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Volumn 359, Issue 3, 2006, Pages 754-768

Erratum to "Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain" [J. Mol. Biol. 359 (2006) 754-768] (DOI:10.1016/j.jmb.2006.04.003);Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

Author keywords

aptamer; isothermal titration calorimetry; mRNA; riboswitch; RNA structure

Indexed keywords

2,6 DIAMINOPURINE; ADENINE DERIVATIVE; APTAMER; GUANINE; HYPOXANTHINE; NUCLEIC ACID BASE; PYRIMIDINE; RNA;

EID: 33646768226     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.075     Document Type: Erratum
Times cited : (231)

References (54)
  • 1
    • 24644502657 scopus 로고    scopus 로고
    • From birth to death: the complex lives of eukaryotic mRNAs
    • Moore M.J. From birth to death: the complex lives of eukaryotic mRNAs. Science 309 (2005) 1514-1518
    • (2005) Science , vol.309 , pp. 1514-1518
    • Moore, M.J.1
  • 2
    • 13444287967 scopus 로고    scopus 로고
    • Assembly and function of RNA silencing complexes
    • Sontheimer E.J. Assembly and function of RNA silencing complexes. Nature Rev. Mol. Cell Biol. 6 (2005) 127-138
    • (2005) Nature Rev. Mol. Cell Biol. , vol.6 , pp. 127-138
    • Sontheimer, E.J.1
  • 4
    • 0034625237 scopus 로고    scopus 로고
    • 6 S RNA regulates E. coli RNA polymerase activity
    • Wassarman K.M., and Storz G. 6 S RNA regulates E. coli RNA polymerase activity. Cell 101 (2000) 613-623
    • (2000) Cell , vol.101 , pp. 613-623
    • Wassarman, K.M.1    Storz, G.2
  • 5
    • 0242361319 scopus 로고    scopus 로고
    • Inhibition of P-TEFb (CDK9/cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA
    • Yik J.H., Chen R., Nishimura R., Jennings J.L., Link A.J., and Zhou Q. Inhibition of P-TEFb (CDK9/cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol. Cell 12 (2003) 971-982
    • (2003) Mol. Cell , vol.12 , pp. 971-982
    • Yik, J.H.1    Chen, R.2    Nishimura, R.3    Jennings, J.L.4    Link, A.J.5    Zhou, Q.6
  • 6
    • 0035320036 scopus 로고    scopus 로고
    • mRNA localization: message on the move
    • Jansen R.P. mRNA localization: message on the move. Nature Rev. Mol. Cell Biol. 2 (2001) 247-256
    • (2001) Nature Rev. Mol. Cell Biol. , vol.2 , pp. 247-256
    • Jansen, R.P.1
  • 8
    • 0033059981 scopus 로고    scopus 로고
    • Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis
    • Zhao J., Hyman L., and Moore C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63 (1999) 405-445
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 405-445
    • Zhao, J.1    Hyman, L.2    Moore, C.3
  • 9
    • 0033575897 scopus 로고    scopus 로고
    • Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA
    • Antson A.A., Dodson E.J., Dodson G., Greaves R.B., Chen X., and Gollnick P. Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401 (1999) 235-242
    • (1999) Nature , vol.401 , pp. 235-242
    • Antson, A.A.1    Dodson, E.J.2    Dodson, G.3    Greaves, R.B.4    Chen, X.5    Gollnick, P.6
  • 10
    • 29144475324 scopus 로고    scopus 로고
    • Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis
    • Gollnick P., Babitzke P., Antson A., and Yanofsky C. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu. Rev. Genet. 39 (2005) 47-68
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 47-68
    • Gollnick, P.1    Babitzke, P.2    Antson, A.3    Yanofsky, C.4
  • 11
    • 0028251157 scopus 로고
    • Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli
    • Zengel J.M., and Lindahl L. Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli. Prog. Nucl. Acid Res. Mol. Biol. 47 (1994) 331-370
    • (1994) Prog. Nucl. Acid Res. Mol. Biol. , vol.47 , pp. 331-370
    • Zengel, J.M.1    Lindahl, L.2
  • 12
    • 1642602044 scopus 로고    scopus 로고
    • RNA finds a simpler way
    • Cech T.R. RNA finds a simpler way. Nature 428 (2004) 263-264
    • (2004) Nature , vol.428 , pp. 263-264
    • Cech, T.R.1
  • 14
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler E., and Mironov A.S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29 (2004) 11-17
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 15
    • 0347418195 scopus 로고    scopus 로고
    • Riboswitches: the oldest mechanism for the regulation of gene expression?
    • Vitreschak A.G., Rodionov D.A., Mironov A.A., and Gelfand M.S. Riboswitches: the oldest mechanism for the regulation of gene expression?. Trends Genet. 20 (2004) 44-50
    • (2004) Trends Genet. , vol.20 , pp. 44-50
    • Vitreschak, A.G.1    Rodionov, D.A.2    Mironov, A.A.3    Gelfand, M.S.4
  • 16
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler W., Nahvi A., and Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419 (2002) 952-956
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 17
    • 32044442926 scopus 로고    scopus 로고
    • Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
    • Corbino K.A., Barrick J.E., Lim J., Welz R., Tucker B.J., Puskarz I., et al. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol. 6 (2005) R70
    • (2005) Genome Biol. , vol.6
    • Corbino, K.A.1    Barrick, J.E.2    Lim, J.3    Welz, R.4    Tucker, B.J.5    Puskarz, I.6
  • 19
    • 0023655214 scopus 로고
    • Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis
    • Ebbole D.J., and Zalkin H. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J. Biol. Chem. 262 (1987) 8274-8287
    • (1987) J. Biol. Chem. , vol.262 , pp. 8274-8287
    • Ebbole, D.J.1    Zalkin, H.2
  • 20
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • Mandal M., Boese B., Barrick J.E., Winkler W.C., and Breaker R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113 (2003) 577-586
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 23
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey R.T., Gilbert S.D., and Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432 (2004) 411-415
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 24
    • 10644250950 scopus 로고    scopus 로고
    • Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs
    • Serganov A., Yuan Y.R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11 (2004) 1729-1741
    • (2004) Chem. Biol. , vol.11 , pp. 1729-1741
    • Serganov, A.1    Yuan, Y.R.2    Pikovskaya, O.3    Polonskaia, A.4    Malinina, L.5    Phan, A.T.6
  • 25
    • 13444271576 scopus 로고    scopus 로고
    • An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
    • Noeske J., Richter C., Grundl M.A., Nasiri H.R., Schwalbe H., and Wohnert J. An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl Acad. Sci. USA 102 (2005) 1372-1377
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1372-1377
    • Noeske, J.1    Richter, C.2    Grundl, M.A.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 26
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • Wickiser J.K., Winkler W.C., Breaker R.R., and Crothers D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18 (2005) 49-60
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 27
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • Wickiser J.K., Cheah M.T., Breaker R.R., and Crothers D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44 (2005) 13404-13414
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 28
    • 0037432340 scopus 로고    scopus 로고
    • Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex
    • Jucker F.M., Phillips R.M., McCallum S.A., and Pardi A. Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Biochemistry 42 (2003) 2560-2567
    • (2003) Biochemistry , vol.42 , pp. 2560-2567
    • Jucker, F.M.1    Phillips, R.M.2    McCallum, S.A.3    Pardi, A.4
  • 29
    • 0034604296 scopus 로고    scopus 로고
    • The 2.8 Å crystal structure of the malachite green aptamer
    • Baugh C., Grate D., and Wilson C. The 2.8 Å crystal structure of the malachite green aptamer. J. Mol. Biol. 301 (2000) 117-128
    • (2000) J. Mol. Biol. , vol.301 , pp. 117-128
    • Baugh, C.1    Grate, D.2    Wilson, C.3
  • 30
    • 0029904020 scopus 로고    scopus 로고
    • Solution structure of an ATP-binding RNA aptamer reveals a novel fold
    • Dieckmann T., Suzuki E., Nakamura G.K., and Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 2 (1996) 628-640
    • (1996) RNA , vol.2 , pp. 628-640
    • Dieckmann, T.1    Suzuki, E.2    Nakamura, G.K.3    Feigon, J.4
  • 31
    • 0029864853 scopus 로고    scopus 로고
    • Molecular recognition in the FMN-RNA aptamer complex
    • Fan P., Suri A.K., Fiala R., Live D., and Patel D.J. Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258 (1996) 480-500
    • (1996) J. Mol. Biol. , vol.258 , pp. 480-500
    • Fan, P.1    Suri, A.K.2    Fiala, R.3    Live, D.4    Patel, D.J.5
  • 32
    • 0029946537 scopus 로고    scopus 로고
    • Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex
    • Jiang F., Kumar R.A., Jones R.A., and Patel D.J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382 (1996) 183-186
    • (1996) Nature , vol.382 , pp. 183-186
    • Jiang, F.1    Kumar, R.A.2    Jones, R.A.3    Patel, D.J.4
  • 33
    • 0030752211 scopus 로고    scopus 로고
    • Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
    • Zimmermann G.R., Jenison R.D., Wick C.L., Simorre J.P., and Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nature Struct. Biol. 4 (1997) 644-649
    • (1997) Nature Struct. Biol. , vol.4 , pp. 644-649
    • Zimmermann, G.R.1    Jenison, R.D.2    Wick, C.L.3    Simorre, J.P.4    Pardi, A.5
  • 34
    • 0034662146 scopus 로고    scopus 로고
    • A water channel in the core of the vitamin B(12) RNA aptamer
    • Sussman D., and Wilson C. A water channel in the core of the vitamin B(12) RNA aptamer. Struct. Fold. Des. 8 (2000) 719-727
    • (2000) Struct. Fold. Des. , vol.8 , pp. 719-727
    • Sussman, D.1    Wilson, C.2
  • 35
    • 0034681490 scopus 로고    scopus 로고
    • Crystal structure of the ribonucleoprotein core of the signal recognition particle
    • Batey R.T., Rambo R.P., Lucast L., Rha B., and Doudna J.A. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287 (2000) 1232-1239
    • (2000) Science , vol.287 , pp. 1232-1239
    • Batey, R.T.1    Rambo, R.P.2    Lucast, L.3    Rha, B.4    Doudna, J.A.5
  • 36
    • 0036786231 scopus 로고    scopus 로고
    • Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly
    • Batey R.T., and Doudna J.A. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry 41 (2002) 11703-11710
    • (2002) Biochemistry , vol.41 , pp. 11703-11710
    • Batey, R.T.1    Doudna, J.A.2
  • 37
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • Mandal M., and Breaker R.R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Struct. Mol. Biol. 11 (2004) 29-35
    • (2004) Nature Struct. Mol. Biol. , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 39
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture
    • Leulliot N., and Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40 (2001) 7947-7956
    • (2001) Biochemistry , vol.40 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 40
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson J.R. Induced fit in RNA-protein recognition. Nature Struct. Biol. 7 (2000) 834-837
    • (2000) Nature Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 41
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar R.S., and Record Jr. M.T. Coupling of local folding to site-specific binding of proteins to DNA. Science 263 (1994) 777-784
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record Jr., M.T.2
  • 43
    • 0030868374 scopus 로고    scopus 로고
    • Allosteric properties of inosine monophosphate dehydrogenase revealed through the thermodynamics of binding of inosine 5′-monophosphate and mycophenolic acid. Temperature dependent heat capacity of binding as a signature of ligand-coupled conformational equilibria
    • Bruzzese F.J., and Connelly P.R. Allosteric properties of inosine monophosphate dehydrogenase revealed through the thermodynamics of binding of inosine 5′-monophosphate and mycophenolic acid. Temperature dependent heat capacity of binding as a signature of ligand-coupled conformational equilibria. Biochemistry 36 (1997) 10428-10438
    • (1997) Biochemistry , vol.36 , pp. 10428-10438
    • Bruzzese, F.J.1    Connelly, P.R.2
  • 44
    • 0026688412 scopus 로고
    • Thermodynamics of oligosaccharide binding to a monoclonal antibody specific for a Salmonella O-antigen point to hydrophobic interactions in the binding site
    • Sigurskjold B.W., and Bundle D.R. Thermodynamics of oligosaccharide binding to a monoclonal antibody specific for a Salmonella O-antigen point to hydrophobic interactions in the binding site. J. Biol. Chem. 267 (1992) 8371-8376
    • (1992) J. Biol. Chem. , vol.267 , pp. 8371-8376
    • Sigurskjold, B.W.1    Bundle, D.R.2
  • 45
    • 12844278693 scopus 로고    scopus 로고
    • The interaction of carbohydrate-binding modules with insoluble non-crystalline cellulose is enthalpically driven
    • Boraston A.B. The interaction of carbohydrate-binding modules with insoluble non-crystalline cellulose is enthalpically driven. Biochem. J. 385 (2005) 479-484
    • (2005) Biochem. J. , vol.385 , pp. 479-484
    • Boraston, A.B.1
  • 48
    • 27244434786 scopus 로고    scopus 로고
    • Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR (13)C relaxation
    • Duchardt E., and Schwalbe H. Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by MNMR (13)C relaxation. J. Biomol. NMR 32 (2005) 295-308
    • (2005) J. Biomol. NMR , vol.32 , pp. 295-308
    • Duchardt, E.1    Schwalbe, H.2
  • 49
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • Winkler W.C., and Breaker R.R. Genetic control by metabolite-binding riboswitches. Chem. Biochem 4 (2003) 1024-1032
    • (2003) Chem. Biochem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 50
    • 2442638925 scopus 로고    scopus 로고
    • A general method for rapid and nondenaturing purification of RNAs
    • Kieft J.S., and Batey R.T. A general method for rapid and nondenaturing purification of RNAs. RNA 10 (2004) 988-995
    • (2004) RNA , vol.10 , pp. 988-995
    • Kieft, J.S.1    Batey, R.T.2
  • 51
    • 0033213239 scopus 로고    scopus 로고
    • The finer things in X-ray diffraction data collection
    • Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallog. sect. D 55 (1999) 1718-1725
    • (1999) Acta Crystallog. sect. D , vol.55 , pp. 1718-1725
    • Pflugrath, J.W.1
  • 53
    • 84901961522 scopus 로고
    • Slow-cooling protocols for crystallographic refinement by simulated annealing
    • Brunger A.T., Krukowski A., and Erickson J.W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A 46 (1990) 585-593
    • (1990) Acta Crystallog. sect. A , vol.46 , pp. 585-593
    • Brunger, A.T.1    Krukowski, A.2    Erickson, J.W.3
  • 54
    • 0035442411 scopus 로고    scopus 로고
    • Direct measurement of protein binding energetics by isothermal titration calorimetry
    • Leavitt S., and Freire E. Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol. 11 (2001) 560-566
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 560-566
    • Leavitt, S.1    Freire, E.2


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