메뉴 건너뛰기




Volumn 328, Issue 1, 2003, Pages 33-47

Understanding discrimination by the ribosome: Stability testing and groove measurement of codon-anticodon pairs

Author keywords

Molecular dynamics; Proofreading; Ribosome; RNA; Translation

Indexed keywords

HYDROGEN; MESSENGER RNA; RNA 16S; SOLVENT;

EID: 0037453255     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00236-5     Document Type: Article
Times cited : (63)

References (59)
  • 1
    • 0001162471 scopus 로고
    • Polypeptide synthesis in Escherichia coli
    • Gilbert W. Polypeptide synthesis in Escherichia coli. J. Mol. Biol. 6:1963;389-403.
    • (1963) J. Mol. Biol. , vol.6 , pp. 389-403
    • Gilbert, W.1
  • 2
    • 0001835705 scopus 로고
    • Involvement of RNA in the synthesis of proteins
    • Watson J.D. Involvement of RNA in the synthesis of proteins. Science. 140:1963;17-26.
    • (1963) Science , vol.140 , pp. 17-26
    • Watson, J.D.1
  • 3
    • 0001239778 scopus 로고
    • Streptomycin, suppression and the code
    • Davies J., Gilbert W., Gorini L. Streptomycin, suppression and the code. Biochemistry. 51:1964;883-890.
    • (1964) Biochemistry , vol.51 , pp. 883-890
    • Davies, J.1    Gilbert, W.2    Gorini, L.3
  • 4
    • 0034923932 scopus 로고    scopus 로고
    • Fidelity of aminoacyl-tRNA selection on the ribosome: Kinetic and structural mechanisms
    • Rodnina M.V., Wintermeyer W. Fidelity of aminoacyl-tRNA selection on the ribosome: Kinetic and structural mechanisms. Annu. Rev. Biochem. 70:2001;415-435.
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 415-435
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 5
    • 0016200132 scopus 로고
    • A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli: Evaluation of some molecular parameters of translation in vivo
    • Ninio J. A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli: Evaluation of some molecular parameters of translation in vivo. J. Mol. Biol. 84:1974;297-313.
    • (1974) J. Mol. Biol. , vol.84 , pp. 297-313
    • Ninio, J.1
  • 6
    • 0000359208 scopus 로고
    • Kinetic Proofreading: New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity
    • Hopfield J.J. Kinetic Proofreading: New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity. Proc. Natl Acad. Sci. USA. 71:1974;4135-4139.
    • (1974) Proc. Natl Acad. Sci. USA , vol.71 , pp. 4135-4139
    • Hopfield, J.J.1
  • 7
    • 0004955452 scopus 로고
    • Proofreading of codon-anticodon Interaction on Ribosomes
    • Thompson R.C., Stone P.J. Proofreading of codon-anticodon Interaction on Ribosomes. Proc. Natl Acad. Sci. USA. 74:1977;198-202.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 198-202
    • Thompson, R.C.1    Stone, P.J.2
  • 8
    • 0033168212 scopus 로고    scopus 로고
    • Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome
    • Pape T., Wintermeyer W., Rodnina M. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J. 18:1999;3800-3807.
    • (1999) EMBO J. , vol.18 , pp. 3800-3807
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.3
  • 9
    • 0029051827 scopus 로고
    • Ribosomal Decoding Processes at Codons in the a-Site or P-Site Depend Differently on 2(-Oh Groups
    • Potapov A.P., Trianaalonso F.J., Nierhaus K.H. Ribosomal Decoding Processes at Codons in the a-Site or P-Site Depend Differently on 2(-Oh Groups. J. Biolo. Chem. 270:1995;17680-17684.
    • (1995) J. Biolo. Chem. , vol.270 , pp. 17680-17684
    • Potapov, A.P.1    Trianaalonso, F.J.2    Nierhaus, K.H.3
  • 10
    • 0034961959 scopus 로고    scopus 로고
    • Analysis of codon: Anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure
    • Lim V.I., Curran J.F. Analysis of codon: anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA - a publication of the RNA society. 7:2001;942-957.
    • (2001) RNA - A Publication of the RNA Society , vol.7 , pp. 942-957
    • Lim, V.I.1    Curran, J.F.2
  • 11
    • 0025280137 scopus 로고
    • The Allosteric 3-Site Model for the Ribosomal Elongation Cycle: Features and Future
    • Nierhaus K.H. The Allosteric 3-Site Model for the Ribosomal Elongation Cycle: Features and Future. Biochemistry. 29:1990;4997-5008.
    • (1990) Biochemistry , vol.29 , pp. 4997-5008
    • Nierhaus, K.H.1
  • 13
    • 0037154986 scopus 로고    scopus 로고
    • Ribosome structure and the mechanism of translation
    • Ramakrishnan V. Ribosome structure and the mechanism of translation. Cell. 108:2002;557-572.
    • (2002) Cell , vol.108 , pp. 557-572
    • Ramakrishnan, V.1
  • 14
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • Ogle J.M., Murphy F.V., Tarry M.J., Ramakrishnan V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell. 111:2002;721-732.
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 17
  • 19
    • 0030806152 scopus 로고    scopus 로고
    • A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA
    • Lodmell J.S., Dahlberg A.E. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science. 277:1997;1262-1267.
    • (1997) Science , vol.277 , pp. 1262-1267
    • Lodmell, J.S.1    Dahlberg, A.E.2
  • 20
    • 0028090796 scopus 로고
    • Selective Perturbation of G530 of 16 S-Ribosomal-RNA by Translational Miscoding Agents and a Streptomycin-Dependence Mutation in Protein-S12
    • Powers T., Noller H.F. Selective Perturbation of G530 of 16 S-Ribosomal-RNA by Translational Miscoding Agents and a Streptomycin-Dependence Mutation in Protein-S12. J. Mol. Biol. 235:1994;156-172.
    • (1994) J. Mol. Biol. , vol.235 , pp. 156-172
    • Powers, T.1    Noller, H.F.2
  • 21
    • 0016703498 scopus 로고
    • Allosteric Mechanism for Codon-Dependent Transfer-RNA Selection on Ribosomes
    • Kurland C.G., Rigler R., Ehrenberg M., Blomberg C. Allosteric Mechanism for Codon-Dependent Transfer-RNA Selection on Ribosomes. Proc. Natil Acad. Sci. USA. 72:1975;4248-4251.
    • (1975) Proc. Natil Acad. Sci. USA , vol.72 , pp. 4248-4251
    • Kurland, C.G.1    Rigler, R.2    Ehrenberg, M.3    Blomberg, C.4
  • 22
    • 0027104840 scopus 로고
    • Translational accuracy and the fitness of bacteria
    • Kurland C.G. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26:1992;29-50.
    • (1992) Annu. Rev. Genet. , vol.26 , pp. 29-50
    • Kurland, C.G.1
  • 23
    • 0020490733 scopus 로고
    • Accuracy of Protein-Biosynthesis: A Kinetic-Study of the Reaction of Poly(U)-Programmed Ribosomes with a Leucyl-Transfer RNA2-Elongation Factor Tu-GTP Complex
    • Thompson R.C., Dix D.B. Accuracy of Protein-Biosynthesis: A Kinetic-Study of the Reaction of Poly(U)-Programmed Ribosomes with a Leucyl-Transfer RNA2-Elongation Factor Tu-GTP Complex. J. Biol. Chem. 257:1982;6677-6682.
    • (1982) J. Biol. Chem. , vol.257 , pp. 6677-6682
    • Thompson, R.C.1    Dix, D.B.2
  • 25
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M., McCammon J.A. Molecular dynamics simulations of biomolecules. Nature Struct. Biol. 9:2002;646-652.
    • (2002) Nature Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 26
    • 0035498860 scopus 로고    scopus 로고
    • Energetics of ion conduction through the K+ channel
    • Berneche S., Roux B. Energetics of ion conduction through the K+ channel. Nature. 414:2001;73-77.
    • (2001) Nature , vol.414 , pp. 73-77
    • Berneche, S.1    Roux, B.2
  • 27
    • 0036175994 scopus 로고    scopus 로고
    • Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase
    • Bockmann R.A., Grubmuller H. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nature Struct. Biol. 9:2002;198-202.
    • (2002) Nature Struct. Biol. , vol.9 , pp. 198-202
    • Bockmann, R.A.1    Grubmuller, H.2
  • 28
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young M.A., Gonfloni S., Superti-Furga G., Roux B., Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 105:2001;115-126.
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 30
    • 0037062505 scopus 로고    scopus 로고
    • Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation
    • Sporlein S.H.C., Satzger H., Renner C., Behrendt R., Moroder L., Tavan P., et al. Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation. Proc. Natl Acad. Sci. USA. 99:2002;7998-8002.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7998-8002
    • Sporlein, S.H.C.1    Satzger, H.2    Renner, C.3    Behrendt, R.4    Moroder, L.5    Tavan, P.6
  • 31
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham T.E., Kollman P.A. Molecular dynamics simulation of nucleic acids. Annu. Rev. Phys. Chem. 51:2000;435-471.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 435-471
    • Cheatham, T.E.1    Kollman, P.A.2
  • 32
    • 0034725528 scopus 로고    scopus 로고
    • Water and ion binding around RNA and DNA (C;G) oligomers
    • Auffinger P., Westhof E. Water and ion binding around RNA and DNA (C;G) oligomers. J. Mol. Biol. 300:2000;1113-1131.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1113-1131
    • Auffinger, P.1    Westhof, E.2
  • 33
    • 0033525065 scopus 로고    scopus 로고
    • Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site
    • VanLoock M.S., Easterwood T.R., Harvey S.C. Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site. J. Mol. Biol. 285:1999;2069-2078.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2069-2078
    • VanLoock, M.S.1    Easterwood, T.R.2    Harvey, S.C.3
  • 34
    • 0037149518 scopus 로고    scopus 로고
    • The transorientation hypothesis for codon recognition during protein synthesis
    • Simonson A.B., Lake J.A. The transorientation hypothesis for codon recognition during protein synthesis. Nature. 416:2002;281-285.
    • (2002) Nature , vol.416 , pp. 281-285
    • Simonson, A.B.1    Lake, J.A.2
  • 35
    • 0033729881 scopus 로고    scopus 로고
    • Molecular dynamics of the anticodon domain of yeast tRNA(Phe): Codon-anticodon interaction
    • Lahiri A., Nilsson L. Molecular dynamics of the anticodon domain of yeast tRNA(Phe): codon-anticodon interaction. Biophys. J. 79:2000;2276-2289.
    • (2000) Biophys. J. , vol.79 , pp. 2276-2289
    • Lahiri, A.1    Nilsson, L.2
  • 36
    • 0029938421 scopus 로고    scopus 로고
    • Thermodynamics of base pairing
    • Turner D.H. Thermodynamics of base pairing. Curr. Opin. Struct. Biol. 6:1996;299-304.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 299-304
    • Turner, D.H.1
  • 37
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner M., Olson A.J., Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:1996;305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.1    Olson, A.J.2    Spehner, J.C.3
  • 38
    • 0025012472 scopus 로고
    • Dominant lethal mutations in a conserved loop in 16 S ribosomal-RNA
    • Powers T., Noller H.F. Dominant lethal mutations in a conserved loop in 16 S ribosomal-RNA. Proc. Natl Acad. Sci. USA. 87:1990;1042-1046.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 1042-1046
    • Powers, T.1    Noller, H.F.2
  • 39
    • 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
  • 40
    • 0027956537 scopus 로고
    • A Major Family of Motifs Involving GA Mismatches in Ribosomal-RNA
    • Gautheret D.F., Konings D., Gutell R.R. A Major Family of Motifs Involving GA Mismatches in Ribosomal-RNA. J. Mol. Biol. 242:1994;1-8.
    • (1994) J. Mol. Biol. , vol.242 , pp. 1-8
    • Gautheret, D.F.1    Konings, D.2    Gutell, R.R.3
  • 42
    • 0036534459 scopus 로고    scopus 로고
    • Ribosome structure: Revisiting the connection between translational accuracy and unconventional decoding
    • Stahl G., McCarthy G.P., Farabaugh P.J. Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding. Trends Biochem. Sci. 26:2002;178-183.
    • (2002) Trends Biochem. Sci. , vol.26 , pp. 178-183
    • Stahl, G.1    McCarthy, G.P.2    Farabaugh, P.J.3
  • 43
    • 0024722501 scopus 로고
    • Errors and Alternatives in Reading the Universal Genetic-Code
    • Parker J. Errors and Alternatives in Reading the Universal Genetic-Code. Microbiol. Rev. 53:1989;273-298.
    • (1989) Microbiol. Rev. , vol.53 , pp. 273-298
    • Parker, J.1
  • 44
    • 33845554708 scopus 로고
    • Crystallographic evidence of the existence of C-H - O, C-H - N, and C-H - Cl hydrogen bonds
    • Taylor R., Kennard O. Crystallographic evidence of the existence of C-H - O, C-H - N, and C-H - Cl hydrogen bonds. J. Am. Chem. Soc. 104:1982;5063-5070.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 5063-5070
    • Taylor, R.1    Kennard, O.2
  • 45
    • 4244122368 scopus 로고
    • Hydrogen-bonding in crystal structures of nucleic acid components: Purines, pyrimidines, nucleosides and nucleotides
    • W. Saenger. Berlin: Springer
    • Jeffrey G.A. Hydrogen-bonding in crystal structures of nucleic acid components: purines, pyrimidines, nucleosides and nucleotides. Saenger W. Numerical Data and Functional Relationships in Science and Technology. 1989;277-348 Springer, Berlin.
    • (1989) Numerical Data and Functional Relationships in Science and Technology , pp. 277-348
    • Jeffrey, G.A.1
  • 48
    • 0029011701 scopus 로고
    • A 2nd 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 2nd 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
  • 51
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • Harvey S.C., Tan R.K.Z., Cheatham T.E. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem. 19:1998;726-740.
    • (1998) J. Comput. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.Z.2    Cheatham, T.E.3
  • 52
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R., Billeter M., Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55.
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 53
    • 85031202807 scopus 로고    scopus 로고
    • Division of Structural Biology, Biozentrum, University of Basel, Switzerland
    • Philippsen, A., (2002). DINO 0.8 edit. Division of Structural Biology, Biozentrum, University of Basel, Switzerland.
    • (2002) DINO 0.8 Edit
    • Philippsen, A.1
  • 54
    • 0026698647 scopus 로고
    • Groove width and depth of B-DNA structures depend on local variation in slide
    • Bhattachary D., Bansal M. Groove width and depth of B-DNA structures depend on local variation in slide. J. Biomol. Struct. Dynam. 10:1992;213-226.
    • (1992) J. Biomol. Struct. Dynam. , vol.10 , pp. 213-226
    • Bhattachary, D.1    Bansal, M.2
  • 56
    • 0000648297 scopus 로고
    • Package for calculating with B-splines
    • de Boor C. Package for calculating with B-splines. SIAM J. Numerical Anal. 14:1977;441-472.
    • (1977) SIAM J. Numerical Anal. , vol.14 , pp. 441-472
    • De Boor, C.1
  • 57
    • 0034822656 scopus 로고    scopus 로고
    • Stereochemical, structural, and thermodynamics origins of stability differences between stereoisomeric Benzoa.pyrene Diol Epoxide Deoxyadenosine adducts in a DNA mutational hot spot sequence
    • Yan S., Shapiro R., Geacintov N.E., Broyde S. Stereochemical, structural, and thermodynamics origins of stability differences between stereoisomeric Benzoa.pyrene Diol Epoxide Deoxyadenosine adducts in a DNA mutational hot spot sequence. J. Am. Chem. Soc. 123:2001;7054-7066.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 7054-7066
    • Yan, S.1    Shapiro, R.2    Geacintov, N.E.3    Broyde, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.