메뉴 건너뛰기




Volumn 41, Issue 3, 2013, Pages 1483-1495

Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; FOOT AND MOUTH DISEASE VIRUS; INTERNAL RIBOSOME ENTRY SITE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; RNA TRANSLATION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

EID: 84873689836     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1302     Document Type: Article
Times cited : (24)

References (56)
  • 1
    • 0029969687 scopus 로고    scopus 로고
    • Structural analysis of the interaction of the pyrimidine tract-binding protein with the internal ribosomal entry site of encephalomyocarditis virus and foot-and-mouth disease virus RNAs
    • Kolupaeva,V.G., Hellen,C.U. and Shatsky,I.N. (1996) Structural analysis of the interaction of the pyrimidine tract-binding protein with the internal ribosomal entry site of encephalomyocarditis virus and foot-and-mouth disease virus RNAs. RNA, 2, 1199-1212.
    • (1996) RNA , vol.2 , pp. 1199-1212
    • Hellen, C.U.1    Shatsky, I.N.2
  • 2
    • 0033623486 scopus 로고    scopus 로고
    • Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo
    • Lopez de Quinto,S. and Martinez-Salas,E. (2000) Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo. RNA, 6, 1380-1392.
    • (2000) RNA , vol.6 , pp. 1380-1392
    • Lopez De Quinto, S.1    Martinez-Salas, E.2
  • 3
    • 0034663980 scopus 로고    scopus 로고
    • A cell cycle-dependent protein serves as a template-specific translation initiation factor
    • Pilipenko,E.V., Pestova,T.V., Kolupaeva,V.G., Khitrina,E.V., Poperechnaya,A.N., Agol,V.I. and Hellen,C.U. (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev., 14, 2028-2045.
    • (2000) Genes Dev. , vol.14 , pp. 2028-2045
    • Agol, V.I.1    Hellen, C.U.2
  • 4
    • 0034852292 scopus 로고    scopus 로고
    • IRES interaction with translation initiation factors: Functional characterization of novel RNA contacts with eIF3, eIF4B, and eIF4GII
    • Lopez de Quinto,S., Lafuente,E. and Martinez-Salas,E. (2001) IRES interaction with translation initiation factors: functional characterization of novel RNA contacts with eIF3, eIF4B, and eIF4GII. RNA, 7, 1213-1226.
    • (2001) RNA , vol.7 , pp. 1213-1226
    • Lopez De Quinto, S.1    Lafuente, E.2    Martinez-Salas, E.3
  • 5
    • 0035040192 scopus 로고    scopus 로고
    • A novel protein-RNA binding assay: Functional interactions of the foot-and-mouth disease virus internal ribosome entry site with cellular proteins
    • Stassinopoulos,I.A. and Belsham,G.J. (2001) A novel protein-RNA binding assay: functional interactions of the foot-and-mouth disease virus internal ribosome entry site with cellular proteins. RNA, 7, 114-122.
    • (2001) RNA , vol.7 , pp. 114-122
    • Stassinopoulos, I.A.1    Belsham, G.J.2
  • 6
    • 34447530523 scopus 로고    scopus 로고
    • Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA
    • Andreev,D.E., Fernandez-Miragall,O., Ramajo,J., Dmitriev,S.E., Terenin,I.M., Martinez-Salas,E. and Shatsky,I.N. (2007) Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA. RNA, 13, 1366-1374.
    • (2007) RNA , vol.13 , pp. 1366-1374
    • Martinez-Salas, E.1    Shatsky, I.N.2
  • 7
    • 59649126267 scopus 로고    scopus 로고
    • A novel role for Gemin5 in mRNA translation
    • Pacheco,A., Lopez de Quinto,S., Ramajo,J., Fernandez,N. and Martinez-Salas,E. (2009) A novel role for Gemin5 in mRNA translation. Nucleic Acids Res., 37, 582-590.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 582-590
    • Ramajo, J.1    Fernandez, N.2    Martinez-Salas, E.3
  • 8
    • 0030999946 scopus 로고    scopus 로고
    • Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation
    • Lopez de Quinto,S. and Martinez-Salas,E. (1997) Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. J. Virol., 71, 4171-4175.
    • (1997) J. Virol. , vol.71 , pp. 4171-4175
    • Lopez De Quinto, S.1    Martinez-Salas, E.2
  • 9
    • 31044449305 scopus 로고    scopus 로고
    • Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation
    • Fernandez-Miragall,O., Ramos,R., Ramajo,J. and Martinez-Salas,E. (2006) Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA, 12, 223-234.
    • (2006) RNA , vol.12 , pp. 223-234
    • Ramajo, J.1    Martinez-Salas, E.2
  • 10
    • 80455168337 scopus 로고    scopus 로고
    • Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation
    • Fernandez,N., Fernandez-Miragall,O., Ramajo,J., Garcia-Sacristan,A., Bellora,N., Eyras,E., Briones,C. and Martinez-Salas,E. (2011) Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation. Nucleic Acids Res., 39, 8572-8585.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 8572-8585
    • Briones, C.1    Martinez-Salas, E.2
  • 11
    • 78650261546 scopus 로고    scopus 로고
    • Structural analysis provides insights into the modular organization of picornavirus IRES
    • Fernandez,N., Garcia-Sacristan,A., Ramajo,J., Briones,C. and Martinez-Salas,E. (2011) Structural analysis provides insights into the modular organization of picornavirus IRES. Virology, 409, 251-261.
    • (2011) Virology , vol.409 , pp. 251-261
    • Briones, C.1    Martinez-Salas, E.2
  • 12
    • 0037370110 scopus 로고    scopus 로고
    • Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution
    • Correll,C.C. and Swinger,K. (2003) Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution. RNA, 9, 355-363.
    • (2003) RNA , vol.9 , pp. 355-363
    • Correll, C.C.1    Swinger, K.2
  • 13
    • 10744229009 scopus 로고    scopus 로고
    • Structural organization of a viral IRES depends on the integrity of the GNRA motif
    • Fernandez-Miragall,O. and Martinez-Salas,E. (2003) Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA, 9, 1333-1344.
    • (2003) RNA , vol.9 , pp. 1333-1344
    • Fernandez-Miragall, O.1    Martinez-Salas, E.2
  • 14
    • 2442457098 scopus 로고    scopus 로고
    • NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: A single C to U substitution drastically changes the shape and flexibility of RNA
    • Du,Z., Ulyanov,N.B., Yu,J., Andino,R. and James,T.L. (2004) NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA. Biochemistry, 43, 5757-5771.
    • (2004) Biochemistry , vol.43 , pp. 5757-5771
    • Andino, R.1    James, T.L.2
  • 15
    • 0032863246 scopus 로고    scopus 로고
    • A selection system for functional internal ribosome entry site (IRES) elements: Analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES
    • Robertson,M.E., Seamons,R.A. and Belsham,G.J. (1999) A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES. RNA, 5, 1167-1179.
    • (1999) RNA , vol.5 , pp. 1167-1179
    • Seamons, R.A.1    Belsham, G.J.2
  • 16
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Zuker, M.1    Turner, D.H.2
  • 17
    • 0029050831 scopus 로고
    • A nomenclature of junctions and branchpoints in nucleic acids
    • Lilley,D.M., Clegg,R.M., Diekmann,S., Seeman,N.C., Von Kitzing,E. and Hagerman,P.J. (1995) A nomenclature of junctions and branchpoints in nucleic acids. Nucleic Acids Res., 23, 3363-3364.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3363-3364
    • Von Kitzing, E.1    Hagerman, P.J.2
  • 18
    • 0036237981 scopus 로고    scopus 로고
    • Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation
    • Kieft,J.S., Zhou,K., Grech,A., Jubin,R. and Doudna,J.A. (2002) Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struct. Biol., 9, 370-374.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 370-374
    • Jubin, R.1    Doudna, J.A.2
  • 19
    • 74249115345 scopus 로고    scopus 로고
    • Topology links RNA secondary structure with global conformation, dynamics, and adaptation
    • Bailor,M.H., Sun,X. and Al-Hashimi,H.M. (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science, 327, 202-206.
    • (2010) Science , vol.327 , pp. 202-206
    • Sun, X.1    Al-Hashimi, H.M.2
  • 20
    • 70349238567 scopus 로고    scopus 로고
    • Tertiary motifs revealed in analyses of higher-order RNA junctions
    • Laing,C., Jung,S., Iqbal,A. and Schlick,T. (2009) Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol., 393, 67-82.
    • (2009) J. Mol. Biol. , vol.393 , pp. 67-82
    • Iqbal, A.1    Schlick, T.2
  • 21
    • 67449103067 scopus 로고    scopus 로고
    • Analysis of four-way junctions in RNA structures
    • Laing,C. and Schlick,T. (2009) Analysis of four-way junctions in RNA structures. J. Mol. Biol., 390, 547-559.
    • (2009) J. Mol. Biol. , vol.390 , pp. 547-559
    • Laing, C.1    Schlick, T.2
  • 22
    • 29844453234 scopus 로고    scopus 로고
    • Topology of three-way junctions in folded RNAs
    • Lescoute,A. and Westhof,E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
    • (2006) RNA , vol.12 , pp. 83-93
    • Lescoute, A.1    Westhof, E.2
  • 23
    • 0016362013 scopus 로고
    • The general structure of transfer RNA molecules
    • Kim,S.H., Sussman,J.L., Suddath,F.L., Quigley,G.J., McPherson,A., Wang,A.H., Seeman,N.C. and Rich,A. (1974) The general structure of transfer RNA molecules. Proc. Natl Acad. Sci. USA, 71, 4970-4974.
    • (1974) Proc. Natl Acad. Sci. USA , vol.71 , pp. 4970-4974
    • Seeman, N.C.1    Rich, A.2
  • 24
    • 0029820625 scopus 로고    scopus 로고
    • Crystal structure of a group i ribozyme domain: Principles of RNA packing
    • Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678-1685.
    • (1996) Science , vol.273 , pp. 1678-1685
    • Cech, T.R.1    Doudna, J.A.2
  • 25
    • 79958073354 scopus 로고    scopus 로고
    • Computational approaches to RNA structure prediction, analysis, and design
    • Laing,C. and Schlick,T. (2011) Computational approaches to RNA structure prediction, analysis, and design. Curr. Opin. Struct. Biol., 21, 306-318.
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 306-318
    • Laing, C.1    Schlick, T.2
  • 26
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • Laing,C. and Schlick,T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens. Matter, 22, 283101.
    • (2010) J. Phys. Condens. Matter , vol.22 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 27
    • 84862969708 scopus 로고    scopus 로고
    • Predicting coaxial helical stacking in RNA junctions
    • Laing,C., Wen,D., Wang,J.T. and Schlick,T. (2011) Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res., 40, 487-498.
    • (2011) Nucleic Acids Res. , vol.40 , pp. 487-498
    • Wang, J.T.1    Schlick, T.2
  • 28
    • 0024355303 scopus 로고
    • Conservation of the secondary structure elements of the 50-untranslated region of cardio- and aphthovirus RNAs
    • Pilipenko,E.V., Blinov,V.M., Chernov,B.K., Dmitrieva,T.M. and Agol,V.I. (1989) Conservation of the secondary structure elements of the 50-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res., 17, 5701-5711.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 5701-5711
    • Dmitrieva, T.M.1    Agol, V.I.2
  • 29
    • 40449139010 scopus 로고    scopus 로고
    • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    • Parisien,M. and Major,F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 31
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin,M.A., Blackshields,G., Brown,N.P., Chenna,R., McGettigan,P.A., McWilliam,H., Valentin,F., Wallace,I.M., Wilm,A., Lopez,R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Lopez, R.1
  • 32
    • 48449084852 scopus 로고    scopus 로고
    • RNALogo: A new approach to display structural RNA alignment
    • Chang,T.H., Horng,J.T. and Huang,H.D. (2008) RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res., 36, W91-W96.
    • (2008) Nucleic Acids Res. , vol.36
    • Horng, J.T.1    Huang, H.D.2
  • 33
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman,L. (2001) Random forests. Mach. Learn., 45, 5-32.
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 34
    • 58249111738 scopus 로고    scopus 로고
    • Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    • Jonikas,M.A., Radmer,R.J., Laederach,A., Das,R., Pearlman,S., Herschlag,D. and Altman,R.B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
    • (2009) RNA , vol.15 , pp. 189-199
    • Herschlag, D.1    Altman, R.B.2
  • 35
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
    • Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E. 3rd, Laughton,C.A. and Orozco,M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Cheatham Iii, T.E.1    Laughton, C.A.2    Orozco, M.3
  • 36
    • 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., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 5179-5197.
    • (1995) J. Am. Chem. Soc. , pp. 5179-5197
    • Caldwell, J.W.1    Kollman, P.A.2
  • 37
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips,J.C., Braun,R., Wang,W., Gumbart,J., Tajkhorshid,E., Villa,E., Chipot,C., Skeel,R.D., Kale,L. and Schulten,K. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem., 26, 1781-1802.
    • (2005) J. Comput. Chem. , vol.26 , pp. 1781-1802
    • Kale, L.1    Schulten, K.2
  • 38
    • 77952472539 scopus 로고    scopus 로고
    • Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H++ forms are most consistent with crystal structures of hairpin ribozyme
    • Mlynsky,V., Banas,P., Hollas,D., Reblova,K., Walter,N.G., Sponer,J. and Otyepka,M. (2010) Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H++ forms are most consistent with crystal structures of hairpin ribozyme. J. Phys. Chem. B, 114, 6642-6652.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 6642-6652
    • Mlynsky, V.1    Banas, P.2    Hollas, D.3    Reblova, K.4    Walter, N.G.5    Sponer, J.6    Otyepka, M.7
  • 39
    • 84864479919 scopus 로고    scopus 로고
    • Structure and mechanical properties of the ribosomal L1 stalk three-way junction
    • Reblova,K., Sponer,J. and Lankas,F. (2012) Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res., 40, 6290-6303.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 6290-6303
    • Reblova, K.1    Sponer, J.2    Lankas, F.3
  • 40
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
    • Zgarbova,M., Otyepka,M., Sponer,J., Mladek,A., Banas,P., Cheatham,T.E. 3rd and Jurecka,P. (2011) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput., 7, 2886-2902.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbova, M.1    Otyepka, M.2    Sponer, J.3    Mladek, A.4    Banas, P.5    Cheatham Iii, T.E.6    Jurecka, P.7
  • 41
    • 84855656902 scopus 로고    scopus 로고
    • Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs
    • Yildirim,I., Kennedy,S.D., Stern,H.A., Hart,J.M., Kierzek,R. and Turner,D.H. (2012) Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs. J. Chem. Theory Comput., 8, 172-181.
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 172-181
    • Yildirim, I.1    Kennedy, S.D.2    Stern, H.A.3    Hart, J.M.4    Kierzek, R.5    Turner, D.H.6
  • 42
    • 79959292152 scopus 로고    scopus 로고
    • ModeRNA: A tool for comparative modeling of RNA 3D structure
    • Rother,M., Rother,K., Puton,T. and Bujnicki,J.M. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4007-4022
    • Rother, M.1    Rother, K.2    Puton, T.3    Bujnicki, J.M.4
  • 43
    • 0023462809 scopus 로고
    • Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena
    • Kim,S.H. and Cech,T.R. (1987) Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena. Proc. Natl Acad. Sci. USA, 84, 8788-8792.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 8788-8792
    • Kim, S.H.1    Cech, T.R.2
  • 44
    • 0030959348 scopus 로고    scopus 로고
    • Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution
    • Costa,M. and Michel,F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J., 16, 3289-3302.
    • (1997) EMBO J. , vol.16 , pp. 3289-3302
    • Costa, M.1    Michel, F.2
  • 45
    • 80053207214 scopus 로고    scopus 로고
    • In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses
    • Burks,J.M., Zwieb,C., Muller,F., Wower,I.K. and Wower,J. (2011) In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses. Arch. Virol., 156, 1737-1747.
    • (2011) Arch. Virol. , vol.156 , pp. 1737-1747
    • Wower, I.K.1    Wower, J.2
  • 46
    • 79956058665 scopus 로고    scopus 로고
    • Biomolecularmodeling and simulation: A field coming of age
    • Schlick,T., Collepardo-Guevara,R., Halvorsen,L.A., Jung,S. and Xiao,X. (2011) Biomolecularmodeling and simulation: a field coming of age. Q. Rev. Biophys., 44, 191-228.
    • (2011) Q. Rev. Biophys. , vol.44 , pp. 191-228
    • Jung, S.1    Xiao, X.2
  • 47
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
    • (2001) RNA , vol.7 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 48
    • 42749086185 scopus 로고    scopus 로고
    • The impact of RNA structure on picornavirus IRES activity
    • Martinez-Salas,E. (2008) The impact of RNA structure on picornavirus IRES activity. Trends Microbiol., 16, 230-237.
    • (2008) Trends Microbiol. , vol.16 , pp. 230-237
    • Martinez-Salas, E.1
  • 49
    • 0344980095 scopus 로고    scopus 로고
    • Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES
    • Ramos,R. and Martinez-Salas,E. (1999) Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES). RNA, 5, 1374-1383.
    • (1999) RNA , vol.5 , pp. 1374-1383
    • Ramos, R.1    Martinez-Salas, E.2
  • 50
    • 34249103881 scopus 로고    scopus 로고
    • Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element
    • Serrano,P., Gomez,J. and Martinez-Salas,E. (2007) Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element. RNA, 13, 849-859.
    • (2007) RNA , vol.13 , pp. 849-859
    • Gomez, J.1    Martinez-Salas, E.2
  • 51
    • 33847318371 scopus 로고    scopus 로고
    • Molecular dynamics simulations of RNA: An in silico single molecule approach
    • McDowell,S.E., Spackova,N., Sponer,J. and Walter,N.G. (2007) Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers, 85, 169-184.
    • (2007) Biopolymers , vol.85 , pp. 169-184
    • Sponer, J.1    Walter, N.G.2
  • 52
    • 0345631645 scopus 로고    scopus 로고
    • Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations
    • Sponer,J., Burda,J.M.S., Leszczynski,J. and Hobza,P. (1998) Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J. Phys. Chem. A, 102, 5951-5957.
    • (1998) J. Phys. Chem. A , vol.102 , pp. 5951-5957
    • Sponer, J.1    Burda, J.M.S.2    Leszczynski, J.3    Hobza, P.4
  • 53
    • 33746388359 scopus 로고    scopus 로고
    • Structure, dynamics, and elasticity of free 16 s rRNA helix 44 studied by molecular dynamics simulations
    • Reblova,K., Lankas,F., Razga,F., Krasovska,M.V., Koca,J. and Sponer,J. (2006) Structure, dynamics, and elasticity of free 16 s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers, 82, 504-520.
    • (2006) Biopolymers , vol.82 , pp. 504-520
    • Koca, J.1    Sponer, J.2
  • 54
    • 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
  • 55
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 27-38.
    • (1996) J. Mol. Graph. , vol.14 , pp. 27-38
    • Dalke, A.1    Schulten, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.