메뉴 건너뛰기




Volumn 326, Issue 5, 2003, Pages 1373-1387

Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: Elucidation of the number of drug amino groups involved and their identities

Author keywords

15N NMR; Aminoglycoside pKa values; Aminoglycoside RNA recognition; Isothermal titration calorimetry; rRNA binding linked aminoglycoside protonation

Indexed keywords

2 DEOXYSTREPTAMINE; AMINOGLYCOSIDE ANTIBIOTIC AGENT; BUFFER; FRAMYCETIN; LIVIDOMYCIN; PAROMOMYCIN; PROTON; RNA;

EID: 0037424612     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01452-3     Document Type: Article
Times cited : (115)

References (33)
  • 1
    • 0026620038 scopus 로고
    • Interaction between the two conserved single-stranded regions at the decoding site of small subunit ribosomal RNA is essential for ribosome function
    • Cunningham P.R., Nurse K., Bakin A., Weitzmann C.J., Pflumm M., Ofengand J. Interaction between the two conserved single-stranded regions at the decoding site of small subunit ribosomal RNA is essential for ribosome function. Biochemistry. 31:1992;12012-12022.
    • (1992) Biochemistry , vol.31 , pp. 12012-12022
    • Cunningham, P.R.1    Nurse, K.2    Bakin, A.3    Weitzmann, C.J.4    Pflumm, M.5    Ofengand, J.6
  • 2
    • 0027282806 scopus 로고
    • Functional effects of base changes which further define the decoding center of Escherichia coli 16 S ribosomal RNA. Mutation of C1404, G1405, C1496, G1497, and U1498
    • Cunningham P.R., Nurse K., Weitzmann C.J., Ofengand J. Functional effects of base changes which further define the decoding center of Escherichia coli 16 S ribosomal RNA. Mutation of C1404, G1405, C1496, G1497, and U1498. Biochemistry. 32:1993;7172-7180.
    • (1993) Biochemistry , vol.32 , pp. 7172-7180
    • Cunningham, P.R.1    Nurse, K.2    Weitzmann, C.J.3    Ofengand, J.4
  • 4
    • 0028071557 scopus 로고
    • Collection of small subunit (16 S- and 16 S-Like) ribosomal RNA structures
    • Gutell R.R. Collection of small subunit (16 S- and 16 S-Like) ribosomal RNA structures. Nucl. Acids Res. 22:1994;3502-3507.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 6
    • 0027988447 scopus 로고
    • Dissociation rate of cognate peptidyl-tRNA from the A-site of hyper-accurate and error-prone ribosomes
    • Karimi R., Ehrenberg M. Dissociation rate of cognate peptidyl-tRNA from the A-site of hyper-accurate and error-prone ribosomes. Eur. J. Biochem. 226:1994;355-360.
    • (1994) Eur. J. Biochem. , vol.226 , pp. 355-360
    • Karimi, R.1    Ehrenberg, M.2
  • 7
    • 0033543589 scopus 로고    scopus 로고
    • Recognition of the codon-anticodon helix by ribosomal RNA
    • Yoshizawa S., Fourmy D., Puglisi J.D. Recognition of the codon-anticodon helix by ribosomal RNA. Science. 285:1999;1722-1725.
    • (1999) Science , vol.285 , pp. 1722-1725
    • Yoshizawa, S.1    Fourmy, D.2    Puglisi, J.D.3
  • 8
    • 0033961143 scopus 로고    scopus 로고
    • Conformational switch in the decoding region of 16 S rRNA during aminoacyl-tRNA selection on the ribosome
    • Pape T., Wintermeyer W., Rodnina M.V. Conformational switch in the decoding region of 16 S rRNA during aminoacyl-tRNA selection on the ribosome. Nature Struct. Biol. 7:2000;104-107.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 104-107
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.V.3
  • 9
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the A site of Escherichia coli 16 S ribosomal RNA complexed with an aminoglycoside antibiotic
    • Fourmy D., Recht M.I., Blanchard S.C., Puglisi J.D. Structure of the A site of Escherichia coli 16 S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 274:1996;1367-1371.
    • (1996) Science , vol.274 , pp. 1367-1371
    • Fourmy, D.1    Recht, M.I.2    Blanchard, S.C.3    Puglisi, J.D.4
  • 10
    • 0032571359 scopus 로고    scopus 로고
    • Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA
    • Fourmy D., Yoshizawa S., Puglisi J.D. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J. Mol. Biol. 277:1998;333-345.
    • (1998) J. Mol. Biol. , vol.277 , pp. 333-345
    • Fourmy, D.1    Yoshizawa, S.2    Puglisi, J.D.3
  • 11
    • 0032538956 scopus 로고    scopus 로고
    • Structural origins of gentamicin antibiotic action
    • Yoshizawa S., Fourmy D., Puglisi J.D. Structural origins of gentamicin antibiotic action. EMBO J. 17:1998;6437-6448.
    • (1998) EMBO J. , vol.17 , pp. 6437-6448
    • Yoshizawa, S.1    Fourmy, D.2    Puglisi, J.D.3
  • 12
    • 0034699519 scopus 로고    scopus 로고
    • Functional insights from the structure of the 30 S ribosomal subunit and its interactions with antibiotics
    • Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Functional insights from the structure of the 30 S ribosomal subunit and its interactions with antibiotics. Nature. 407:2000;340-348.
    • (2000) Nature , vol.407 , pp. 340-348
    • Carter, A.P.1    Clemons, W.M.2    Brodersen, D.E.3    Morgan-Warren, R.J.4    Wimberly, B.T.5    Ramakrishnan, V.6
  • 13
    • 0034886697 scopus 로고    scopus 로고
    • Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site
    • Vicens Q., Westhof E. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure. 9:2001;647-658.
    • (2001) Structure , vol.9 , pp. 647-658
    • Vicens, Q.1    Westhof, E.2
  • 14
    • 0035986708 scopus 로고    scopus 로고
    • Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site
    • Vicens Q., Westhof E. Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site. Chem. Biol. 9:2002;747-755.
    • (2002) Chem. Biol. , vol.9 , pp. 747-755
    • Vicens, Q.1    Westhof, E.2
  • 15
    • 0029286628 scopus 로고
    • Hydroxyl radical footprinting of ribosomal proteins on 16 S rRNA
    • Powers T., Noller H.F. Hydroxyl radical footprinting of ribosomal proteins on 16 S rRNA. RNA. 1:1995;194-209.
    • (1995) RNA , vol.1 , pp. 194-209
    • Powers, T.1    Noller, H.F.2
  • 16
    • 1842388479 scopus 로고    scopus 로고
    • RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide
    • Recht M.I., Fourmy D., Blanchard S.C., Dahlquist K.D., Puglisi J.D. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J. Mol. Biol. 262:1996;421-436.
    • (1996) J. Mol. Biol. , vol.262 , pp. 421-436
    • Recht, M.I.1    Fourmy, D.2    Blanchard, S.C.3    Dahlquist, K.D.4    Puglisi, J.D.5
  • 17
    • 0032571306 scopus 로고    scopus 로고
    • Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA
    • Fourmy D., Recht M.I., Puglisi J.D. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. J. Mol. Biol. 277:1998;347-362.
    • (1998) J. Mol. Biol. , vol.277 , pp. 347-362
    • Fourmy, D.1    Recht, M.I.2    Puglisi, J.D.3
  • 18
    • 0033548073 scopus 로고    scopus 로고
    • Effect of mutations in the A-site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction
    • Recht M.I., Douthwaite S., Dahlquist K.D., Puglisi J.D. Effect of mutations in the A-site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction. J. Mol. Biol. 286:1999;33-43.
    • (1999) J. Mol. Biol. , vol.286 , pp. 33-43
    • Recht, M.I.1    Douthwaite, S.2    Dahlquist, K.D.3    Puglisi, J.D.4
  • 19
    • 0037129948 scopus 로고    scopus 로고
    • Thermodynamics of aminoglycoside-rRNA recognition: The binding of neomycin-class aminoglycosides to the A site of 16 S rRNA
    • Kaul M., Pilch D.S. Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16 S rRNA. Biochemistry. 41:2002;7695-7706.
    • (2002) Biochemistry , vol.41 , pp. 7695-7706
    • Kaul, M.1    Pilch, D.S.2
  • 20
    • 0020708497 scopus 로고
    • Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides
    • Botto R.E., Coxon B. Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides. J. Am. Chem. Soc. 105:1983;1021-1028.
    • (1983) J. Am. Chem. Soc. , vol.105 , pp. 1021-1028
    • Botto, R.E.1    Coxon, B.2
  • 21
    • 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 M.T.J., Anderson C.F., 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, M.T.J.1    Anderson, C.F.2    Lohman, T.M.3
  • 22
    • 0026684671 scopus 로고
    • Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water
    • Spolar R.S., Livingstone J.R., Record M.T.J. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 31:1992;3947-3955.
    • (1992) Biochemistry , vol.31 , pp. 3947-3955
    • Spolar, R.S.1    Livingstone, J.R.2    Record, M.T.J.3
  • 23
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar R.S., Record M.T. Jr. 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 M.T., Jr.2
  • 24
    • 0029131539 scopus 로고
    • Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry
    • Doyle M.L., Louie G., Dal Monte P.R., Sokoloski, T.D. Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry. Methods Enzymol. 259:1995;183-194.
    • (1995) Methods Enzymol. , vol.259 , pp. 183-194
    • Doyle, M.L.1    Louie, G.2    Dal Monte, P.R.3    Sokoloski, T.D.4
  • 25
    • 0034696752 scopus 로고    scopus 로고
    • Aminoglycoside binding in the major groove of duplex RNA: The thermodynamic and electrostatic forces that govern recognition
    • Jin E., Katritich V., Olson W.K., Kharatisvili M., Abagyan R., Pilch D.S. Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. J. Mol. Biol. 298:2000;95-110.
    • (2000) J. Mol. Biol. , vol.298 , pp. 95-110
    • Jin, E.1    Katritich, V.2    Olson, W.K.3    Kharatisvili, M.4    Abagyan, R.5    Pilch, D.S.6
  • 27
    • 0037093442 scopus 로고    scopus 로고
    • Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry
    • Fong D.H., Berghuis A.M. Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry. EMBO J. 21:2002;2323-2331.
    • (2002) EMBO J. , vol.21 , pp. 2323-2331
    • Fong, D.H.1    Berghuis, A.M.2
  • 28
    • 0023406843 scopus 로고
    • Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
    • Marky L.A., Breslauer K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 26:1987;1601-1620.
    • (1987) Biopolymers , vol.26 , pp. 1601-1620
    • Marky, L.A.1    Breslauer, K.J.2
  • 30
    • 84986513567 scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
    • Breneman C.M., Wiberg K.B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 11:1990;361-373.
    • (1990) J. Comput. Chem. , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 31
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5    Ferguson, D.M.6
  • 33
    • 0023668218 scopus 로고
    • Differential calorimetric study of the thermal unfolding of taka-amylase A from Aspergillus oryzae
    • Fukada H., Takahashi K., Sturtevant J.M. Differential calorimetric study of the thermal unfolding of taka-amylase A from Aspergillus oryzae. Biochemistry. 26:1987;4063-4068.
    • (1987) Biochemistry , vol.26 , pp. 4063-4068
    • Fukada, H.1    Takahashi, K.2    Sturtevant, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.