메뉴 건너뛰기




Volumn 376, Issue 4, 2008, Pages 1034-1047

Late Steps in the Formation of E. coli RNA Polymerase-λPR Promoter Open Complexes: Characterization of Conformational Changes by Rapid [Perturbant] Upshift Experiments

Author keywords

bacterial RNA polymerase; conformational changes; kinetics; open complex formation; solute effects

Indexed keywords

DNA; POTASSIUM CHLORIDE; RNA POLYMERASE; SODIUM CHLORIDE; UREA;

EID: 39049123619     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.11.064     Document Type: Article
Times cited : (34)

References (41)
  • 1
    • 22144482360 scopus 로고    scopus 로고
    • TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape
    • Lin Y.C., Choi W.S., and Gralla J.D. TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nature Struct. Mol. Biol. 12 (2005) 603-607
    • (2005) Nature Struct. Mol. Biol. , vol.12 , pp. 603-607
    • Lin, Y.C.1    Choi, W.S.2    Gralla, J.D.3
  • 2
  • 3
    • 0032491380 scopus 로고    scopus 로고
    • DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA
    • Craig M.L., Tsodikov O.V., McQuade K.L., Schlax Jr. P.E., Capp M.W., Saecker R.M., and Record Jr. M.T. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283 (1998) 741-756
    • (1998) J. Mol. Biol. , vol.283 , pp. 741-756
    • Craig, M.L.1    Tsodikov, O.V.2    McQuade, K.L.3    Schlax Jr., P.E.4    Capp, M.W.5    Saecker, R.M.6    Record Jr., M.T.7
  • 4
    • 39049098737 scopus 로고    scopus 로고
    • R promoter. PhD thesis, University of Wisconsin-Madison.
    • R promoter. PhD thesis, University of Wisconsin-Madison.
  • 8
    • 0021840415 scopus 로고
    • R promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening
    • R promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J. Mol. Biol. 184 (1985) 441-453
    • (1985) J. Mol. Biol. , vol.184 , pp. 441-453
    • Roe, J.H.1    Burgess, R.R.2    Record Jr., M.T.3
  • 10
    • 0033047068 scopus 로고    scopus 로고
    • 70 RNA polymerase and lambdaP(R) promoter DNA
    • 70 RNA polymerase and lambdaP(R) promoter DNA. Biophys. J. 76 (1999) 1320-1329
    • (1999) Biophys. J. , vol.76 , pp. 1320-1329
    • Tsodikov, O.V.1    Record Jr., M.T.2
  • 13
    • 39049148162 scopus 로고    scopus 로고
    • R promoter interactions: effects of temperature and initiating nucleotides on the kinetics and thermodynamics of open complex formation. PhD thesis, University of Wisconsin-Madison.
    • R promoter interactions: effects of temperature and initiating nucleotides on the kinetics and thermodynamics of open complex formation. PhD thesis, University of Wisconsin-Madison.
  • 14
    • 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
  • 15
    • 4043069926 scopus 로고    scopus 로고
    • DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP
    • Paul B.J., Barker M.M., Ross W., Schneider D.A., Webb C., Foster J.W., and Gourse R.L. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118 (2004) 311-322
    • (2004) Cell , vol.118 , pp. 311-322
    • Paul, B.J.1    Barker, M.M.2    Ross, W.3    Schneider, D.A.4    Webb, C.5    Foster, J.W.6    Gourse, R.L.7
  • 16
    • 20344363655 scopus 로고    scopus 로고
    • DksA potentiates direct activation of amino acid promoters by ppGpp
    • Paul B.J., Berkmen M.B., and Gourse R.L. DksA potentiates direct activation of amino acid promoters by ppGpp. Proc. Natl. Acad. Sci. USA 102 (2005) 7823-7828
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 7823-7828
    • Paul, B.J.1    Berkmen, M.B.2    Gourse, R.L.3
  • 17
    • 34249941797 scopus 로고    scopus 로고
    • Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase
    • Davis C.A., Bingman C.A., Landick R., Record Jr. M.T., and Saecker R.M. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. U S A 104 (2007) 7833-7838
    • (2007) Proc. Natl. Acad. Sci. U S A , vol.104 , pp. 7833-7838
    • Davis, C.A.1    Bingman, C.A.2    Landick, R.3    Record Jr., M.T.4    Saecker, R.M.5
  • 18
    • 0021827364 scopus 로고
    • Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase
    • Spassky A., Kirkegaard K., and Buc H. Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase. Biochemistry 24 (1985) 2723-2731
    • (1985) Biochemistry , vol.24 , pp. 2723-2731
    • Spassky, A.1    Kirkegaard, K.2    Buc, H.3
  • 19
    • 0021857751 scopus 로고
    • Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps
    • Buc H., and McClure W.R. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry 24 (1985) 2712-2723
    • (1985) Biochemistry , vol.24 , pp. 2712-2723
    • Buc, H.1    McClure, W.R.2
  • 20
    • 0034595499 scopus 로고    scopus 로고
    • R promoter of bacteriophage lambda affect steps in open complex formation that precede DNA strand separation
    • R promoter of bacteriophage lambda affect steps in open complex formation that precede DNA strand separation. J. Mol. Biol. 299 (2000) 337-349
    • (2000) J. Mol. Biol. , vol.299 , pp. 337-349
    • McKane, M.1    Gussin, G.N.2
  • 21
    • 0035896034 scopus 로고    scopus 로고
    • Differential melting of the transcription start site associated with changes in RNA polymerase-promoter contacts in initiating transcription complexes
    • Brodolin K., and Buckle M. Differential melting of the transcription start site associated with changes in RNA polymerase-promoter contacts in initiating transcription complexes. J. Mol. Biol. 307 (2001) 25-30
    • (2001) J. Mol. Biol. , vol.307 , pp. 25-30
    • Brodolin, K.1    Buckle, M.2
  • 22
    • 0033593474 scopus 로고    scopus 로고
    • The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase
    • Buckle M., Pemberton I.K., Jacquet M.A., and Buc H. The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase. J. Mol. Biol. 285 (1999) 955-964
    • (1999) J. Mol. Biol. , vol.285 , pp. 955-964
    • Buckle, M.1    Pemberton, I.K.2    Jacquet, M.A.3    Buc, H.4
  • 23
    • 34848916114 scopus 로고    scopus 로고
    • Anatomy of energetic changes accompanying urea-induced protein denaturation
    • Auton M., Holthauzen L.M., and Bolen D.W. Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc. Natl. Acad. Sci. USA 104 (2007) 15317-15322
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 15317-15322
    • Auton, M.1    Holthauzen, L.M.2    Bolen, D.W.3
  • 24
    • 34548270876 scopus 로고    scopus 로고
    • Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas
    • Cannon J.G., Anderson C.F., and Record Jr. M.T. Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J. Phys. Chem. ser. B 111 (2007) 9675-9685
    • (2007) J. Phys. Chem. ser. B , vol.111 , pp. 9675-9685
    • Cannon, J.G.1    Anderson, C.F.2    Record Jr., M.T.3
  • 25
    • 8744318698 scopus 로고    scopus 로고
    • Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability
    • Hong J., Capp M.W., Anderson C.F., Saecker R.M., Felitsky D.J., Anderson M.W., and Record Jr. M.T. Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability. Biochemistry 43 (2004) 14744-14758
    • (2004) Biochemistry , vol.43 , pp. 14744-14758
    • Hong, J.1    Capp, M.W.2    Anderson, C.F.3    Saecker, R.M.4    Felitsky, D.J.5    Anderson, M.W.6    Record Jr., M.T.7
  • 27
    • 0033772098 scopus 로고    scopus 로고
    • Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model
    • Courtenay E.S., Capp M.W., Saecker R.M., and Record Jr. M.T. Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins: Struct. Funct. Genet. 4 (2000) 72-85
    • (2000) Proteins: Struct. Funct. Genet. , vol.4 , pp. 72-85
    • Courtenay, E.S.1    Capp, M.W.2    Saecker, R.M.3    Record Jr., M.T.4
  • 28
    • 0035176391 scopus 로고    scopus 로고
    • Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area
    • Courtenay E.S., Capp M.W., and Record Jr. M.T. Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area. Protein Sci. 10 (2001) 2485-2497
    • (2001) Protein Sci. , vol.10 , pp. 2485-2497
    • Courtenay, E.S.1    Capp, M.W.2    Record Jr., M.T.3
  • 29
    • 0037465426 scopus 로고    scopus 로고
    • Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes
    • Felitsky D.J., and Record Jr. M.T. Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes. Biochemistry 42 (2003) 2202-2217
    • (2003) Biochemistry , vol.42 , pp. 2202-2217
    • Felitsky, D.J.1    Record Jr., M.T.2
  • 30
    • 29344437812 scopus 로고    scopus 로고
    • Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding
    • Hong J., Capp M.W., Saecker R.M., and Record Jr. M.T. Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. Biochemistry 44 (2005) 16896-16911
    • (2005) Biochemistry , vol.44 , pp. 16896-16911
    • Hong, J.1    Capp, M.W.2    Saecker, R.M.3    Record Jr., M.T.4
  • 31
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 32
    • 0014958992 scopus 로고
    • Physical studies on ribonucleic acid polymerase from Escherichia coli B
    • Berg D., and Chamberlin M. Physical studies on ribonucleic acid polymerase from Escherichia coli B. Biochemistry 9 (1970) 5055-5064
    • (1970) Biochemistry , vol.9 , pp. 5055-5064
    • Berg, D.1    Chamberlin, M.2
  • 33
    • 0000411690 scopus 로고
    • Helix-random coil transitions in synthetic DNAs of alternating sequence
    • Inman R.B., and Baldwin R.L. Helix-random coil transitions in synthetic DNAs of alternating sequence. J. Mol. Biol. 5 (1962) 172-184
    • (1962) J. Mol. Biol. , vol.5 , pp. 172-184
    • Inman, R.B.1    Baldwin, R.L.2
  • 34
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity
    • Record Jr. M.T., Anderson C.F., and Lohman T.M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quart. Rev. Biophys. 11 (1978) 103-178
    • (1978) Quart. Rev. Biophys. , vol.11 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 36
    • 0018074213 scopus 로고
    • Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions
    • Lohman T.M., DeHaseth P.L., and Record Jr. M.T. Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions. Biophys. Chem. 8 (1978) 281-294
    • (1978) Biophys. Chem. , vol.8 , pp. 281-294
    • Lohman, T.M.1    DeHaseth, P.L.2    Record Jr., M.T.3
  • 39
    • 33645819791 scopus 로고    scopus 로고
    • Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
    • Published online 2006 March 31
    • Shcherbakova I., Mitra S., Beer R.H., and Brenowitz M. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucl. Acids. Res. 34 (2006) e48 Published online 2006 March 31
    • (2006) Nucl. Acids. Res. , vol.34
    • Shcherbakova, I.1    Mitra, S.2    Beer, R.H.3    Brenowitz, M.4
  • 40
    • 0028789430 scopus 로고
    • 2+ binding and its structural consequences at the transcription start site
    • 2+ binding and its structural consequences at the transcription start site. Biochemistry 34 (1995) 15624-15632
    • (1995) Biochemistry , vol.34 , pp. 15624-15632
    • Craig, M.L.1    Suh, W.C.2    Record Jr., M.T.3
  • 41
    • 0016748261 scopus 로고
    • A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography
    • Burgess R.R., and Jendrisak J.J. A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry 14 (1975) 4634-4638
    • (1975) Biochemistry , vol.14 , pp. 4634-4638
    • Burgess, R.R.1    Jendrisak, J.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.