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Volumn 4, Issue 11, 1997, Pages 931-938

Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; RIBONUCLEASE P; RIBOZYME; RNA;

EID: 0030669671     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb1197-931     Document Type: Article
Times cited : (177)

References (46)
  • 2
    • 0025963132 scopus 로고
    • Visualizing the higher order folding of a catalytic RNA molecule
    • Celander, D.W. & Cech, T.R. Visualizing the higher order folding of a catalytic RNA molecule. Science 251, 401-407 (1991).
    • (1991) Science , vol.251 , pp. 401-407
    • Celander, D.W.1    Cech, T.R.2
  • 3
    • 0027434244 scopus 로고
    • Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure
    • Banerjee, A.R., Jaeger, J.A. & Turner, D.H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32, 153-163 (1993).
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.A.2    Turner, D.H.3
  • 4
    • 0028234517 scopus 로고
    • Thermodynamics of RNA folding in a conserved ribosomal RNA domain
    • Laing, L.G. & Draper, D.E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237, 560-576 (1994).
    • (1994) J. Mol. Biol. , vol.237 , pp. 560-576
    • Laing, L.G.1    Draper, D.E.2
  • 5
    • 0027173193 scopus 로고
    • An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme
    • Murphy, F.L. & T.R. Cech An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291-5300 (1993).
    • (1993) Biochemistry , vol.32 , pp. 5291-5300
    • Murphy, F.L.1    Cech, T.R.2
  • 6
    • 0029820625 scopus 로고    scopus 로고
    • Crystal structure of a group I ribozyme domain: Principles of RNA packing
    • Cate, J.H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678-1685 (1996).
    • (1996) Science , vol.273 , pp. 1678-1685
    • Cate, J.H.1
  • 7
    • 0028945859 scopus 로고
    • Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P
    • Pan, T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P, Biochemistry 34, 902-909 (1995).
    • (1995) Biochemistry , vol.34 , pp. 902-909
    • Pan, T.1
  • 8
    • 0029949699 scopus 로고    scopus 로고
    • Domain structure of the ribozyme from eubacterial ribonuclease P
    • Loria, A. & Pan, T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551-563 (1996).
    • (1996) RNA , vol.2 , pp. 551-563
    • Loria, A.1    Pan, T.2
  • 9
    • 0030952270 scopus 로고    scopus 로고
    • The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core
    • Doherty, E.A. & Doudna, J.A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 36, 3159-3169 (1997).
    • (1997) Biochemistry , vol.36 , pp. 3159-3169
    • Doherty, E.A.1    Doudna, J.A.2
  • 11
    • 0001103473 scopus 로고    scopus 로고
    • Kinetics of folding of proteins and RNA
    • Thirumalai, D. & Woodson, S.A. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29, 433-439 (1996).
    • (1996) Acc. Chem. Res. , vol.29 , pp. 433-439
    • Thirumalai, D.1    Woodson, S.A.2
  • 13
  • 14
    • 0015497450 scopus 로고
    • Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams
    • Cole, P.E., Yang, S.K. & Crothers, D.M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11, 4358-4368 (1972).
    • (1972) Biochemistry , vol.11 , pp. 4358-4368
    • Cole, P.E.1    Yang, S.K.2    Crothers, D.M.3
  • 15
    • 0016233090 scopus 로고
    • Cooperative binding of magnesium to transfer RNA studied by a fluorescent probe
    • Lynch, D.C. & Schimmel, P.R. Cooperative binding of magnesium to transfer RNA studied by a fluorescent probe. Biochemistry 13, 1841-1852 (1974).
    • (1974) Biochemistry , vol.13 , pp. 1841-1852
    • Lynch, D.C.1    Schimmel, P.R.2
  • 16
    • 0027991626 scopus 로고
    • Kinetic intermediates in RNA folding
    • Zarrinkar, P.P. & Williamson, J.R. Kinetic intermediates in RNA folding. Science 265, 918-924 (1994).
    • (1994) Science , vol.265 , pp. 918-924
    • Zarrinkar, P.P.1    Williamson, J.R.2
  • 17
    • 0029007094 scopus 로고
    • The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme
    • Banerjeee, A.R. & Turner, D.H. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. Biochemistry 34, 6504-6512 (1995).
    • (1995) Biochemistry , vol.34 , pp. 6504-6512
    • Banerjeee, A.R.1    Turner, D.H.2
  • 18
    • 0029874598 scopus 로고    scopus 로고
    • The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
    • Zarrinkar, P.P. & Williamson, J.R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nature Struct. Biol. 3, 432-438 (1996).
    • (1996) Nature Struct. Biol. , vol.3 , pp. 432-438
    • Zarrinkar, P.P.1    Williamson, J.R.2
  • 19
    • 0029958503 scopus 로고    scopus 로고
    • Slow folding kinetics of RNase P RNA
    • Zarrinkar, P.P., Wang, J. & Williamson, J.R. Slow folding kinetics of RNase P RNA. RNA 2, 564-573 (1996).
    • (1996) RNA , vol.2 , pp. 564-573
    • Zarrinkar, P.P.1    Wang, J.2    Williamson, J.R.3
  • 20
    • 0029904022 scopus 로고    scopus 로고
    • Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks
    • Downs, W.D. & Cech, T.R. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA 2, 718-732 (1996).
    • (1996) RNA , vol.2 , pp. 718-732
    • Downs, W.D.1    Cech, T.R.2
  • 21
    • 0029800606 scopus 로고    scopus 로고
    • Analysis of rate-determining Conformational changes during self-splicing of the Tetrahymena intron
    • Emerick, V.L., Pan, J. & Woodson, S.A. Analysis of rate-determining Conformational changes during self-splicing of the Tetrahymena intron. Biochemistry 35, 13469-13477 (1996).
    • (1996) Biochemistry , vol.35 , pp. 13469-13477
    • Emerick, V.L.1    Pan, J.2    Woodson, S.A.3
  • 22
    • 0031566962 scopus 로고    scopus 로고
    • Time- Resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: Application to protein-DNA interactions and RNA folding
    • Sclavi, B., Woodson, S., Sullivan, M., Chance, M.R. & Brenowitz, M. Time- resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J. Mol. Biol. 266, 144-159 (1997).
    • (1997) J. Mol. Biol. , vol.266 , pp. 144-159
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.R.4    Brenowitz, M.5
  • 24
    • 0028945546 scopus 로고
    • Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes
    • Gray, D.M., Hung, S.-H. & Johnson, K.H. Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Meths. Enz. 246, 19-34 (1995).
    • (1995) Meths. Enz. , vol.246 , pp. 19-34
    • Gray, D.M.1    Hung, S.-H.2    Johnson, K.H.3
  • 25
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning, G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11, 179-246 (1978).
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 26
    • 0023517017 scopus 로고
    • Effect of point mutations on the folding of globular proteins
    • Matthews, C.R. Effect of point mutations on the folding of globular proteins. Meths. Enz. 154, 498-511 (1987).
    • (1987) Meths. Enz. , vol.154 , pp. 498-511
    • Matthews, C.R.1
  • 27
    • 0016505899 scopus 로고
    • The stability of globular proteins
    • Pace, C.N. The stability of globular proteins. CRC Crit. Rev. biochem. 3:1-4-, (1975).
    • (1975) CRC Crit. Rev. Biochem. , vol.3
    • Pace, C.N.1
  • 28
    • 0017182937 scopus 로고
    • Structural domains of tranfer RNA molecules
    • Quigley, G.J. & Rich, A. Structural domains of tranfer RNA molecules. Science 194, 796-806 (1976).
    • (1976) Science , vol.194 , pp. 796-806
    • Quigley, G.J.1    Rich, A.2
  • 29
    • 0031576334 scopus 로고    scopus 로고
    • Folding of RNA involves parallel pathways
    • in the press
    • Pan, J., Thirumalai, D. & Woodson, S.A. Folding of RNA involves parallel pathways. J. Mol. Biol. in the press (1997).
    • (1997) J. Mol. Biol.
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 30
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson, S.E. & Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428-10435 (1991).
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 31
    • 0029940033 scopus 로고    scopus 로고
    • Molecular collapse: The rate- Limiting step in 2-state cytochrome c folding
    • Sosnick, T. R., Mayne, L. & Englander, S. W. Molecular collapse: The rate- limiting step in 2-state cytochrome c folding. Proteins: Struct. Funct. Genet. 24, 413-426 (1996).
    • (1996) Proteins: Struct. Funct. Genet. , vol.24 , pp. 413-426
    • Sosnick, T.R.1    Mayne, L.2    Englander, S.W.3
  • 33
    • 0029249945 scopus 로고
    • The nature of protein folding pathways: The classical versus the new view
    • Baldwin, R.L. The nature of protein folding pathways: The classical versus the new view. J. Biomol. NMR 5, 103-109 (1995).
    • (1995) J. Biomol. NMR , vol.5 , pp. 103-109
    • Baldwin, R.L.1
  • 34
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: Evidence from the lattice model
    • Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33, 10026-10036 (1994).
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 35
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki, L. S., Otzen, D. E. & Fersht, A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-88 (1995).
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 36
    • 0029010695 scopus 로고
    • Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
    • Guo, Z.Y. & Thirumalai, D. Kinetics of protein folding: Nucleation mechanism, time scales, and pathways. Biopolymers 36, 83-102 (1995).
    • (1995) Biopolymers , vol.36 , pp. 83-102
    • Guo, Z.Y.1    Thirumalai, D.2
  • 37
    • 0029643523 scopus 로고
    • Protein folding intermediates: Native-state hydrogen exchange
    • Bai, Y., Sosnick, T. R., Mayne, L. & Englander, S. W. Protein folding intermediates: Native-state hydrogen exchange. Science 269, 192-197 (1995).
    • (1995) Science , vol.269 , pp. 192-197
    • Bai, Y.1    Sosnick, T.R.2    Mayne, L.3    Englander, S.W.4
  • 38
    • 0029740071 scopus 로고    scopus 로고
    • Non-native α-helical intermediate in the refolding of β-lactoglobin, a predominantly β-sheet protein
    • Hamada, D., Segawa, S., Goto, Y. Non-native α-helical intermediate in the refolding of β-lactoglobin, a predominantly β-sheet protein. Nature Struct. Biol. 3, 868-873 (1996).
    • (1996) Nature Struct. Biol. , vol.3 , pp. 868-873
    • Hamada, D.1    Segawa, S.2    Goto, Y.3
  • 39
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson, J.D. & Wolynes, P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93, 6902-6915 (1989).
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 40
    • 36448999595 scopus 로고
    • Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice moldel simulations
    • Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice moldel simulations. J. Chem. Phys. 101:6052-6062 (1994).
    • (1994) J. Chem. Phys. , vol.101 , pp. 6052-6062
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 42
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4: 10-19 (1997).
    • (1997) Nature Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 43
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J.F., Groebe, D.R., Witherell, G.W. & Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798 (1987).
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 44
    • 0028088780 scopus 로고
    • Selection of circularly permuted ribozymes from Bacillus subtilis RNase P by substrate binding
    • Pan, T. & Zhong, K. Selection of circularly permuted ribozymes from Bacillus subtilis RNase P by substrate binding. Biochemistry 33, 14207-14212 (1994).
    • (1994) Biochemistry , vol.33 , pp. 14207-14212
    • Pan, T.1    Zhong, K.2
  • 45
    • 0027930184 scopus 로고
    • Asp catalyzed by the RNA component of Bacillus subtilis ribonuclease P
    • Asp catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry 33, 10294-10304 (1994).
    • (1994) Biochemistry , vol.33 , pp. 10294-10304
    • Beebe, J.A.1    Fierke, C.A.2
  • 46
    • 0031009290 scopus 로고    scopus 로고
    • Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P
    • Loria, A. & Pan, T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 36, 6317-6235 (1997).
    • (1997) Biochemistry , vol.36 , pp. 6317-16235
    • Loria, A.1    Pan, T.2


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