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Volumn 84, Issue 6, 2003, Pages 3564-3582

Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E

Author keywords

[No Author keywords available]

Indexed keywords

CATION; MAGNESIUM; RIBOSOME RNA; RNA; RNA 5S;

EID: 0037764044     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75089-9     Document Type: Article
Times cited : (101)

References (87)
  • 1
    • 0032054952 scopus 로고    scopus 로고
    • Simulations of the molecular dynamics of nucleic acids
    • Auffinger, P., and E. Westhof. 1998. Simulations of the molecular dynamics of nucleic acids. Curr. Opin. Struct. Biol. 8:227-236.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 227-236
    • Auffinger, P.1    Westhof, E.2
  • 2
    • 14244271781 scopus 로고    scopus 로고
    • RNA solvation: A molecular dynamics simulation perspective
    • Auffinger, P., and E. Westhof. 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
  • 4
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution
    • Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. 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
  • 5
    • 0036306053 scopus 로고    scopus 로고
    • Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
    • Banavali, N. K., and A. D. MacKerell. 2002. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol. 319:141-160.
    • (2002) J. Mol. Biol. , vol.319 , pp. 141-160
    • Banavali, N.K.1    MacKerell, A.D.2
  • 6
    • 0034036078 scopus 로고    scopus 로고
    • Nucleic acids: Theory and computer simulation, Y2K
    • Beveridge, D. L., and K. J. McConnell. 2000. Nucleic acids: theory and computer simulation, Y2K. Curr. Opin. Struct. Biol. 10:182-196.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 182-196
    • Beveridge, D.L.1    McConnell, K.J.2
  • 7
    • 0037108909 scopus 로고    scopus 로고
    • Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA
    • Bink, H. H. J., K. Hellendoorn, J. van der Meulen, and C. W. Pleij. 2002. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc. Natl. Acad. Sci. USA. 99:13465-13470.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 13465-13470
    • Bink, H.H.J.1    Hellendoorn, K.2    Van der Meulen, J.3    Pleij, C.W.4
  • 8
    • 0034316780 scopus 로고    scopus 로고
    • Water-mediated base pairs in RNA. A quantum-chemical study
    • Brandl, M., M. Meyer, and J. Suhnel. 2000. Water-mediated base pairs in RNA. A quantum-chemical study. J. Phys. Chem. 104:11177-11187.
    • (2000) J. Phys. Chem. , vol.104 , pp. 11177-11187
    • Brandl, M.1    Meyer, M.2    Suhnel, J.3
  • 10
    • 0034699519 scopus 로고    scopus 로고
    • Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
    • Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 407:340-348.
    • (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
  • 12
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham III, T. E., and P. A. Kollman. 2000. Molecular dynamics simulation of nucleic acids. Annu. Rev. Phys. Chem. 51:435-471.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 435-471
    • Cheatham T.E. III1    Kollman, P.A.2
  • 13
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham III, T. E., and M. A. Young. 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. III1    Young, M.A.2
  • 14
    • 0032707625 scopus 로고    scopus 로고
    • Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
    • Chin, K., K. A. Sharp, B. Honig, and A. M. Pyle. 1999. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nat. Struct. Biol. 6:1055-1061.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 1055-1061
    • Chin, K.1    Sharp, K.A.2    Honig, B.3    Pyle, A.M.4
  • 15
    • 0035965121 scopus 로고    scopus 로고
    • Zipper-like Watson-Crick base-pairs
    • Chou, S. H., and K. H. Chin. 2001. Zipper-like Watson-Crick base-pairs. J. Mol. Biol. 312:753-768.
    • (2001) J. Mol. Biol. , vol.312 , pp. 753-768
    • Chou, S.H.1    Chin, K.H.2
  • 17
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs and recognition in the crystal structure of 5S rRNA domain
    • Correll, C. C., B. Freeborn, P. B. Moore, and T. A. Steitz. 1997. Metals, motifs and recognition in the crystal structure of 5S rRNA domain. Cell. 91:705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correll, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 19
    • 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., I. G. Wool, and A. Munishkin. 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
  • 20
    • 0035834495 scopus 로고    scopus 로고
    • Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding
    • Csaszar, K., N. Spackova, R. Stefl, J. Sponer, and N. B. Leontis. 2001. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. J. Mol. Biol. 313:1073-1091.
    • (2001) J. Mol. Biol. , vol.313 , pp. 1073-1091
    • Csaszar, K.1    Spackova, N.2    Stefl, R.3    Sponer, J.4    Leontis, N.B.5
  • 21
    • 0034718074 scopus 로고    scopus 로고
    • Molecular dynamics study of oligonucleotides containing difluorotoluene
    • Cubero, E., C. A. Laughton, F. J. Luque, and M. Orozco. 2000. Molecular dynamics study of oligonucleotides containing difluorotoluene. J. Am. Chem. Soc. 122:6891-6899.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 6891-6899
    • Cubero, E.1    Laughton, C.A.2    Luque, F.J.3    Orozco, M.4
  • 22
    • 0037120830 scopus 로고    scopus 로고
    • Conformational heterogeneity observed in simulations of a pyrene-substituted DNA
    • Cui, G. L., and C. Simmerling. 2002. Conformational heterogeneity observed in simulations of a pyrene-substituted DNA. J. Am. Chem. Soc. 124:12154-12164.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 12154-12164
    • Cui, G.L.1    Simmerling, C.2
  • 23
    • 0031574326 scopus 로고    scopus 로고
    • The loop E-loop D region of Escherichia coli 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins
    • Dallas, A., and P. B. Moore. 1997. The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure. 5:1639-1653.
    • (1997) Structure , vol.5 , pp. 1639-1653
    • Dallas, A.1    Moore, P.B.2
  • 24
    • 0000642138 scopus 로고    scopus 로고
    • Ionic charging free energies: Spherical versus periodic boundary condition
    • Darden, T., D. Pearlman, and L. Pedersen. 1998. Ionic charging free energies: spherical versus periodic boundary condition. J. Phys. Chem. 109:10921-10935.
    • (1998) J. Phys. Chem. , vol.109 , pp. 10921-10935
    • Darden, T.1    Pearlman, D.2    Pedersen, L.3
  • 25
    • 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 I. G. Wool. 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
  • 27
    • 0006627150 scopus 로고    scopus 로고
    • A molecular simulation picture of DNA hydration around A- and B-DNA
    • Feig, M., and B. M. Pettitt. 1998. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers. 48:199-209.
    • (1998) Biopolymers , vol.48 , pp. 199-209
    • Feig, M.1    Pettitt, B.M.2
  • 28
    • 0032851951 scopus 로고    scopus 로고
    • Sodium and chlorine ions as part of the DNA solvation shell
    • Feig, M., and B. M. Pettitt. 1999. Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J. 77:1769-1781.
    • (1999) Biophys. J. , vol.77 , pp. 1769-1781
    • Feig, M.1    Pettitt, B.M.2
  • 30
    • 84988087911 scopus 로고    scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M. K., K. A. Sharp, and B. H. Honig. 1998. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:327-335.
    • (1998) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 31
    • 0034538789 scopus 로고    scopus 로고
    • Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation
    • Guo, J. X., I. Daizadeh, and W. Gmeiner. 2000. Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation. J. Biomol. Struct. Dyn. 18:335-344.
    • (2000) J. Biomol. Struct. Dyn. , vol.18 , pp. 335-344
    • Guo, J.X.1    Daizadeh, I.2    Gmeiner, W.3
  • 32
    • 0036290781 scopus 로고    scopus 로고
    • Crystal structure of the potassium form of an Oxytricha nova G-quadruplex
    • Haider, S., G. N. Parkinson, and S. Neidle. 2002. Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J. Mol. Biol. 320:189-200.
    • (2002) J. Mol. Biol. , vol.320 , pp. 189-200
    • Haider, S.1    Parkinson, G.N.2    Neidle, S.3
  • 34
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • Harvey, S. C., R. K. Z. Tan, and T. E. Cheatham, III. 1998. The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem. 19:726-740.
    • (1998) J. Comput. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.Z.2    Cheatham T.E. III3
  • 35
    • 0030849184 scopus 로고    scopus 로고
    • Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme
    • Hermann, T., P. Auffinger, W. G. Scott, and E. Westhof. 1997. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme. Nucleic Acids Res. 25:3421-3427.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3421-3427
    • Hermann, T.1    Auffinger, P.2    Scott, W.G.3    Westhof, E.4
  • 36
    • 0032532765 scopus 로고    scopus 로고
    • Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations
    • Hermann, T., and E. Westhof. 1998. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure. 6:1303-1314.
    • (1998) Structure , vol.6 , pp. 1303-1314
    • Hermann, T.1    Westhof, E.2
  • 37
    • 0031915278 scopus 로고    scopus 로고
    • Molecular dynamics investigations of hammerhead ribozyme RNA
    • Hermann, T., P. Auffinger, and E. Westhof. 1998. Molecular dynamics investigations of hammerhead ribozyme RNA. Eur. Biophys. J. 27:153-165.
    • (1998) Eur. Biophys. J. , vol.27 , pp. 153-165
    • Hermann, T.1    Auffinger, P.2    Westhof, E.3
  • 38
    • 0033544719 scopus 로고    scopus 로고
    • Stitching together RNA tertiary architectures
    • Hermann, T., and D. J. Patel. 1999. Stitching together RNA tertiary architectures. J. Mol. Biol. 294:829-849.
    • (1999) J. Mol. Biol. , vol.294 , pp. 829-849
    • Hermann, T.1    Patel, D.J.2
  • 39
    • 0343213055 scopus 로고    scopus 로고
    • Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results
    • Hobza, P., M. Kabelac, J. Sponer, P. Mejzlik, and J. Vondrasek. 1997. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: comparison with nonempirical beyond Hartree-Fock results. J. Comput. Chem. 18:1136-1150.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1136-1150
    • Hobza, P.1    Kabelac, M.2    Sponer, J.3    Mejzlik, P.4    Vondrasek, J.5
  • 40
    • 0026000848 scopus 로고
    • Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs
    • Holbrook, S. R., C. J. Cheong, I. Tinoco, and S. H. Kim. 1991. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature. 353:579-581.
    • (1991) Nature , vol.353 , pp. 579-581
    • Holbrook, S.R.1    Cheong, C.J.2    Tinoco, I.3    Kim, S.H.4
  • 43
    • 0033729881 scopus 로고    scopus 로고
    • Molecular dynamics of the anticodon domain of yeast tRNAPhe: Codon-anticodon interaction
    • Lahiri, A., and L. Nilsson. 2000. Molecular dynamics of the anticodon domain of yeast tRNAPhe: codon-anticodon interaction. Biophys. J. 79:2276-2289.
    • (2000) Biophys. J. , vol.79 , pp. 2276-2289
    • Lahiri, A.1    Nilsson, L.2
  • 44
    • 0031664960 scopus 로고    scopus 로고
    • The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure
    • Leontis, N. B., and E. Westhof. 1998a. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure. RNA. 4:1134-1153.
    • (1998) RNA , vol.4 , pp. 1134-1153
    • Leontis, N.B.1    Westhof, E.2
  • 45
    • 0032300804 scopus 로고    scopus 로고
    • Conserved geometrical base-pairing patterns in RNA
    • Leontis, N. B., and E. Westhof. 1998b. Conserved geometrical base-pairing patterns in RNA. Q. Rev. Biophys. 31:399-455.
    • (1998) Q. Rev. Biophys. , vol.31 , pp. 399-455
    • Leontis, N.B.1    Westhof, E.2
  • 46
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • Leontis, N. B., and E. Westhof. 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
  • 47
    • 0034007990 scopus 로고    scopus 로고
    • Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-angstrom resolution
    • Lu, M., and T. A. Steitz. 2000. Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-angstrom resolution. Proc. Natl. Acad. Sci. USA. 97:2023-2028.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 2023-2028
    • Lu, M.1    Steitz, T.A.2
  • 48
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu, X. J., Z. Shakked, and W. K. Olson. 2000. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300:819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.J.1    Shakked, Z.2    Olson, W.K.3
  • 49
    • 0032568852 scopus 로고    scopus 로고
    • On the potential role of the amino nitrogen atom as a hydrogen acceptor in macromolecules
    • Luisi, B., M. Orozco, J. Sponer, F. J. Luque, and Z. Shakked. 1998. On the potential role of the amino nitrogen atom as a hydrogen acceptor in macromolecules. J. Mol. Biol. 279:1123-1136.
    • (1998) J. Mol. Biol. , vol.279 , pp. 1123-1136
    • Luisi, B.1    Orozco, M.2    Sponer, J.3    Luque, F.J.4    Shakked, Z.5
  • 50
    • 0034671291 scopus 로고    scopus 로고
    • DNA structure: What's in charge?
    • McConnell, K. J., and D. L. Beveridge. 2000. DNA structure: what's in charge? J. Mol. Biol. 304:803-820.
    • (2000) J. Mol. Biol. , vol.304 , pp. 803-820
    • McConnell, K.J.1    Beveridge, D.L.2
  • 51
    • 0033581172 scopus 로고    scopus 로고
    • Wild-type RNA microhelix (Ala) and 3:70 variants: Molecular dynamics analysis of local helical structure and tightly bound water
    • Nagan, M. C., S. S. Kerimo, K. Musier-Forsyth, and C. J. Cramer. 1999. Wild-type RNA microhelix (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
  • 52
    • 0034235396 scopus 로고    scopus 로고
    • Importance of discriminator base stacking interactions: Molecular dynamics analysis of A73 microhelix (Ala) variants
    • Nagan, M. C., P. Beuning, K. Musier-Forsyth, and C. J. Cramer. 2000. Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix (Ala) variants. Nucleic Acids Res. 28:2527-2534.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2527-2534
    • Nagan, M.C.1    Beuning, P.2    Musier-Forsyth, K.3    Cramer, C.J.4
  • 54
    • 0032515193 scopus 로고    scopus 로고
    • Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C center. A(+) mismatches
    • Pan, B. C., S. N. Mitra, and M. Sundaralingam. 1998. Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C center. A(+) mismatches. J. Mol. Biol. 283:977-984.
    • (1998) J. Mol. Biol. , vol.283 , pp. 977-984
    • Pan, B.C.1    Mitra, S.N.2    Sundaralingam, M.3
  • 55
    • 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., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, and S. DeBolt. 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. III5    DeBolt, S.6
  • 56
    • 0035312355 scopus 로고    scopus 로고
    • Atomic structures at last: The ribosome in 2000
    • Ramakrishnan, V., and P. B. Moore. 2000. Atomic structures at last: the ribosome in 2000. Curr. Opin. Struct. Biol. 11:144-154.
    • (2000) Curr. Opin. Struct. Biol. , vol.11 , pp. 144-154
    • Ramakrishnan, V.1    Moore, P.B.2
  • 57
    • 0034719109 scopus 로고    scopus 로고
    • Adenine protonation in domain B of the hairpin ribozyme
    • Ravindranathan, S., S. E. Butcher, and J. Feigon. 2000. Adenine protonation in domain B of the hairpin ribozyme. Biochemistry. 39:16026-16032.
    • (2000) Biochemistry , vol.39 , pp. 16026-16032
    • Ravindranathan, S.1    Butcher, S.E.2    Feigon, J.3
  • 59
    • 0028086928 scopus 로고
    • Ion-induced stabilization of the G-DNA quadruplex: Free-energy perturbation studies
    • Ross, W. S., and C. C. Hardin. 1994. Ion-induced stabilization of the G-DNA quadruplex: free-energy perturbation studies. J. Am. Chem. Soc. 116:6070-6080.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6070-6080
    • Ross, W.S.1    Hardin, C.C.2
  • 60
    • 0033855843 scopus 로고    scopus 로고
    • Conformational dynamics of a 5S rRNA hairpin domain containing Loop D and a single nucleotide bulge
    • Sarzynska, J., T. Kulinski, and L. Nilsson. 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
  • 62
    • 0034545696 scopus 로고    scopus 로고
    • A molecular dynamics simulation study of coaxial stacking in RNA
    • Schneider, C., and J. Suhnel. 2000. A molecular dynamics simulation study of coaxial stacking in RNA. J. Biomol. Struct. Dyn. 18:345-352.
    • (2000) J. Biomol. Struct. Dyn. , vol.18 , pp. 345-352
    • Schneider, C.1    Suhnel, J.2
  • 63
    • 0035951296 scopus 로고    scopus 로고
    • Molecular dynamics simulation reveals conformational switching of water-mediated uracilcytosine base-pairs in an RNA duplex
    • Schneider, C., M. Brandl, and J. Suhnel. 2001. Molecular dynamics simulation reveals conformational switching of water-mediated uracilcytosine 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
  • 64
    • 0032528295 scopus 로고    scopus 로고
    • A zipper-like duplex in DNA: The crystal structure of d(GCGAAAGCT) at 2.1 angstrom resolution
    • Shepard, W., W. B. T. Cruse, R. Fourme, E. de la Fortelle, and T. Prange. 1998. A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 angstrom resolution. Structure. 6:849-861.
    • (1998) Structure , vol.6 , pp. 849-861
    • Shepard, W.1    Cruse, W.B.T.2    Fourme, R.3    De la Fortelle, E.4    Prange, T.5
  • 66
    • 0040164390 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
    • Spackova, N., I. Berger, and J. Sponer. 1999. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. J. Am. Chem. Soc. 121:5519-5534.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 5519-5534
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 67
    • 0034625886 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G.A mismatch pairs
    • Spackova, N., I. Berger, and J. Sponer. 2000. Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G.A mismatch pairs. J. Am. Chem. Soc. 122:7564-7572.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 7564-7572
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 68
    • 0034836422 scopus 로고    scopus 로고
    • Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
    • Spackova, N., I. Berger, and J. Sponer. 2001. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J. Am. Chem. Soc. 123:3295-3307.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3295-3307
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 69
    • 0037442584 scopus 로고    scopus 로고
    • Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. I. Minor groove binding between 4′,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution
    • Spackova, N., T. E. Cheatham III., F. Ryjacek, F. Lankas, L. van Meervelt, P. Hobza, and J. Sponer. 2003. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. I. Minor groove binding between 4′,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. J. Am. Chem. Soc. 125:1759-1769.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1759-1769
    • Spackova, N.1    Cheatham T.E. III2    Ryjacek, F.3    Lankas, F.4    Van Meervelt, L.5    Hobza, P.6    Sponer, J.7
  • 70
    • 0028005530 scopus 로고
    • Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study
    • Sponer, J., and P. Hobza. 1994a. Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study. J. Am. Chem. Soc. 116:709-714.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 709-714
    • Sponer, J.1    Hobza, P.2
  • 71
    • 33751158761 scopus 로고
    • Nonplanar geometries of DNA bases. Second order Moller-Plesset study
    • Sponer, J., and P. Hobza. 1994b. Nonplanar geometries of DNA bases. Second order Moller-Plesset study. J. Phys. Chem. 98:3161-3164.
    • (1994) J. Phys. Chem. , vol.98 , pp. 3161-3164
    • Sponer, J.1    Hobza, P.2
  • 73
    • 0033913014 scopus 로고    scopus 로고
    • Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view
    • Sponer, J., J. E. Sponer, and J. Leszczynski. 2000a. Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view. J. Biomol. Struct. Dyn. 17:1087-1096.
    • (2000) J. Biomol. Struct. Dyn. , vol.17 , pp. 1087-1096
    • Sponer, J.1    Sponer, J.E.2    Leszczynski, J.3
  • 74
    • 0034249870 scopus 로고    scopus 로고
    • The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing
    • Sponer, J., M. Sabat, L. Gorb, J. Leszczynski, B. Lippert, and P. Hobza. 2000b. The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing. J. Phys. Chem. B. 104:7535-7544.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7535-7544
    • Sponer, J.1    Sabat, M.2    Gorb, L.3    Leszczynski, J.4    Lippert, B.5    Hobza, P.6
  • 75
    • 0000875282 scopus 로고    scopus 로고
    • Interaction energies of hydrogen-bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals
    • Sponer, J., and P. Hobza. 2000. Interaction energies of hydrogen-bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals. J. Phys. Chem. 104: 4592-4597.
    • (2000) J. Phys. Chem. , vol.104 , pp. 4592-4597
    • Sponer, J.1    Hobza, P.2
  • 76
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Sponer, J., J. Leszczynski, and P. Hobza. 2001. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers. 61:3-31.
    • (2001) Biopolymers , vol.61 , pp. 3-31
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 77
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate: DNA helices
    • Srinivasan, J., T. E. Cheatham III, P. Cieplak, P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate: DNA helices. J. Am. Chem. Soc. 120:9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham T.E. III2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 78
    • 0037009672 scopus 로고    scopus 로고
    • Structural basis of biotin-RNA aptamer binding: A theoretical study
    • Starikov, E. B., and L. Nilsson. 2002. Structural basis of biotin-RNA aptamer binding: a theoretical study. Chem. Phys. Lett. 363:39-44.
    • (2002) Chem. Phys. Lett. , vol.363 , pp. 39-44
    • Starikov, E.B.1    Nilsson, L.2
  • 79
    • 0028953727 scopus 로고
    • The sarcin/ricin loop, a modular RNA
    • Szewczak, A. A., and P. B. Moore. 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
  • 80
    • 0037178070 scopus 로고    scopus 로고
    • Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
    • Varnai, P., and R. Lavery. 2002. Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations. J. Am. Chem. Soc. 124:7272-7273.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 7272-7273
    • Varnai, P.1    Lavery, R.2
  • 81
    • 0024974668 scopus 로고
    • Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs
    • Westhof, E., P. Romby, P. J. Romaniuk, J. P. Ebel, C. Ehresmann, and B. Ehresmann. 1989. Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs. J. Mol. Biol. 207:417-431.
    • (1989) J. Mol. Biol. , vol.207 , pp. 417-431
    • Westhof, E.1    Romby, P.2    Romaniuk, P.J.3    Ebel, J.P.4    Ehresmann, C.5    Ehresmann, B.6
  • 82
    • 0033064123 scopus 로고    scopus 로고
    • Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model
    • Williams, D. J., and K. B. Hall. 1999. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. Biophys. J. 76:3192-3205.
    • (1999) Biophys. J. , vol.76 , pp. 3192-3205
    • Williams, D.J.1    Hall, K.B.2
  • 83
    • 0027439912 scopus 로고
    • The conformation of loop E of eukaryotic 5S ribosomal RNA
    • Wimberly, B., G. Varani, and I. Tinoco. 1993. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry. 32:1078-1087.
    • (1993) Biochemistry , vol.32 , pp. 1078-1087
    • Wimberly, B.1    Varani, G.2    Tinoco, I.3
  • 85
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek, S. T., T. W. Clark, L. R. Scott, and J. A. McCammon. 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
  • 86
    • 0034027592 scopus 로고    scopus 로고
    • Simulation of the structure and dynamics of nonhelical RNA motifs
    • Zacharias, M. 2000. Simulation of the structure and dynamics of nonhelical RNA motifs. Curr. Opin. Struct. Biol. 10:311-317.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 311-317
    • Zacharias, M.1
  • 87
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for beta hairpin folding in explicit water
    • Zhou, R., B. J. Berne, and R. Germain. 2001. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA. 18:14931-14936.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.18 , pp. 14931-14936
    • Zhou, R.1    Berne, B.J.2    Germain, R.3


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