메뉴 건너뛰기




Volumn 34, Issue 19, 2006, Pages 5361-5368

Molecular dynamics simulations of human tRNA UUU Lys,3: The role of modified bases in mRNA recognition

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DERIVATIVE; LYSINE TRANSFER RNA; MESSENGER RNA; NUCLEIC ACID BASE; PSEUDOURIDINE; THIOURIDINE; WATER;

EID: 33751001340     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl580     Document Type: Article
Times cited : (39)

References (84)
  • 1
    • 0028906308 scopus 로고
    • Structures of posttranscriptionally modified nucleosides from RNA
    • Limbach,P.A., Crain,P.F., Pomerantz,S.C. and McCloskey,J.A. (1995) Structures of posttranscriptionally modified nucleosides from RNA. Biochimie, 77, 135-138.
    • (1995) Biochimie , vol.77 , pp. 135-138
    • Limbach, P.A.1    Crain, P.F.2    Pomerantz, S.C.3    McCloskey, J.A.4
  • 2
    • 0001494356 scopus 로고    scopus 로고
    • Appendix 1: Chemical structures and classification of posttranscriptionally modified nucleosides in RNA
    • In Grosjean,H. and Benne,R. (eds), American Society for Microbiology Press, Washington, DC
    • Motorin,Y. and Grosjean,H. (1998) Appendix 1: Chemical structures and classification of posttranscriptionally modified nucleosides in RNA. In Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. American Society for Microbiology Press, Washington, DC, pp. 534-549.
    • (1998) Modification and Editing of RNA , pp. 534-549
    • Motorin, Y.1    Grosjean, H.2
  • 3
    • 0002365884 scopus 로고
    • Modified nucleosides and codon recognition
    • In Soll,D. and RajBhandary,U.L. (eds), American Society for Microbiology, Washington, DC
    • Yokoyama,S. and Nishimura,S. (1995) Modified nucleosides and codon recognition. In Soll,D. and RajBhandary,U.L. (eds), tRNA: Structure, Biosynthesis and Function. American Society for Microbiology, Washington, DC, pp. 207-223.
    • (1995) TRNA: Structure, Biosynthesis and Function , pp. 207-223
    • Yokoyama, S.1    Nishimura, S.2
  • 4
    • 1242309517 scopus 로고    scopus 로고
    • Decoding the genome: A modified view
    • Agris,P.F. (2004) Decoding the genome: A modified view. Nucleic Acids Res., 32, 223-238.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 223-238
    • Agris, P.F.1
  • 5
    • 15044362242 scopus 로고    scopus 로고
    • Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm
    • Sakurai,M., Ohtsuki,T. and Watanabe,K. (2005) Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm. Nucleic Acids Res., 33, 1653-1661.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1653-1661
    • Sakurai, M.1    Ohtsuki, T.2    Watanabe, K.3
  • 6
    • 2442709155 scopus 로고    scopus 로고
    • A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon
    • Blaise,M., Becker,H.D., Keith,G., Cambillau,C., Lapointe,J., Giege,R. and Kern,D. (2004) A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon. Nucleic Acids Res., 32, 2768-2775.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 2768-2775
    • Blaise, M.1    Becker, H.D.2    Keith, G.3    Cambillau, C.4    Lapointe, J.5    Giege, R.6    Kern, D.7
  • 7
    • 0027331556 scopus 로고
    • Modified nucleotides of tRNA3lys modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription
    • Isel,C., Marquet,R., Keith,G., Ehresmann,C. and Ehresmann,B. (1993) Modified nucleotides of tRNA3lys modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem., 268, 25269-25272.
    • (1993) J. Biol. Chem. , vol.268 , pp. 25269-25272
    • Isel, C.1    Marquet, R.2    Keith, G.3    Ehresmann, C.4    Ehresmann, B.5
  • 10
    • 0036809730 scopus 로고    scopus 로고
    • Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation
    • Phelps,S.S., Jeinic,O. and Joseph,S. (2002) Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol. Cell, 10, 799-807.
    • (2002) Mol. Cell , vol.10 , pp. 799-807
    • Phelps, S.S.1    Jeinic, O.2    Joseph, S.3
  • 12
    • 0042492708 scopus 로고    scopus 로고
    • Glu modulates the translation rate of glutamic acid codons in vivo
    • Glu modulates the translation rate of glutamic acid codons in vivo. J. Mol. Biol., 284, 621-631.
    • (1998) J. Mol. Biol. , vol.284 , pp. 621-631
    • Kruger, M.1    Pedersen, S.2    Hagervall, T.G.3
  • 13
    • 0031577333 scopus 로고    scopus 로고
    • Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: Influence of tRNA anticodon modification on frameshifting
    • Brierley,I., Meredith,M.R., Bloys,A.J. and Hagervall,T.G. (1997) Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: Influence of tRNA anticodon modification on frameshifting. J. Mol. Biol., 270, 360-373.
    • (1997) J. Mol. Biol. , vol.270 , pp. 360-373
    • Brierley, I.1    Meredith, M.R.2    Bloys, A.J.3    Hagervall, T.G.4
  • 14
    • 13444288185 scopus 로고    scopus 로고
    • Compilation of tRNA sequences and sequences of tRNA genes
    • Sprinzl,M. and Vassilenko,K.S. (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 33, D139-D149.
    • (2005) Nucleic Acids Res. , vol.33
    • Sprinzl, M.1    Vassilenko, K.S.2
  • 15
    • 0002495140 scopus 로고
    • Biosynthesis and function of modified nucleosides
    • In Söll,D. and RajBhandary,U.L. (eds), American Society for Microbiology Press, Washington, DC
    • Bjork,G.R. (1995) Biosynthesis and function of modified nucleosides. In Söll,D. and RajBhandary,U.L. (eds), tRNA: Structure, Biosynthesis, and Function. American Society for Microbiology Press, Washington, DC, pp. 165-206.
    • (1995) TRNA: Structure, Biosynthesis, and Function , pp. 165-206
    • Bjork, G.R.1
  • 20
    • 0027442943 scopus 로고
    • 5-Methylcytidine is required for cooperative binding of magnesium(2+) and a conformational transition at the anticodon stem-loop of yeast phenylalanine tRNA
    • Chen,Y., Sierzputowska-Gracz,H., Guenther,R., Everett,K. and Agris,P.F. (1993) 5-Methylcytidine is required for cooperative binding of magnesium(2+) and a conformational transition at the anticodon stem-loop of yeast phenylalanine tRNA. Biochemistry, 32, 10249-10253.
    • (1993) Biochemistry , vol.32 , pp. 10249-10253
    • Chen, Y.1    Sierzputowska-Gracz, H.2    Guenther, R.3    Everett, K.4    Agris, P.F.5
  • 23
    • 0031023569 scopus 로고    scopus 로고
    • Identification of 2-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome
    • Von Ahsen,U., Green,R., Schroeder,R. and Noller,H.F. (1997) Identification of 2-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome. RNA, 3, 49-56.
    • (1997) RNA , vol.3 , pp. 49-56
    • Von Ahsen, U.1    Green, R.2    Schroeder, R.3    Noller, H.F.4
  • 31
    • 0014210985 scopus 로고
    • Conformation of the anticodon loop in tRNA
    • Fuller,W. and Hodgson,A. (1967) Conformation of the anticodon loop in tRNA. Nature, 215, 817-821.
    • (1967) Nature , vol.215 , pp. 817-821
    • Fuller, W.1    Hodgson, A.2
  • 35
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen,W.L., Chandrasekhar,J. and Madura,J.D. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 36
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • York,D.M., Darden,T.A. and Pedersen,L.G. (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. J. Chem. Phys., 99, 8345-8348.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a systems with constraints: Molecular dynamics of n-alkanes
    • Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the Cartesian equations of motion of a systems with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys., 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 39
    • 0030953141 scopus 로고    scopus 로고
    • Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes
    • Cheatham,T.E., III and Kollman,P.A. (1997) Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc., 119, 4805-4825.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 4805-4825
    • Cheatham III, T.E.1    Kollman, P.A.2
  • 40
    • 0346366808 scopus 로고    scopus 로고
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations
    • 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol., 335, 555-571.
    • (2004) J. Mol. Biol. , vol.335 , pp. 555-571
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 42
    • 28444490422 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    • Dixit,S.B., Beveridge,D.L., Case,D.A., Cheatham,T.E., III, Giudice,E., Lankas,F., Lavery,R., Maddocks,J.H., Osman,R., Sklenar,H. et al. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J., 89, 3721-3740.
    • (2005) Biophys. J. , vol.89 , pp. 3721-3740
    • Dixit, S.B.1    Beveridge, D.L.2    Case, D.A.3    Cheatham III, T.E.4    Giudice, E.5    Lankas, F.6    Lavery, R.7    Maddocks, J.H.8    Osman, R.9    Sklenar, H.10
  • 43
    • 33645006571 scopus 로고    scopus 로고
    • Structural and evolutionary classification of G/U wobble basepairs in the ribosome
    • Mokdad,A., Krasovska,M.V., Sponer,J. and Leontis,N.B. (2006) Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Res., 34, 1326-1341.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 1326-1341
    • Mokdad, A.1    Krasovska, M.V.2    Sponer, J.3    Leontis, N.B.4
  • 44
    • 0033581172 scopus 로고    scopus 로고
    • Ala and 3:70 variants: Molecular dynamics analysis of local helical structure and tightly bound water
    • Ala and 3:70 variants: molecular dynamics analysis of local helical structure and tightly bound water. J. Am. Chem. Soc., 121, 7310-7317.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 7310-7317
    • Nagan, M.C.1    Kerimo, S.S.2    Musier-Forsyth, K.3    Cramer, C.J.4
  • 45
    • 32644451166 scopus 로고    scopus 로고
    • Molecular dynamics simulations of sarcin-ricin rRNA motif
    • Spackova,N. and Sponer,J. (2006) Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res., 34, 697-708.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 697-708
    • Spackova, N.1    Sponer, J.2
  • 48
    • 36849115659 scopus 로고
    • Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules
    • Ditchfield,R., Hehre,W.J. and Pople,J.A. (1971) Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules. J. Chem. Phys., 54, 724-728.
    • (1971) J. Chem. Phys. , vol.54 , pp. 724-728
    • Ditchfield, R.1    Hehre, W.J.2    Pople, J.A.3
  • 49
    • 49649133169 scopus 로고
    • The effects of d-functions on molecular orbital energies for hydrocarbons
    • Hariharan,P.C. and Pople,J.A. (1972) The effects of d-functions on molecular orbital energies for hydrocarbons. Chem. Phys. Lett., 66, 217-219.
    • (1972) Chem. Phys. Lett. , vol.66 , pp. 217-219
    • Hariharan, P.C.1    Pople, J.A.2
  • 50
    • 0347170005 scopus 로고
    • Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules
    • Hehre,W.J., Ditchfield,R. and Pople,J.A. (1972) Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules. J. Am. Chem. Soc., 56, 2257-2261.
    • (1972) J. Am. Chem. Soc. , vol.56 , pp. 2257-2261
    • Hehre, W.J.1    Ditchfield, R.2    Pople, J.A.3
  • 51
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model
    • Bayly,C.I., Cieplak,P., Cornell,W.D. and Kollman,P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model. J. Phys. Chem., 97, 10269-10280.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 54
    • 0037422363 scopus 로고    scopus 로고
    • Effectiveness of diffuse basis functions for calculating relative energies by density functional theory
    • Lynch,B.J., Zhao,Y. and Truhlar,D.G. (2003) Effectiveness of diffuse basis functions for calculating relative energies by density functional theory. J. Phys. Chem. A, 107, 1384-1388.
    • (2003) J. Phys. Chem. A , vol.107 , pp. 1384-1388
    • Lynch, B.J.1    Zhao, Y.2    Truhlar, D.G.3
  • 55
    • 33748545144 scopus 로고
    • Influence of polarization functions on MO hydrogenation energies
    • Hariharan,P.C. and Pople,J.A. (1973) Influence of polarization functions on MO hydrogenation energies. Theor. Chim. Acta, 28, 213-222.
    • (1973) Theor. Chim. Acta , vol.28 , pp. 213-222
    • Hariharan, P.C.1    Pople, J.A.2
  • 56
  • 57
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu,X. and Olson,W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.1    Olson, W.K.2
  • 60
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly,M.L. (1983) Analytical molecular surface calculation. J. Appl. Cryst., 16, 548-558.
    • (1983) J. Appl. Cryst. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 62
    • 0002143869 scopus 로고    scopus 로고
    • Base and base pair morphologies, helical parameters, and definitions
    • In Neidle,S. (ed.), Oxford University Press, NY
    • Lavery,R. and Zakrzewska,K. (1999) Base and base pair morphologies, helical parameters, and definitions. In Neidle,S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, NY, pp. 39-76.
    • (1999) Oxford Handbook of Nucleic Acid Structure , pp. 39-76
    • Lavery, R.1    Zakrzewska, K.2
  • 63
    • 0017310258 scopus 로고
    • Spatial configuration of ordered polynucleotide chains. 3. Polycyclonucleotides
    • Olson,W.K. and Dasika,R.D. (1976) Spatial configuration of ordered polynucleotide chains. 3. Polycyclonucleotides. J. Am. Chem. Soc., 98, 5371-5380.
    • (1976) J. Am. Chem. Soc. , vol.98 , pp. 5371-5380
    • Olson, W.K.1    Dasika, R.D.2
  • 67
    • 0000643212 scopus 로고    scopus 로고
    • Effects of pseudouridylation
    • In Grosjean,H. and Benne,R. (eds), ASM Press, Washington, DC
    • Auffinger,P. and Westhof,E. (1998) Effects of pseudouridylation. In Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 103-112.
    • (1998) Modification and Editing of RNA , pp. 103-112
    • Auffinger, P.1    Westhof, E.2
  • 68
    • 0023891456 scopus 로고
    • Hydration of transfer RNA molecules: A crystallographic study
    • Westhof,E., Dumas,P. and Moras,D. (1988) Hydration of transfer RNA molecules: A crystallographic study. Biochimie, 70, 145-165.
    • (1988) Biochimie , vol.70 , pp. 145-165
    • Westhof, E.1    Dumas, P.2    Moras, D.3
  • 70
    • 0025922011 scopus 로고
    • Phe from hisT mutants: A structural role for pseudouridine
    • Phe from hisT mutants: A structural role for pseudouridine. Biochemistry, 30, 4223-4231.
    • (1991) Biochemistry , vol.30 , pp. 4223-4231
    • Davis, D.R.1    Poulter, C.D.2
  • 71
    • 0033523082 scopus 로고    scopus 로고
    • Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model
    • Zacharias,M. and Skelnar,H. (1999) Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model. J. Mol. Biol., 289, 261-275.
    • (1999) J. Mol. Biol. , vol.289 , pp. 261-275
    • Zacharias, M.1    Skelnar, H.2
  • 73
    • 0021879256 scopus 로고
    • Crystallographic refinement of yeast aspartic acid transfer RNA
    • Westhof,E., Dumas,P. and Moras,D. (1985) Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol., 194, 119-145.
    • (1985) J. Mol. Biol. , vol.194 , pp. 119-145
    • Westhof, E.1    Dumas, P.2    Moras, D.3
  • 75
    • 0025815046 scopus 로고
    • The 3 Å crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination
    • Basavappa,R. and Sigler,P.B. (1991) The 3 Å crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination. EMBO J., 10, 2105-3111.
    • (1991) EMBO J. , vol.10 , pp. 2105-3111
    • Basavappa, R.1    Sigler, P.B.2
  • 77
    • 0034654495 scopus 로고    scopus 로고
    • Factors contributing to aromatic stacking in water: Evaluation in the context of DNA
    • Guckian,K.M., Ren,R.X.-F., Chaudhuri,N.C., Tahmassebi,D.T. and Kool,E.T. (2000) Factors contributing to aromatic stacking in water: Evaluation in the context of DNA. J. Am. Chem. Soc., 122, 2213-2222.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2213-2222
    • Guckian, K.M.1    Ren, R.X.-F.2    Chaudhuri, N.C.3    Tahmassebi, D.T.4    Kool, E.T.5
  • 78
    • 0036851660 scopus 로고    scopus 로고
    • Replacing the nucleobases in DNA with designer molecules
    • Kool,E.T. (2002) Replacing the nucleobases in DNA with designer molecules. Acc. Chem. Res., 35, 936-943.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 936-943
    • Kool, E.T.1
  • 81
    • 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., IV, Tarry,M.J. and Ramakrishnan,V. (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell, 111, 721-732.
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy IV, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 82
    • 0035798380 scopus 로고    scopus 로고
    • Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions
    • Spahn,C.M.T., Beckmann,R., Eswar,N., Penczek,P.A., Sali,A., Blobel,G. and Frank,J. (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell, 107, 373-386.
    • (2001) Cell , vol.107 , pp. 373-386
    • Spahn, C.M.T.1    Beckmann, R.2    Eswar, N.3    Penczek, P.A.4    Sali, A.5    Blobel, G.6    Frank, J.7
  • 84
    • 0035252889 scopus 로고    scopus 로고
    • Ribosome fidelity: tRNA discrimination, proofreading and induced fit
    • Rodnina,M.V. and Wintermeyer,W. (2001) Ribosome fidelity: TRNA discrimination, proofreading and induced fit. TIBS, 26, 124-130.
    • (2001) TIBS , vol.26 , pp. 124-130
    • Rodnina, M.V.1    Wintermeyer, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.