메뉴 건너뛰기




Volumn 353, Issue 5, 2005, Pages 1199-1209

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme

Author keywords

Polyelectrolyte; Ribozyme; RNA folding; RNA metal ions; SAXS

Indexed keywords

BACTERIAL ENZYME; ISOENZYME; MAGNESIUM; RIBONUCLEASE; RIBOZYME; RNA;

EID: 27144451444     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.09.015     Document Type: Article
Times cited : (47)

References (49)
  • 2
  • 3
    • 0030627401 scopus 로고    scopus 로고
    • Emerging themes in RNA folding
    • J.A. Doudna, and E.A. Doherty Emerging themes in RNA folding Fold. Des. 2 1997 R65 R70
    • (1997) Fold. Des. , vol.2
    • Doudna, J.A.1    Doherty, E.A.2
  • 5
    • 0035830964 scopus 로고    scopus 로고
    • Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
    • S.L. Heilman-Miller, D. Thirumalai, and S.A. Woodson Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations J. Mol. Biol. 306 2001 1157 1166
    • (2001) J. Mol. Biol. , vol.306 , pp. 1157-1166
    • Heilman-Miller, S.L.1    Thirumalai, D.2    Woodson, S.A.3
  • 6
    • 0242317691 scopus 로고    scopus 로고
    • Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction
    • M. Xiao, M.J. Leibowitz, and Y. Zhang Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction Nucl. Acids Res. 31 2003 3901 3908
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3901-3908
    • Xiao, M.1    Leibowitz, M.J.2    Zhang, Y.3
  • 7
    • 0034100560 scopus 로고    scopus 로고
    • Small angle X-ray scattering reveals a compact intermediate in RNA folding
    • R. Russell, I.S. Millett, S. Doniach, and D. Herschlag Small angle X-ray scattering reveals a compact intermediate in RNA folding Nature Struct. Biol. 7 2000 367 370
    • (2000) Nature Struct. Biol. , vol.7 , pp. 367-370
    • Russell, R.1    Millett, I.S.2    Doniach, S.3    Herschlag, D.4
  • 10
    • 0042009114 scopus 로고    scopus 로고
    • The fastest global events in RNA folding: Electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme
    • R. Das, L.W. Kwok, I.S. Millett, Y. Bai, T.T. Mills, and J. Jacob The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme J. Mol. Biol. 332 2003 311 319
    • (2003) J. Mol. Biol. , vol.332 , pp. 311-319
    • Das, R.1    Kwok, L.W.2    Millett, I.S.3    Bai, Y.4    Mills, T.T.5    Jacob, J.6
  • 11
    • 0027991626 scopus 로고
    • Kinetic intermediates in RNA folding
    • P.P. Zarrinkar, and J.R. Williamson Kinetic intermediates in RNA folding Science 265 1994 918 924
    • (1994) Science , vol.265 , pp. 918-924
    • Zarrinkar, P.P.1    Williamson, J.R.2
  • 12
    • 0031576334 scopus 로고    scopus 로고
    • Folding of RNA involves parallel pathways
    • J. Pan, D. Thirumalai, and S.A. Woodson Folding of RNA involves parallel pathways J. Mol. Biol. 273 1997 7 13
    • (1997) J. Mol. Biol. , vol.273 , pp. 7-13
    • Pan, J.1    Thirumalai, D.2    Woodson, S.A.3
  • 13
    • 0035808384 scopus 로고    scopus 로고
    • Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction
    • D.K. Treiber, and J.R. Williamson Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction J. Mol. Biol. 305 2001 11 21
    • (2001) J. Mol. Biol. , vol.305 , pp. 11-21
    • Treiber, D.K.1    Williamson, J.R.2
  • 14
    • 0035906731 scopus 로고    scopus 로고
    • Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway
    • R. Russell, and D. Herschlag Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway J. Mol. Biol. 308 2001 839 851
    • (2001) J. Mol. Biol. , vol.308 , pp. 839-851
    • Russell, R.1    Herschlag, D.2
  • 15
    • 0032590020 scopus 로고    scopus 로고
    • 2+-dependent folding of a large ribozyme without kinetic traps
    • 2+-dependent folding of a large ribozyme without kinetic traps Nature Struct. Biol. 6 1999 1091 1095
    • (1999) Nature Struct. Biol. , vol.6 , pp. 1091-1095
    • Fang, X.W.1    Pan, T.2    Sosnick, T.R.3
  • 16
    • 0037173087 scopus 로고    scopus 로고
    • The rate-limiting step in the folding of a large ribozyme without kinetic traps
    • X.W. Fang, P. Thiyagarajan, T.R. Sosnick, and T. Pan The rate-limiting step in the folding of a large ribozyme without kinetic traps Proc. Natl Acad. Sci. USA 99 2002 8518 8523
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8518-8523
    • Fang, X.W.1    Thiyagarajan, P.2    Sosnick, T.R.3    Pan, T.4
  • 17
    • 0035156627 scopus 로고    scopus 로고
    • A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex
    • A.E. Webb, and K.M. Weeks A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex Nature Struct. Biol. 8 2001 135 140
    • (2001) Nature Struct. Biol. , vol.8 , pp. 135-140
    • Webb, A.E.1    Weeks, K.M.2
  • 18
    • 0344844493 scopus 로고    scopus 로고
    • Near native structure in an RNA collapsed state
    • K.L. Buchmueller, and K.M. Weeks Near native structure in an RNA collapsed state Biochemistry 42 2003 13869 13878
    • (2003) Biochemistry , vol.42 , pp. 13869-13878
    • Buchmueller, K.L.1    Weeks, K.M.2
  • 19
    • 0029805902 scopus 로고    scopus 로고
    • Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus
    • M. Tanner, and T. Cech Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus RNA 2 1996 74 83
    • (1996) RNA , vol.2 , pp. 74-83
    • Tanner, M.1    Cech, T.2
  • 20
    • 0037452797 scopus 로고    scopus 로고
    • Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme
    • P. Rangan, B. Masquida, E. Westhof, and S.A. Woodson Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme Proc. Natl Acad. Sci. USA 100 2003 1574 1579
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 1574-1579
    • Rangan, P.1    Masquida, B.2    Westhof, E.3    Woodson, S.A.4
  • 22
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • P.L. Adams, M.R. Stahley, A.B. Kosek, J. Wang, and S.A. Strobel Crystal structure of a self-splicing group I intron with both exons Nature 430 2004 45 50
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 23
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • D. Thirumalai, and C. Hyeon RNA and protein folding: common themes and variations Biochemistry 44 2005 4957 4970
    • (2005) Biochemistry , vol.44 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 24
    • 0025134897 scopus 로고
    • Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns
    • F. Michel, A.D. Ellington, S. Couture, and J.W. Szostak Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns Nature 347 1990 578 580
    • (1990) Nature , vol.347 , pp. 578-580
    • Michel, F.1    Ellington, A.D.2    Couture, S.3    Szostak, J.W.4
  • 25
    • 0028294458 scopus 로고
    • Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
    • L. Jaeger, F. Michel, and E. Westhof Involvement of a GNRA tetraloop in long-range RNA tertiary interactions J. Mol. Biol. 236 1994 1271 1276
    • (1994) J. Mol. Biol. , vol.236 , pp. 1271-1276
    • Jaeger, L.1    Michel, F.2    Westhof, E.3
  • 26
    • 6344242969 scopus 로고    scopus 로고
    • Principles of RNA compaction: Insights from the equilibrium folding pathway of the p4-p6 RNA domain in monovalent cations
    • K. Takamoto, R. Das, Q. He, S. Doniach, M. Brenowitz, D. Herschlag, and M.R. Chance Principles of RNA compaction: insights from the equilibrium folding pathway of the p4-p6 RNA domain in monovalent cations J. Mol. Biol. 343 2004 1195 1206
    • (2004) J. Mol. Biol. , vol.343 , pp. 1195-1206
    • Takamoto, K.1    Das, R.2    He, Q.3    Doniach, S.4    Brenowitz, M.5    Herschlag, D.6    Chance, M.R.7
  • 28
    • 0038737980 scopus 로고    scopus 로고
    • 2+ binding in the group I intron core
    • 2+ binding in the group I intron core J. Mol. Biol. 329 2003 229 238
    • (2003) J. Mol. Biol. , vol.329 , pp. 229-238
    • Rangan, P.1    Woodson, S.A.2
  • 29
    • 0024285808 scopus 로고
    • Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes
    • A.J. Zaug, C.A. Grosshans, and T.R. Cech Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes Biochemistry 27 1988 8924 8931
    • (1988) Biochemistry , vol.27 , pp. 8924-8931
    • Zaug, A.J.1    Grosshans, C.A.2    Cech, T.R.3
  • 30
    • 0032732707 scopus 로고    scopus 로고
    • Characterization of the Azoarcus ribozyme: Tight binding to guanosine and substrate by an unusually small group I ribozyme
    • L.Y. Kuo, L.A. Davidson, and S. Pico Characterization of the Azoarcus ribozyme: tight binding to guanosine and substrate by an unusually small group I ribozyme Biochim. Biophys. Acta 1489 1999 281 292
    • (1999) Biochim. Biophys. Acta , vol.1489 , pp. 281-292
    • Kuo, L.Y.1    Davidson, L.A.2    Pico, S.3
  • 31
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 32
    • 0027434244 scopus 로고
    • Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure
    • A.R. Banerjee, J.A. Jaeger, and D.H. Turner Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure Biochemistry 32 1993 153 163
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.A.2    Turner, D.H.3
  • 33
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • M. Wu, and I. Tinoco Jr RNA folding causes secondary structure rearrangement Proc. Natl Acad. Sci. USA 95 1998 11555 11560
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11555-11560
    • Wu, M.1    Tinoco Jr., I.2
  • 34
    • 0032578390 scopus 로고    scopus 로고
    • Native secondary structure formation in RNA may be a slave to tertiary folding
    • D. Thirumalai Native secondary structure formation in RNA may be a slave to tertiary folding Proc. Natl Acad. Sci. USA 95 1998 11506 11508
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11506-11508
    • Thirumalai, D.1
  • 36
    • 0030669671 scopus 로고    scopus 로고
    • Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity
    • T. Pan, and T.R. Sosnick Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity Nature Struct. Biol. 4 1997 931 938
    • (1997) Nature Struct. Biol. , vol.4 , pp. 931-938
    • Pan, T.1    Sosnick, T.R.2
  • 37
    • 0037466322 scopus 로고    scopus 로고
    • Perturbed folding kinetics of circularly permuted RNAs with altered topology
    • S.L. Heilman-Miller, and S.A. Woodson Perturbed folding kinetics of circularly permuted RNAs with altered topology J. Mol. Biol. 328 2003 385 394
    • (2003) J. Mol. Biol. , vol.328 , pp. 385-394
    • Heilman-Miller, S.L.1    Woodson, S.A.2
  • 38
    • 3042733138 scopus 로고    scopus 로고
    • Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding
    • G. Pljevaljcic, D.P. Millar, and A.A. Deniz Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding Biophys. J. 87 2004 457 467
    • (2004) Biophys. J. , vol.87 , pp. 457-467
    • Pljevaljcic, G.1    Millar, D.P.2    Deniz, A.A.3
  • 39
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • G.S. Manning The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Quart. Rev. Biophys. 11 1978 179 246
    • (1978) Quart. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 41
    • 4444370899 scopus 로고    scopus 로고
    • Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
    • I. Shcherbakova, S. Gupta, M.R. Chance, and M. Brenowitz Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme J. Mol. Biol. 342 2004 1431 1442
    • (2004) J. Mol. Biol. , vol.342 , pp. 1431-1442
    • Shcherbakova, I.1    Gupta, S.2    Chance, M.R.3    Brenowitz, M.4
  • 42
    • 0032563297 scopus 로고    scopus 로고
    • Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core
    • J. Pan, and S.A. Woodson Folding intermediates of a self-splicing RNA: mispairing of the catalytic core J. Mol. Biol. 280 1998 597 609
    • (1998) J. Mol. Biol. , vol.280 , pp. 597-609
    • Pan, J.1    Woodson, S.A.2
  • 43
    • 0034635353 scopus 로고    scopus 로고
    • Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA
    • J. Pan, M.L. Deras, and S.A. Woodson Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA J. Mol. Biol. 296 2000 133 144
    • (2000) J. Mol. Biol. , vol.296 , pp. 133-144
    • Pan, J.1    Deras, M.L.2    Woodson, S.A.3
  • 45
    • 11144256451 scopus 로고    scopus 로고
    • Fast formation of the P3-P7 pseudoknot: A strategy for efficient folding of the catalytically active ribozyme
    • L. Zhang, M. Xiao, C. Lu, and Y. Zhang Fast formation of the P3-P7 pseudoknot: a strategy for efficient folding of the catalytically active ribozyme RNA 11 2005 59 69
    • (2005) RNA , vol.11 , pp. 59-69
    • Zhang, L.1    Xiao, M.2    Lu, C.3    Zhang, Y.4
  • 46
    • 0026244044 scopus 로고
    • GNOM - A program package for small-angle scattering data-processing
    • A.V. Semenyuk, and D.I. Svergun GNOM - a program package for small-angle scattering data-processing J. Appl. Crystallog. 24 1991 537 540
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 537-540
    • Semenyuk, A.V.1    Svergun, D.I.2
  • 47
    • 0028587156 scopus 로고
    • Catalysis of RNA cleavage by a ribozyme derived from the group I intron of Anabaena pre-tRNA(Leu)
    • A.J. Zaug, J.A. Davila-Aponte, and T.R. Cech Catalysis of RNA cleavage by a ribozyme derived from the group I intron of Anabaena pre-tRNA(Leu) Biochemistry 33 1994 14935 14947
    • (1994) Biochemistry , vol.33 , pp. 14935-14947
    • Zaug, A.J.1    Davila-Aponte, J.A.2    Cech, T.R.3
  • 48
    • 0028234517 scopus 로고
    • Thermodynamics of RNA folding in a conserved ribosomal RNA domain
    • L.G. Laing, and D.E. Draper Thermodynamics of RNA folding in a conserved ribosomal RNA domain J. Mol. Biol. 237 1994 560 576
    • (1994) J. Mol. Biol. , vol.237 , pp. 560-576
    • Laing, L.G.1    Draper, D.E.2
  • 49
    • 0026599998 scopus 로고
    • Self-splicing introns in tRNA genes of widely divergent bacteria
    • B. Reinhold-Hurek, and D.A. Shub Self-splicing introns in tRNA genes of widely divergent bacteria Nature 357 1992 173 176
    • (1992) Nature , vol.357 , pp. 173-176
    • Reinhold-Hurek, B.1    Shub, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.