메뉴 건너뛰기




Volumn 353, Issue 3, 2005, Pages 540-555

Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR

Author keywords

13C relaxation; Base flipping; Chemical shift anisotropy; Nuclear magnetic resonance (NMR); U6 snRNA

Indexed keywords

MAGNESIUM ION; NUCLEOTIDE; SMALL NUCLEAR RNA; URIDINE;

EID: 26244435237     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.08.030     Document Type: Article
Times cited : (58)

References (52)
  • 1
    • 0038206733 scopus 로고    scopus 로고
    • 2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings
    • 2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings J. Mol. Biol. 329 2003 867 873
    • (2003) J. Mol. Biol. , vol.329 , pp. 867-873
    • Al-Hashimi, H.M.1    Pitt, S.W.2    Majumdar, A.3    Xu, W.4    Patel, D.J.5
  • 2
    • 0034043484 scopus 로고    scopus 로고
    • Recent insights on RNA folding mechanisms from catalytic RNA
    • S.A. Woodson Recent insights on RNA folding mechanisms from catalytic RNA Cell Mol. Life Sci. 57 2000 796 808
    • (2000) Cell Mol. Life Sci. , vol.57 , pp. 796-808
    • Woodson, S.A.1
  • 3
    • 0034911866 scopus 로고    scopus 로고
    • Nuclear magnetic resonance methods to study structure and dynamics of RNA-protein complexes
    • M. Allen, L. Varani, and G. Varani Nuclear magnetic resonance methods to study structure and dynamics of RNA-protein complexes Methods Enzymol. 339 2001 357 376
    • (2001) Methods Enzymol. , vol.339 , pp. 357-376
    • Allen, M.1    Varani, L.2    Varani, G.3
  • 4
    • 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
  • 6
    • 0032573527 scopus 로고    scopus 로고
    • Order, dynamics and metal-binding in the lead-dependent ribozyme
    • P. Legault, C.G. Hoogstraten, E. Metlitzky, and A. Pardi Order, dynamics and metal-binding in the lead-dependent ribozyme J. Mol. Biol. 284 1998 325 335
    • (1998) J. Mol. Biol. , vol.284 , pp. 325-335
    • Legault, P.1    Hoogstraten, C.G.2    Metlitzky, E.3    Pardi, A.4
  • 7
    • 0032580790 scopus 로고    scopus 로고
    • 13C Relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin
    • 13C Relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin Biochemistry 37 1998 9323 9332
    • (1998) Biochemistry , vol.37 , pp. 9323-9332
    • Hall, K.B.1    Tang, C.2
  • 8
    • 0034664076 scopus 로고    scopus 로고
    • Active site dynamics in the lead-dependent ribozyme
    • C.G. Hoogstraten, J.R. Wank, and A. Pardi Active site dynamics in the lead-dependent ribozyme Biochemistry 39 2000 9951 9958
    • (2000) Biochemistry , vol.39 , pp. 9951-9958
    • Hoogstraten, C.G.1    Wank, J.R.2    Pardi, A.3
  • 10
    • 7244254183 scopus 로고    scopus 로고
    • Dynamics in the U6 RNA intramolecular stem-loop: A base flipping conformational change
    • N.J. Reiter, H. Blad, F. Abildgaard, and S.E. Butcher Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change Biochemistry 43 2004 13739 13747
    • (2004) Biochemistry , vol.43 , pp. 13739-13747
    • Reiter, N.J.1    Blad, H.2    Abildgaard, F.3    Butcher, S.E.4
  • 11
    • 0036948420 scopus 로고    scopus 로고
    • Allosteric cascade of spliceosome activation
    • D.A. Brow Allosteric cascade of spliceosome activation Annu. Rev. Genet. 36 2002 333 360
    • (2002) Annu. Rev. Genet. , vol.36 , pp. 333-360
    • Brow, D.A.1
  • 12
    • 0026486883 scopus 로고
    • A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome
    • H.D. Madhani, and C. Guthrie A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome Cell 71 1992 803 817
    • (1992) Cell , vol.71 , pp. 803-817
    • Madhani, H.D.1    Guthrie, C.2
  • 13
    • 0029959586 scopus 로고    scopus 로고
    • Interactions of the yeast U6 RNA with the pre-mRNA branch site
    • D.S. McPheeters Interactions of the yeast U6 RNA with the pre-mRNA branch site RNA 2 1996 1110 1123
    • (1996) RNA , vol.2 , pp. 1110-1123
    • McPheeters, D.S.1
  • 14
    • 0030833215 scopus 로고    scopus 로고
    • Metal ion catalysis during splicing of pre-messenger RNA
    • E.J. Sontheimer, S.G. Sun, and J.A. Piccirilli Metal ion catalysis during splicing of pre-messenger RNA Nature 388 1997 801 805
    • (1997) Nature , vol.388 , pp. 801-805
    • Sontheimer, E.J.1    Sun, S.G.2    Piccirilli, J.A.3
  • 15
    • 0033965261 scopus 로고    scopus 로고
    • Metal ion catalysis during exon-ligation step of nuclear pre-mRNA splicing: Extending the parallels between the spliceosome and group II introns
    • P.M. Gordon, E.J. Sontheimer, and J.A. Piccirilli Metal ion catalysis during exon-ligation step of nuclear pre-mRNA splicing: Extending the parallels between the spliceosome and group II introns RNA 6 2000 199 205
    • (2000) RNA , vol.6 , pp. 199-205
    • Gordon, P.M.1    Sontheimer, E.J.2    Piccirilli, J.A.3
  • 16
    • 0034649666 scopus 로고    scopus 로고
    • Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome
    • S.L. Yean, G. Wuenschell, J. Termini, and R.J. Lin Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome Nature 408 2000 881 884
    • (2000) Nature , vol.408 , pp. 881-884
    • Yean, S.L.1    Wuenschell, G.2    Termini, J.3    Lin, R.J.4
  • 17
    • 0035909314 scopus 로고    scopus 로고
    • Splicing-related catalysis by protein-free snRNAs
    • S. Valadkhan, and J.L. Manley Splicing-related catalysis by protein-free snRNAs Nature 413 2001 701 707
    • (2001) Nature , vol.413 , pp. 701-707
    • Valadkhan, S.1    Manley, J.L.2
  • 19
  • 20
    • 0034919305 scopus 로고    scopus 로고
    • NMR methods for quantifying microsecond to millisecond motions in biologial macromolecules
    • A.G. Palmer, C.D. Kroenke, and J.P. Loria NMR methods for quantifying microsecond to millisecond motions in biologial macromolecules Methods Enzymol. 339 2001 204 238
    • (2001) Methods Enzymol. , vol.339 , pp. 204-238
    • Palmer, A.G.1    Kroenke, C.D.2    Loria, J.P.3
  • 21
    • 0001248067 scopus 로고
    • Studies of chemical exchange by nuclear magnetic relaxation in the rotating frame
    • C. Deverell, R.E. Morgan, and J.H. Strange Studies of chemical exchange by nuclear magnetic relaxation in the rotating frame Mol. Phys. 18 1970 553
    • (1970) Mol. Phys. , vol.18 , pp. 553
    • Deverell, C.1    Morgan, R.E.2    Strange, J.H.3
  • 22
    • 0027384192 scopus 로고
    • Conformational backbone dynamics of the cyclic decapeptide antamanide. Application of a new multiconformational search algorithm based on NMR data
    • M.J. Blackledge, R. Brüschweiler, C. Griesinger, J.M. Schmidt, P. Xu, and R.R. Ernst Conformational backbone dynamics of the cyclic decapeptide antamanide. Application of a new multiconformational search algorithm based on NMR data Biochemistry 32 1993 10960 10974
    • (1993) Biochemistry , vol.32 , pp. 10960-10974
    • Blackledge, M.J.1    Brüschweiler, R.2    Griesinger, C.3    Schmidt, J.M.4    Xu, P.5    Ernst, R.R.6
  • 25
    • 10144257606 scopus 로고
    • Estimation of NMR function accuracies from least-squares fitting
    • A. Celmiņš Estimation of NMR function accuracies from least-squares fitting J. Magn. Reson. 50 1982 373 381
    • (1982) J. Magn. Reson. , vol.50 , pp. 373-381
    • Celmiņš, A.1
  • 28
    • 0020855355 scopus 로고
    • Hydrogen-exchange and structural dynamics of proteins and nucleic-acids
    • S.W. Englander, and N.R. Kallenbach Hydrogen-exchange and structural dynamics of proteins and nucleic-acids Quart. Rev. Biophys. 16 1983 521 655
    • (1983) Quart. Rev. Biophys. , vol.16 , pp. 521-655
    • Englander, S.W.1    Kallenbach, N.R.2
  • 29
    • 0028864424 scopus 로고
    • Studies of base pair kinetics by NMR measurement of proton exchange
    • M. Gueron, and J.L. Leroy Studies of base pair kinetics by NMR measurement of proton exchange Methods Enzymol. 261 1995 383 413
    • (1995) Methods Enzymol. , vol.261 , pp. 383-413
    • Gueron, M.1    Leroy, J.L.2
  • 31
    • 0030747007 scopus 로고    scopus 로고
    • a shift at the active site of a lead-dependent ribozyme
    • a shift at the active site of a lead-dependent ribozyme J. Am. Chem. Soc. 119 1997 6621 6628
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 6621-6628
    • Legault, P.1    Pardi, A.2
  • 32
    • 0029869856 scopus 로고    scopus 로고
    • Solution structure of loop a from the hairpin ribozyme from tobacco ringspot virus satellite
    • Z. Cai, and I. Tinoco Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite Biochemistry 35 1996 6026 6036
    • (1996) Biochemistry , vol.35 , pp. 6026-6036
    • Cai, Z.1    Tinoco, I.2
  • 33
    • 26244456236 scopus 로고
    • Field dependence of solvent proton and deuteron NMR relaxation rates of the manganese (II) binding site of chloroplast coupling factor 1
    • A.E. Haddy, and R.R. Sharp Field dependence of solvent proton and deuteron NMR relaxation rates of the manganese (II) binding site of chloroplast coupling factor 1 Biochemistry 28 1989 3656 3664
    • (1989) Biochemistry , vol.28 , pp. 3656-3664
    • Haddy, A.E.1    Sharp, R.R.2
  • 34
    • 0032719896 scopus 로고    scopus 로고
    • Calculations of NMR dipolar coupling strengths in model peptides
    • D.A. Case Calculations of NMR dipolar coupling strengths in model peptides J. Biomol. NMR 15 1999 95 102
    • (1999) J. Biomol. NMR , vol.15 , pp. 95-102
    • Case, D.A.1
  • 35
    • 0038539610 scopus 로고    scopus 로고
    • 2+ binding sites of the 5S rRNA loop e motif as investigated by molecular dynamics simulations
    • 2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations Chem. Biol. 10 2003 551 561
    • (2003) Chem. Biol. , vol.10 , pp. 551-561
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 36
    • 67049156092 scopus 로고    scopus 로고
    • Ionic solvation in aqueous and nonaqueous solutions
    • H. Ohtaki Ionic solvation in aqueous and nonaqueous solutions Monatshefte für Chemie 32 2001 1237 1268
    • (2001) Monatshefte für Chemie , vol.32 , pp. 1237-1268
    • Ohtaki, H.1
  • 37
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • G. Lipari, and A. Szabo Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity J. Am. Chem. Soc. 104 1982 4546 4559
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 38
    • 0025046144 scopus 로고
    • Deviation from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
    • G.M. Clore, A. Szabo, A. Bax, L.E. Kay, P.C. Driscoll, and A.M. Gronenborn Deviation from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins J. Am. Chem. Soc. 112 1990 4989 4991
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 4989-4991
    • Clore, G.M.1    Szabo, A.2    Bax, A.3    Kay, L.E.4    Driscoll, P.C.5    Gronenborn, A.M.6
  • 40
    • 0041464604 scopus 로고    scopus 로고
    • Crystal structure of the leadzyme at 1.8 Å resolution: Metal ion binding and the implications for catalytic mechanism and allo site ion regulation
    • J.E. Wedekind, and D.B. McKay Crystal structure of the leadzyme at 1.8 Å resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation Biochemistry 42 2003 9554 9563
    • (2003) Biochemistry , vol.42 , pp. 9554-9563
    • Wedekind, J.E.1    McKay, D.B.2
  • 42
    • 0035367070 scopus 로고    scopus 로고
    • Structure and function of the small ribozymes
    • S.E. Butcher Structure and function of the small ribozymes Curr. Opin. Struct. Biol. 11 2001 315 320
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 315-320
    • Butcher, S.E.1
  • 43
    • 0000987483 scopus 로고    scopus 로고
    • An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations
    • F.A.A. Mulder, R.A. de Graaf, R. Kaptein, and R. Boelens An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations J. Magn. Reson. 131 1998 351 357
    • (1998) J. Magn. Reson. , vol.131 , pp. 351-357
    • Mulder, F.A.A.1    De Graaf, R.A.2    Kaptein, R.3    Boelens, R.4
  • 45
    • 0037063506 scopus 로고    scopus 로고
    • An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates
    • D.M. Korzhnev, N.R. Skrynnikov, O. Millet, D.A. Torchia, and L.E. Kay An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates J. Am. Chem. Soc. 124 2002 10743 10753
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 10743-10753
    • Korzhnev, D.M.1    Skrynnikov, N.R.2    Millet, O.3    Torchia, D.A.4    Kay, L.E.5
  • 46
    • 0032608454 scopus 로고    scopus 로고
    • 1 field inhomogeneity. Are the biases assumed in heteronuclear relaxation experiments usually underestimated?
    • 1 field inhomogeneity. Are the biases assumed in heteronuclear relaxation experiments usually underestimated? J. Magn. Reson. 136 1999 118 126
    • (1999) J. Magn. Reson. , vol.136 , pp. 118-126
    • Guenneuges, M.1    Berthault, P.2    Desvaux, H.3
  • 48
    • 5144229966 scopus 로고
    • Practical aspects of two-dimensional transverse NOE spectroscopy
    • A. Bax, and D.G. Davis Practical aspects of two-dimensional transverse NOE spectroscopy J. Magn. Reson. 63 1985 207 213
    • (1985) J. Magn. Reson. , vol.63 , pp. 207-213
    • Bax, A.1    Davis, D.G.2
  • 49
    • 0029283694 scopus 로고
    • Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data
    • R.A. Chylla, and J.L. Markley Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data J. Biomol. NMR 6 1995 245 258
    • (1995) J. Biomol. NMR , vol.6 , pp. 245-258
    • Chylla, R.A.1    Markley, J.L.2
  • 51
    • 0000973097 scopus 로고
    • Study of slow molecular motions in solution using off-resonance irradiation in homonuclear NMR: 2. Fast chemical-exchange processes
    • H. Desvaux, N. Birlirakis, C. Wary, and P. Berthault Study of slow molecular motions in solution using off-resonance irradiation in homonuclear NMR: 2. Fast chemical-exchange processes Mol. Phys. 86 1995 1059 1073
    • (1995) Mol. Phys. , vol.86 , pp. 1059-1073
    • Desvaux, H.1    Birlirakis, N.2    Wary, C.3    Berthault, P.4
  • 52
    • 0034921520 scopus 로고    scopus 로고
    • Identification and characterization of metal ion binding sites in RNA
    • R.L. Gonzalez, and I. Tinoco Identification and characterization of metal ion binding sites in RNA Methods Enzymol. 338 2001 421 443
    • (2001) Methods Enzymol. , vol.338 , pp. 421-443
    • Gonzalez, R.L.1    Tinoco, I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.