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Volumn 34, Issue 2, 2006, Pages 697-708

Molecular dynamics simulations of sarcin-ricin rRNA motif

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CATION; HYPOXANTHINE; RIBOSOME RNA; RICIN; RNA 23S; RNA 28S; WATER;

EID: 32644451166     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkj470     Document Type: Article
Times cited : (72)

References (63)
  • 1
    • 0023405923 scopus 로고
    • Evidence that the G2661 region of 23S ribosomal-RNA is located at the ribosomal-binding sites of both elongation-factors
    • Hausner,T.P., Atmadja,J. and Nierhaus,K.H. (1987) Evidence that the G2661 region of 23S ribosomal-RNA is located at the ribosomal-binding sites of both elongation-factors. Biochimie, 69, 911-923.
    • (1987) Biochimie , vol.69 , pp. 911-923
    • Hausner, T.P.1    Atmadja, J.2    Nierhaus, K.H.3
  • 2
    • 0023722010 scopus 로고
    • Interaction of elongation-factors Ef-G and Ef-Tu with a conserved loop in 23S RNA
    • Moazed,D., Robertson,J.M. and Noller,H.F. (1988) Interaction of elongation-factors Ef-G and Ef-Tu with a conserved loop in 23S RNA. Nature, 334, 362-364.
    • (1988) Nature , vol.334 , pp. 362-364
    • Moazed, D.1    Robertson, J.M.2    Noller, H.F.3
  • 3
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3497-3531
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 4
    • 0020479406 scopus 로고
    • The site of action of alpha-sarcin on eukaryotic ribosomes - The sequence at the alpha-sarcin cleavage site in 28 S-ribosomal ribonucleic-acid
    • Endo,Y. and Wool,I.G. (1982) The site of action of alpha-sarcin on eukaryotic ribosomes - the sequence at the alpha-sarcin cleavage site in 28 S-ribosomal ribonucleic-acid. J. Biol. Chem., 257, 9054-9060.
    • (1982) J. Biol. Chem. , vol.257 , pp. 9054-9060
    • Endo, Y.1    Wool, I.G.2
  • 5
    • 0023664263 scopus 로고
    • The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes - The site and the characteristics of the modification in 28-S ribosomal-RNA caused by the toxins
    • Endo,Y., Mitsui,K., Motizuki,M. and Tsurugi,K. (1987) The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes - the site and the characteristics of the modification in 28-S ribosomal-RNA caused by the toxins. J. Biol. Chem., 262, 5908-5912.
    • (1987) J. Biol. Chem. , vol.262 , pp. 5908-5912
    • Endo, Y.1    Mitsui, K.2    Motizuki, M.3    Tsurugi, K.4
  • 6
    • 0023219950 scopus 로고
    • RNA N-glycosidase activity of ricin a-chain - Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes
    • Endo,Y. and Tsurugi,K. (1987) RNA N-glycosidase activity of ricin a-chain - mechanism of action of the toxic lectin ricin on eukaryotic ribosomes. J. Biol. Chem., 262, 8128-8130.
    • (1987) J. Biol. Chem. , vol.262 , pp. 8128-8130
    • Endo, Y.1    Tsurugi, K.2
  • 7
    • 0343898815 scopus 로고    scopus 로고
    • Determination of the 28 S ribosomal RNA identity element (G4319) for alpha-sarcin and the relationship of recognition to the selection of the catalytic site
    • Gluck,A. and Wool,I.G. (1996) Determination of the 28 S ribosomal RNA identity element (G4319) for alpha-sarcin and the relationship of recognition to the selection of the catalytic site. J. Mol. Biol., 256, 838-848.
    • (1996) J. Mol. Biol. , vol.256 , pp. 838-848
    • Gluck, A.1    Wool, I.G.2
  • 8
    • 0030774277 scopus 로고    scopus 로고
    • The ribosome-in-pieces: Binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin/ricin and thiostrepton domains of 23S ribosomal RNA
    • Munishkin,A. and Wool,I.G. (1997) The ribosome-in-pieces: Binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin/ ricin and thiostrepton domains of 23S ribosomal RNA. Proc. Natl Acad. Sci. USA, 94, 12280-12284.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 12280-12284
    • Munishkin, A.1    Wool, I.G.2
  • 9
    • 0034674158 scopus 로고    scopus 로고
    • The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity
    • Perez-Canadillas,J.M., Santoro,J., Campos-Olivas,R., Lacadena,J., del Pozo,A.M., Gavilanes,J.G., Rico,M. and Bruix,M. (2000) The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity. J. Mol. Biol., 299, 1061-1073.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1061-1073
    • Perez-Canadillas, J.M.1    Santoro, J.2    Campos-Olivas, R.3    Lacadena, J.4    del Pozo, A.M.5    Gavilanes, J.G.6    Rico, M.7    Bruix, M.8
  • 10
    • 0033578939 scopus 로고    scopus 로고
    • The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: The structure at 1.11 angstrom resolution
    • Correll,C.C., Wool,I.G. and Munishkin,A. (1999) The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: The structure at 1.11 angstrom resolution. J. Mol. Biol., 292, 275-287.
    • (1999) J. Mol. Biol. , vol.292 , pp. 275-287
    • Correll, C.C.1    Wool, I.G.2    Munishkin, A.3
  • 11
    • 0345531092 scopus 로고    scopus 로고
    • The common and the distinctive features of the bulged-G motif based on a 1.04 angstrom resolution RNA structure
    • Correll,C.C., Beneken,J., Plantinga,M.J., Lubbers,M. and Chan,Y.L. (2003) The common and the distinctive features of the bulged-G motif based on a 1.04 angstrom resolution RNA structure. Nucleic Acids Res., 31, 6806-6818.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6806-6818
    • Correll, C.C.1    Beneken, J.2    Plantinga, M.J.3    Lubbers, M.4    Chan, Y.L.5
  • 12
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution
    • Ban,N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science, 289, 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 15
    • 0028953727 scopus 로고
    • The sarcin ricin loop, a modular RNA
    • Szewczak,A.A. and Moore,P.B. (1995) The sarcin ricin loop, a modular RNA. J. Mol. Biol., 247, 81-98.
    • (1995) J. Mol. Biol. , vol.247 , pp. 81-98
    • Szewczak, A.A.1    Moore, P.B.2
  • 17
    • 0034856481 scopus 로고    scopus 로고
    • Application of dipolar coupling data to the refinement of the solution structure of the sarcin-ricin loop RNA
    • Warren,J.J. and Moore,P.B. (2001) Application of dipolar coupling data to the refinement of the solution structure of the sarcin-ricin loop RNA. J. Biomol. NMR, 20, 311-323.
    • (2001) J. Biomol. NMR , vol.20 , pp. 311-323
    • Warren, J.J.1    Moore, P.B.2
  • 18
    • 0034760104 scopus 로고    scopus 로고
    • Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping
    • Yang,X.J., Gerczei,T., Glover,L. and Correll,C.C. (2001) Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nature Struct. Biol., 8, 968-973.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 968-973
    • Yang, X.J.1    Gerczei, T.2    Glover, L.3    Correll, C.C.4
  • 19
    • 1442299243 scopus 로고    scopus 로고
    • The location and the significance of a cross-link between the sarcin/ricin domain of ribosomal RNA and the elongation factor-G
    • Chan,Y.L., Correll,C.C. and Wool,I.G. (2004) The location and the significance of a cross-link between the sarcin/ricin domain of ribosomal RNA and the elongation factor-G. J. Mol. Biol., 337, 263-272.
    • (2004) J. Mol. Biol. , vol.337 , pp. 263-272
    • Chan, Y.L.1    Correll, C.C.2    Wool, I.G.3
  • 20
    • 16644372753 scopus 로고    scopus 로고
    • Atomic model of the Thermus thermophilus 70S ribosome developed in silico
    • Tung,C.S. and Sanbonmatsu,K.Y. (2004) Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophys. J., 87, 2714-2722.
    • (2004) Biophys. J. , vol.87 , pp. 2714-2722
    • Tung, C.S.1    Sanbonmatsu, K.Y.2
  • 21
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham,T.E. and Young,M.A. (2000) Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers, 56, 232-256.
    • (2000) Biopolymers , vol.56 , pp. 232-256
    • Cheatham, T.E.1    Young, M.A.2
  • 22
    • 0038539610 scopus 로고    scopus 로고
    • The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
    • Auffinger,P., Bielecki,L. and Westhof,E. (2003) The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol., 10, 551-561.
    • (2003) Chem. Biol. , vol.10 , pp. 551-561
    • Auffinger, P.1    Bielecki, L.2    Westhof, E.3
  • 23
    • 23444456517 scopus 로고    scopus 로고
    • Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
    • Krasovska,M.V., Sefcikova,J., Spackova,N., Sponer,J. and Walter,N.G. (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J. Mol. Biol., 351, 731-748.
    • (2005) J. Mol. Biol. , vol.351 , pp. 731-748
    • Krasovska, M.V.1    Sefcikova, J.2    Spackova, N.3    Sponer, J.4    Walter, N.G.5
  • 25
    • 17844375121 scopus 로고    scopus 로고
    • Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases
    • Razga,F., Koca,J., Sponer,J. and Leontis,N.B. (2005) Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases. Biophys. J., 88, 3466-3485.
    • (2005) Biophys. J. , vol.88 , pp. 3466-3485
    • Razga, F.1    Koca, J.2    Sponer, J.3    Leontis, N.B.4
  • 26
    • 12844258405 scopus 로고    scopus 로고
    • Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex
    • Reblova,K., Spackova,N., Koca,J., Leontis,N.B. and Sponer,J. (2004) Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys. J., 87, 3397-3412.
    • (2004) Biophys. J. , vol.87 , pp. 3397-3412
    • Reblova, K.1    Spackova, N.2    Koca, J.3    Leontis, N.B.4    Sponer, J.5
  • 27
    • 17944388579 scopus 로고    scopus 로고
    • Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
    • Reblova,K., Spackova,N., Sponer,J.E., Koca,J. and Sponer,J. (2003) Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res., 31, 6942-6952.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6942-6952
    • Reblova, K.1    Spackova, N.2    Sponer, J.E.3    Koca, J.4    Sponer, J.5
  • 28
    • 0037764044 scopus 로고    scopus 로고
    • Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E
    • Reblova,K., Spackova,N., Stefl,R., Csaszar,K., Koca,J., Leontis,N.B. and Sponer,J. (2003) Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E. Biophys. J., 84, 3564-3582.
    • (2003) Biophys. J. , vol.84 , pp. 3564-3582
    • Reblova, K.1    Spackova, N.2    Stefl, R.3    Csaszar, K.4    Koca, J.5    Leontis, N.B.6    Sponer, J.7
  • 29
    • 0346366808 scopus 로고    scopus 로고
    • Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations
    • Auffinger,P., Bielecki,L. and Westhof,E. (2004) Symmetric K+ and Mg2+ 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
  • 30
    • 12844270442 scopus 로고    scopus 로고
    • The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study
    • Cojocaru,V., Nottrott,S., Klement,R. and Jovin,T.M. (2005) The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study. RNA, 11, 197-209.
    • (2005) RNA , vol.11 , pp. 197-209
    • Cojocaru, V.1    Nottrott, S.2    Klement, R.3    Jovin, T.M.4
  • 31
    • 10944272174 scopus 로고    scopus 로고
    • Closing loop base pairs in RNA loop-loop complexes: Structural behavior, interaction energy and solvation analysis through molecular dynamics simulations
    • Golebiowski,J., Antonczak,S., Fernandez-Carmona,J., Condom,R. and Cabrol-Bass,D. (2004) Closing loop base pairs in RNA loop-loop complexes: Structural behavior, interaction energy and solvation analysis through molecular dynamics simulations. J. Mol. Model. (Online), 10, 408-417.
    • (2004) J. Mol. Model. (Online) , vol.10 , pp. 408-417
    • Golebiowski, J.1    Antonczak, S.2    Fernandez-Carmona, J.3    Condom, R.4    Cabrol-Bass, D.5
  • 32
    • 20444464100 scopus 로고    scopus 로고
    • Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif
    • Cojocaru,V., Klement,R. and Jovin,T.M. (2005) Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Res., 33, 3435-3446.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3435-3446
    • Cojocaru, V.1    Klement, R.2    Jovin, T.M.3
  • 33
    • 14244271781 scopus 로고    scopus 로고
    • RNA solvation: A molecular dynamics simulation perspective
    • Auffinger,P. and Westhof,E. (2000) RNA solvation: A molecular dynamics simulation perspective. Biopolymers, 56, 266-274.
    • (2000) Biopolymers , vol.56 , pp. 266-274
    • Auffinger, P.1    Westhof, E.2
  • 34
    • 13444256246 scopus 로고    scopus 로고
    • Conformational determinants of tandem GU mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations
    • Pan,Y.P., Priyakumar,U.D. and MacKerell,A.D. (2005) Conformational determinants of tandem GU mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations. Biochemistry, 44, 1433-1443.
    • (2005) Biochemistry , vol.44 , pp. 1433-1443
    • Pan, Y.P.1    Priyakumar, U.D.2    MacKerell, A.D.3
  • 35
    • 0035700275 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop
    • Li,W., Ma,B.Y. and Shapiro,B.A. (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. J. Biomol. Struct. Dyn., 19, 381-396.
    • (2001) J. Biomol. Struct. Dyn. , vol.19 , pp. 381-396
    • Li, W.1    Ma, B.Y.2    Shapiro, B.A.3
  • 36
    • 0037453255 scopus 로고    scopus 로고
    • Understanding discrimination by the ribosome: Stability testing and groove measurement of codon-anticodon pairs
    • Sanbonmatsu,K.Y. and Joseph,S. (2003) Understanding discrimination by the ribosome: Stability testing and groove measurement of codon-anticodon pairs. J. Mol. Biol., 328, 33-47.
    • (2003) J. Mol. Biol. , vol.328 , pp. 33-47
    • Sanbonmatsu, K.Y.1    Joseph, S.2
  • 37
    • 27644502679 scopus 로고    scopus 로고
    • Simulating movement of tRNA into the ribosome during decoding
    • Sanbonmatsu,K.Y., Joseph,S. and Tung,C.S. (2005) Simulating movement of tRNA into the ribosome during decoding. Proc. Natl Acad. Sci. USA, 102, 15854-15859.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15854-15859
    • Sanbonmatsu, K.Y.1    Joseph, S.2    Tung, C.S.3
  • 38
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas,F., Sponer,J., Langowski,J. and Cheatham,T.E. (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883.
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham, T.E.4
  • 39
    • 0030596092 scopus 로고    scopus 로고
    • A network of heterogeneous hydrogen bonds in GNRA tetraloops
    • Jucker,F.M., Heus,H.A., Yip,P.F., Moors,E.H.M. and Pardi,A. (1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol., 264, 968-980.
    • (1996) J. Mol. Biol. , vol.264 , pp. 968-980
    • Jucker, F.M.1    Heus, H.A.2    Yip, P.F.3    Moors, E.H.M.4    Pardi, A.5
  • 40
    • 0037370110 scopus 로고    scopus 로고
    • Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 angstrom resolution
    • Correll,C.C. and Swinger,K. (2003) Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 angstrom resolution. RNA, 9, 355-363.
    • (2003) RNA , vol.9 , pp. 355-363
    • Correll, C.C.1    Swinger, K.2
  • 42
    • 0029633186 scopus 로고
    • Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman,D.A., Case,D.A., Caldwell,J.W., Ross,W.S., Cheatham,T.E., Debolt,S., Ferguson,D., Seibel,G. and Kollman,P. (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 45
    • 33846823909 scopus 로고
    • Particle Mesh Ewald - An N.Log(N) method for Ewald sums in large systems
    • Darden,T., York,D. and Pedersen,L. (1993) Particle Mesh Ewald - an N.Log(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 46
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constrains: 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 system with constrains: 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
  • 47
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco,M., Perez,A., Noy,A. and Luque,F.J. (2003) Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev., 32, 350-364.
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Luque, F.J.4
  • 48
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek,S.T., Clark,T.W., Scott,L.R. and McCammon,J.A. (1997) Molecular dynamics of acetylcholinesterase dimer complexed with tacrine. J. Am. Chem. Soc., 119, 9513-9522.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 9513-9522
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 49
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution - Method and error assessment
    • Gilson,M.K., Sharp,K.A. and Honig,B.H. (1988) Calculating the electrostatic potential of molecules in solution - method and error assessment. J. Comput. Chem., 9, 327-335.
    • (1988) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 51
    • 0344012516 scopus 로고    scopus 로고
    • RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
    • Duarte,C.M., Wadley,L.M. and Pyle,A.M. (2003) RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res., 31, 4755-4761.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4755-4761
    • Duarte, C.M.1    Wadley, L.M.2    Pyle, A.M.3
  • 53
    • 12144283874 scopus 로고    scopus 로고
    • Dynamics and stability of GCAA tetraloop with 2-aminopurine and purine substitutions
    • Sarzynska,J. and Kulinski,T. (2005) Dynamics and stability of GCAA tetraloop with 2-aminopurine and purine substitutions. J. Biomol. Struct. Dyn., 22, 425-439.
    • (2005) J. Biomol. Struct. Dyn. , vol.22 , pp. 425-439
    • Sarzynska, J.1    Kulinski, T.2
  • 54
    • 0344119523 scopus 로고    scopus 로고
    • Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations
    • Sarzynska,J., Nilsson,L. and Kulinski,T. (2003) Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations. Biophys. J., 85, 3445-3459.
    • (2003) Biophys. J. , vol.85 , pp. 3445-3459
    • Sarzynska, J.1    Nilsson, L.2    Kulinski, T.3
  • 55
    • 11944270215 scopus 로고
    • Molecular-dynamics of RNA with the OPLS force-field - Aqueous simulation of a hairpin containing a tetranucleotide loop
    • Zichi,D.A. (1995) Molecular-dynamics of RNA with the OPLS force-field - aqueous simulation of a hairpin containing a tetranucleotide loop. J. Am. Chem. Soc., 117, 2957-2969.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 2957-2969
    • Zichi, D.A.1
  • 56
    • 0033855843 scopus 로고    scopus 로고
    • Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge
    • Sarzynska,J., Kulinski,T. and Nilsson,L. (2000) Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge. Biophys. J., 79, 1213-1227.
    • (2000) Biophys. J. , vol.79 , pp. 1213-1227
    • Sarzynska, J.1    Kulinski, T.2    Nilsson, L.3
  • 57
    • 0036297661 scopus 로고    scopus 로고
    • RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop
    • Sorin,E.J., Engelhardt,M.A., Herschlag,D. and Pande,V.S. (2002) RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol., 317, 493-506.
    • (2002) J. Mol. Biol. , vol.317 , pp. 493-506
    • Sorin, E.J.1    Engelhardt, M.A.2    Herschlag, D.3    Pande, V.S.4
  • 58
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • Varnai,P. and Zakrzewska,K. (2004) DNA and its counterions: A molecular dynamics study. Nucleic Acids Res., 32, 4269-4280.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4269-4280
    • Varnai, P.1    Zakrzewska, K.2
  • 59
    • 10044257912 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(C(p)G) steps
    • Beveridge,D.L., Barreiro,G., Byun,K.S., Case,D.A., Cheatham,T.E., Dixit,S.B., Giudice,E., Lankas,F., Lavery,R., Maddocks,J.H. et al. (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(C(p)G) steps. Biophys. J., 87, 3799-3813.
    • (2004) Biophys. J. , vol.87 , pp. 3799-3813
    • Beveridge, D.L.1    Barreiro, G.2    Byun, K.S.3    Case, D.A.4    Cheatham, T.E.5    Dixit, S.B.6    Giudice, E.7    Lankas, F.8    Lavery, R.9    Maddocks, J.H.10
  • 60
    • 4043137165 scopus 로고    scopus 로고
    • Accurate interaction energies of hydrogen-bonded nucleic acid base pairs
    • Sponer,J., Jurecka,P. and Hobza,P. (2004) Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J. Am. Chem. Soc., 126, 10142-10151.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 10142-10151
    • Sponer, J.1    Jurecka, P.2    Hobza, P.3
  • 61
    • 20744441693 scopus 로고    scopus 로고
    • Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs
    • Sponer,J.E., Spackova,N., Leszczynski,J. and Sponer,J. (2005) Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/ sugar edge base pairs. J. Phys. Chem. B, 109, 11399-11410.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 11399-11410
    • Sponer, J.E.1    Spackova, N.2    Leszczynski, J.3    Sponer, J.4
  • 62
    • 0035951296 scopus 로고    scopus 로고
    • Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex
    • Schneider,C., Brandl,M. and Suhnel,J. (2001) Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex. J. Mol. Biol., 305, 659-667.
    • (2001) J. Mol. Biol. , vol.305 , pp. 659-667
    • Schneider, C.1    Brandl, M.2    Suhnel, J.3


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