. Angew. Chem. Int., 2000, 39, 922-925.
89. Sudarsan, N.; Lee, E. R.; Weinberg, Z.; Moy, R. H.; Kim, J. N.; Link, K. H.; Breaker, R. R. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science, 2008, 321, 411-413.
90. Solano, C.; Garcia, B.; Latasa, C.; Toledo-Arana, A.; Zorraquino, V.; Valle, J.; Casals, J.; Pedroso, E.; Lasa, I. Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in Salmonella. Proc. Natl. Acad. Sci., 2009, 106, 7997-8002.
91. Scaringe, S. A.; Wincott, F. E.; Caruthers, M. H. Novel RNA synthesis method using 5'-O-Silyl-2'-O-orthoester protecting groups. J. Am. Chem. Soc., 1998, 120, 11820-11821.
92. Höbartner, C.; Micura, R. Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 SnRNA stemloop segment. J. Am. Chem. Soc., 2004, 126, 1141-1149.
93. Micura, R.; Höbartner, C.; Rieder, R.; Kreutz, C.; Puffer, B.; Lang, K.; Moroder, H. Preparation of 2'-deoxy-2'-methylseleno-modified phosphora-midites and RNA. Curr. Protoc. Nucleic Acid Chem., 2007, Chapter 1, Unit 1 15.
94. Moroder, H.; Kreutz, C.; Lang, K.; Serganov, A.; Micura, R. Synthesis, oxidation behavior, crystallization and structure of 2'-methylseleno guanosine containing RNAs. J. Am. Chem. Soc., 2006, 128, 9909-9918.
95. Puffer, B.; Moroder, H.; Aigner, M.; Micura, R. 2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach. Nucleic Acids Res., 2008, 36, 970-983.
96. Bevers, S.; Xiang, G.; McLaughlin, L. W. Importance of specific adenosine N3-nitrogens for efficient cleavage by a hammerhead ribozyme. Biochemistry, 1996, 35, 6483-6490.
97. DeNapoli, L.; Messere, A.; Montesarchio, D.; Piccialli, G.; Varra, M., 1-Substituted 2'-deoxyinosine analogues. J. Chem. Soc. Perkin. Trans., 1997, 1, 2079-2082.
98. Minakawa, N.; Sasabuchi, Y.; Kiyosue, A.; Kojima, N.; Matsuda, A. Nucleosides and nucleotides.143. Synthesis of 5-amino-4-imidazolecarboxamide (AICA) deoxyribosides from deoxyinosines and their conversion into 3deazapurine derivatives. Chem. Pharm. Bull., 1996, 44, 288-295.
99. Pankiewicz, K.; Matsuda, A.; Wata nabe, K. A. Nucleosides. 121. Improved and general synthesis of 2'-deoxy-C-nucleosides. Synthesis of 5-(2-deoxybeta.-D-erythro-pentofuranosyl)uracil, -1-methyluracil, -1,3-dimethyluracil, and -isocytosine. J. Org. Chem., 1982, 47, 485-488.
100. Robins, M. J.; Wilson, J. S.; Hansske, F. Nucleic acid related compounds. 42. A general procedure for the efficient deoxygenation of secondary alcohols. Regiospecific and stereoselective conversion of ribonucleosides to 2'deoxynucleosides. J. Am. Chem. Soc., 1983, 105, 4059-4065.
101. Lang, K.; Erlacher, M.; Wilson, D. N.; Micura, R.; Polacek, N. The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis. Chem. Biol., 2008, 15, 485-492.
102. Karpeisky, A.; Sweedler, D.; Haeberli, P.; Read, J.; Jarvis, K.; Beigelman, L. Scaleable and efficient synthesis of 2'-deoxy-2'-N-phthaloyl nucleoside phosphoramidites for oligonucleotide synthesis. Bioorg. Med. Chem. Lett., 2002, 12, 3345-3347.
103. Trobro, S.; Aqvist, J. Mechanism of peptide bond synthesis on the ribosome. Proc. Natl. Acad. Sci., 2005, 102, 12395-12400.
104. Bayryamov, S. G.; Rangelov, M. A.; Mladjova, A. P.; Yomtova, V.; Petkov, D. D. Unambiguous evidence for efficient chemical catalysis of adenosine ester aminolysis by its 2'/3'-OH. J. Am. Chem. Soc., 2007, 129, 5790-5791.
105. Kingery, D. A.; Pfund, E.; Voorhees, R. M.; Okuda, K.; Wohlgemuth, I.; Kitchen, D. E.; Rodnina, M. V.; Strobel, S. A. An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction. Chem. Biol., 2008, 15, 493-500.
106. Schlosser, A.; Blechschmidt, B.; Nawrot, B.; Sprinzl, M. Aminoacylation of tRNA induces a conformational switch on the 3'-terminal ribose. In RNA Biochemistry and Biotechnology, Barciszewski, J.; Clark, B. F. C., Eds. Kluwer Academic Publishers, 1999, pp. 159-168.
107. Schlosser, A.; Nawrot, B.; Grillenbeck, N.; Sprinzl, M. Fluorescencemonitored conformational change on the 3'-end of tRNA upon aminoacyla-tion. J. Biomol. Struct. Dyn., 2001, 19, 285-291.
108. Acharya, P.; Nawrot, B.; Sprinzl, M.; Thibaudeau, C.; Chattopadhyaya, J. The strength of the 3'-gauche effect dictates the structure of 3'-Oanthraniloyladenosine and its 5'-phosphate, two analogues of the 3'-end of aminoacyl-tRNA. J. Chem. Soc., Perkin Trans. 1999, 2, 1531-1535.
109. Amort, M.; Wotzel, B.; Bakowska-Zywicka, K.; Erlacher, M. D.; Micura, R.; Polacek, N. An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination. Nucleic Acids Res., 2007, 35, 5130-5140.
110. Littlefield, J. W.; Keller, E. B.; Gross, J.; Zamecnik, P. C. Studies on cytoplasmic ribonucleoprotein particles from the liver of the rat. J. Biol. Chem., 1955, 217, 111-123.
111. Schachtschabel, D.; Zillig, W. [Investigations on the biosynthesis of proteins. I. Synthesis of radiocarbon labeled amino acids in proteins of cell free nucleoprotein-enzyme-system of Escherichia coli.]. Hoppe Seylers Z. Physiol. Chem., 1959, 314, 262-275.
112. Spirin, A. S. High-throughput cell-free systems for synthesis of functionally active proteins. Trends Biotechnol., 2004, 22, 538-545.
113. Shimizu, Y.; Kuruma, Y.; Ying, B. W.; Umekage, S.; Ueda, T. Cell-free translation systems for protein engineering. FEBS J., 2006, 273, 4133-4140.
114. Goshima, N.; Kawamura, Y.; Fukumoto, A.; Miura, A.; Honma, R.; Satoh, R.; Wakamatsu, A.; Yamamoto, J.; Kimura, K.; Nishikawa, T.; Andoh, T.; Iida, Y.; Ishikawa, K.; Ito, E.; Kagawa, N.; Kaminaga, C.; Kanehori, K.; Kawakami, B.; Kenmochi, K.; Kimura, R.; Kobayashi, M.; Kuroita, T.; Kuwayama, H.; Maruyama, Y.; Matsuo, K.; Minami, K.; Mitsubori, M.; Mori, M.; Morishita, R.; Murase, A.; Nishikawa, A.; Nishikawa, S.; Okamoto, T.; Sakagami, N.; Sakamoto, Y.; Sasaki, Y.; Seki, T.; Sono, S.; Sugiyama, A.; Sumiya, T.; Takayama, T.; Takayama, Y.; Takeda, H.; Togashi, T.; Yahata, K.; Yamada, H.; Yanagisawa, Y.; Endo, Y.; Imamoto, F.; Kisu, Y.; Tanaka, S.; Isogai, T.; Imai, J.; Watanabe, S.; Nomura, N. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat. Methods, 2008, 5, 1011-1017.
115. Maruyama, Y.; Wakamatsu, A.; Kawamura, Y.; Kimura, K.; Yamamoto, J.; Nishikawa, T.; Kisu, Y.; Sugano, S.; Goshima, N.; Isogai, T.; Nomura, N. Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res. 2009, 37, D762-766.
116. Shimizu, Y.; Inoue, A.; Tomari, Y.; Suzuki, T.; Yokogawa, T.; Nishikawa, K.; Ueda, T. Cell-free translation reconstituted with purified components. Nat. Biotechnol., 2001, 19, 751-755.
117. Forster, A. C.; Tan, Z.; Nalam, M. N.; Lin, H.; Qu, H.; Cornish, V. W.; Blacklow, S. C. Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc. Natl. Acad. Sci., 2003, 100, 6353-6357.
118. Forster, A. C. Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome. Nucleic Acids Res., 2009, 37, 3747-3755.
119. Bartetzko, A.; Nierhaus, K. H. Mg2+/NH4+/polyamine system for polyuridine-dependent polyphenylalanine synthesis with near in vivo characteristics. Methods Enzymol., 1988, 164, 650-658.
120. Jelenc, P. C.; Kurland, C. G., Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl. Acad. Sci., 1979, 76, 3174-3178.
121. Stapulionis, R.; Wang, Y.; Dempsey, G. T.; Khudaravalli, R.; Nielsen, K. M.; Cooperman, B. S.; Goldman, Y. E.; Knudsen, C. R. Fast in vitro translation system immobilized on a surface via specific biotinylation of the ribosome. Biol. Chem., 2008, 389, 1239-1249.
122. Erlacher, M.; Polacek, N. Role of RNA backbone groups for ribosomal catalysis. Biotechnologia, 2009, 1, 65-80.
123. Martick, M.; Scott, W. G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell, 2006, 126, 309-320.
124. Voorhees, R. M.; Weixlbaumer, A.; Loakes, D.; Kelley, A. C.; Ramakrish-nan, V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat. Struct. Mol. Biol., 2009, 16, 528-533.