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Volumn 78, Issue 5, 2000, Pages 2528-2542

Conformational deformability of RNA: A harmonic mode analysis

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; RNA;

EID: 0034063442     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76798-1     Document Type: Article
Times cited : (19)

References (53)
  • 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. 2:227-236.
    • (1998) Curr. Opin. Struct. Biol. , vol.2 , pp. 227-236
    • Auffinger, P.1    Westhof, E.2
  • 2
    • 0032483483 scopus 로고    scopus 로고
    • Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms
    • Bahar, I., and R. L. Jernigan. 1998. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J. Mol. Biol. 281:871-884.
    • (1998) J. Mol. Biol. , vol.281 , pp. 871-884
    • Bahar, I.1    Jernigan, R.L.2
  • 4
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1522-1542.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 5
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks, B. R., and M. Karplus. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575.
    • (1983) Proc. Natl. Acad. Sci. USA. , vol.80 , pp. 6571-6575
    • Brooks, B.R.1    Karplus, M.2
  • 6
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • Case, D. A. 1994. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:285-290.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 285-290
    • Case, D.A.1
  • 8
    • 0029941154 scopus 로고    scopus 로고
    • Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
    • Cheatham, T. E., and P. A. Kollman. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259:434-444.
    • (1996) J. Mol. Biol. , vol.259 , pp. 434-444
    • Cheatham, T.E.1    Kollman, P.A.2
  • 9
    • 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., and P. A. Kollman. 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, T.E.1    Kollman, P.A.2
  • 10
    • 0001772691 scopus 로고    scopus 로고
    • Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics
    • N. B. Leontis, editor. American Chemical Society, Washington, DC.
    • Cheatham, T. E., J. L. Miller, T. I. Spector, P. Cieplak, and P. A. Kollman. 1997. Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics. In Molecular Modeling of Nucleic acids. N. B. Leontis, editor. American Chemical Society, Washington, DC. 285-303.
    • (1997) Molecular Modeling of Nucleic Acids , pp. 285-303
    • Cheatham, T.E.1    Miller, J.L.2    Spector, T.I.3    Cieplak, P.4    Kollman, P.A.5
  • 12
    • 0032104683 scopus 로고    scopus 로고
    • Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride
    • Delrow, J. J., P. J. Health, B. S. Fujimoto, and J. M. Schurr. 1998. Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride. Biopolymers. 45:503-515.
    • (1998) Biopolymers , vol.45 , pp. 503-515
    • Delrow, J.J.1    Health, P.J.2    Fujimoto, B.S.3    Schurr, J.M.4
  • 14
    • 0029956116 scopus 로고    scopus 로고
    • RNA hydration: A detailed look
    • Egli, M., S. Portmann, and N. Usman. 1996. RNA hydration: a detailed look. Biochemistry. 35:8489-8496.
    • (1996) Biochemistry , vol.35 , pp. 8489-8496
    • Egli, M.1    Portmann, S.2    Usman, N.3
  • 15
    • 0031808069 scopus 로고    scopus 로고
    • Structural equilibrium of DNA represented with different force fields
    • Feig, M., and B. M. Pettitt. 1998. Structural equilibrium of DNA represented with different force fields. Biophys. J. 75:134-149.
    • (1998) Biophys. J. , vol.75 , pp. 134-149
    • Feig, M.1    Pettitt, B.M.2
  • 16
    • 0000882951 scopus 로고    scopus 로고
    • Internal coordinate modeling of DNA: Force field comparisons
    • Flatters, D., K. Zakrzewska, and R. Lavery. 1997. Internal coordinate modeling of DNA: force field comparisons. J. Comput. Chem. 18:1043-1055.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1043-1055
    • Flatters, D.1    Zakrzewska, K.2    Lavery, R.3
  • 17
    • 0025366778 scopus 로고
    • Dependence of the torsional rigidity of DNA on base composition
    • Fujimoto, B. S., and J. M. Schurr. 1990. Dependence of the torsional rigidity of DNA on base composition. Nature. 344:175-178.
    • (1990) Nature , vol.344 , pp. 175-178
    • Fujimoto, B.S.1    Schurr, J.M.2
  • 18
    • 0343757149 scopus 로고
    • Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution
    • Garcia, A. E., and D. M. Soumpasis. 1989. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc. Natl. Acad. Sci. USA. 86:3160-3164.
    • (1989) Proc. Natl. Acad. Sci. USA. , vol.86 , pp. 3160-3164
    • Garcia, A.E.1    Soumpasis, D.M.2
  • 19
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin, A. A., V. B. Zhurkin, and W. K. Olson. 1995. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:34-38.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-38
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 20
    • 0000213488 scopus 로고    scopus 로고
    • Calculation and analysis of low frequency normal modes for DNA
    • Ha Duong, T., and K. Zakrzewska. 1997a. Calculation and analysis of low frequency normal modes for DNA. J. Comput. Chem. 18:796-811.
    • (1997) J. Comput. Chem. , vol.18 , pp. 796-811
    • Ha Duong, T.1    Zakrzewska, K.2
  • 21
    • 0009781658 scopus 로고    scopus 로고
    • Influence of drug binding on DNA flexibility: A normal mode analysis
    • Ha Duong, T., and K. Zakrzewska. 1997b. Influence of drug binding on DNA flexibility: a normal mode analysis. J. Biomol. Struct. Dyn. 14:691-701.
    • (1997) J. Biomol. Struct. Dyn. , vol.14 , pp. 691-701
    • Ha Duong, T.1    Zakrzewska, K.2
  • 22
    • 0032479181 scopus 로고    scopus 로고
    • Sequence specificity of bacteriophage 434 repressor-operator complexation
    • Ha Duong, T., and K. Zakrzewska. 1999. Sequence specificity of bacteriophage 434 repressor-operator complexation. J. Mol. Biol. 280:31-39.
    • (1999) J. Mol. Biol. , vol.280 , pp. 31-39
    • Ha Duong, T.1    Zakrzewska, K.2
  • 23
    • 0019588074 scopus 로고
    • Investigation of the flexibility of DNA using transient electric birefringence
    • Hagerman, P. J. 1981. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 20:1503-1535.
    • (1981) Biopolymers , vol.20 , pp. 1503-1535
    • Hagerman, P.J.1
  • 24
    • 0022399917 scopus 로고
    • Transition from B to Z DNA: Contribution of internal fluctuations to configurational entropy difference
    • Irikura, K. K., B. Tidor, B. R. Brooks, and M. Karplus. 1985. Transition from B to Z DNA: contribution of internal fluctuations to configurational entropy difference. Science. 229:571-572.
    • (1985) Science , vol.229 , pp. 571-572
    • Irikura, K.K.1    Tidor, B.2    Brooks, B.R.3    Karplus, M.4
  • 26
    • 0023951245 scopus 로고
    • The three-dimensional structures of a DNA duplex containing looped-out bases
    • Joshua-Tor, L. F., D. Rabinovich. H. Hope, F. Frolow, E. Appela, and J. L. Sussman. 1988. The three-dimensional structures of a DNA duplex containing looped-out bases. Nature. 334:82-84.
    • (1988) Nature , vol.334 , pp. 82-84
    • Joshua-Tor, L.F.1    Rabinovich, D.2    Hope, H.3    Frolow, F.4    Appela, E.5    Sussman, J.L.6
  • 27
    • 12944249776 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A. 34:827-828.
    • (1976) Acta Crystallogr. Sect. A. , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 29
    • 0025292904 scopus 로고
    • Langevin modes of macromolecules: Applications to crambin and DNA hexamers
    • Kottalam, I., and D. A. Case. 1990. Langevin modes of macromolecules: applications to crambin and DNA hexamers. Biopolymers. 29:1409-1421.
    • (1990) Biopolymers , vol.29 , pp. 1409-1421
    • Kottalam, I.1    Case, D.A.2
  • 30
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery, R., and H. Sklenar. 1988a. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:63-91.
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 31
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R., and H. Sklenar. 1988b. defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6:655-667.
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 32
  • 34
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt, M. A., C. Sander, and P. S. Stern. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.A.1    Sander, C.2    Stern, P.S.3
  • 36
    • 0000319912 scopus 로고    scopus 로고
    • Dynamic properties of double-stranded DNA by normal mode analysis
    • Matsumoto, A., and N. Go. 1999. Dynamic properties of double-stranded DNA by normal mode analysis. J. Chem. Phys. 111:11070-11075.
    • (1999) J. Chem. Phys. , vol.111 , pp. 11070-11075
    • Matsumoto, A.1    Go, N.2
  • 37
    • 0032998812 scopus 로고    scopus 로고
    • Dynamical structure of transfer RNA studied by normal mode analysis
    • Matsumoto, A., M. Tomimoto, and N. Go. 1999. Dynamical structure of transfer RNA studied by normal mode analysis. Eur. Biophys. J. 28:369-379.
    • (1999) Eur. Biophys. J. , vol.28 , pp. 369-379
    • Matsumoto, A.1    Tomimoto, M.2    Go, N.3
  • 38
    • 0344142531 scopus 로고    scopus 로고
    • Ala from Escherichia coli shows unique G:U wobble base pair at 1.16 Å resolution
    • Ala from Escherichia coli shows unique G:U wobble base pair at 1.16 Å resolution. RNA. 5:670-677.
    • (1999) RNA. , vol.5 , pp. 670-677
    • Mueller, U.1    Schübel, H.2    Sprinzl, M.3    Heinemann, U.4
  • 39
    • 0028359395 scopus 로고
    • Dynamics of transfer RNAs analyzed by normal mode calculations
    • Nakamura, S., and J. Doi. 1994. Dynamics of transfer RNAs analyzed by normal mode calculations. Nucleic Acids Res. 22:514-552.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 514-552
    • Nakamura, S.1    Doi, J.2
  • 41
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson, W. K., A. A. Gorin, X. J. Lu, L. M. Hock, and V. B. Zhurkin. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA. 95:11163-11168.
    • (1998) Proc. Natl. Acad. Sci. USA. , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 42
    • 0030090986 scopus 로고    scopus 로고
    • Crystal structures of an A-form duplex with single adenosine bulges and conformational basis for site-specific RNA self-cleavage
    • Portmann, S., S. Grimm, C. Workman, N. Usman, and M. Egli. 1996. Crystal structures of an A-form duplex with single adenosine bulges and conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3:173-184.
    • (1996) Chem. Biol. , vol.3 , pp. 173-184
    • Portmann, S.1    Grimm, S.2    Workman, C.3    Usman, N.4    Egli, M.5
  • 43
    • 0027146665 scopus 로고
    • 2 in solution from NMR and restraint molecular dynamics
    • 2 in solution from NMR and restraint molecular dynamics. Biochemistry. 32:12612-12623.
    • (1993) Biochemistry , vol.32 , pp. 12612-12623
    • Santalucia, J.1    Turner, D.H.2
  • 44
    • 0033561656 scopus 로고    scopus 로고
    • Dynamic twisting correlations in a model DNA with uniform torsion elastic constant
    • Schurr, J. M., and B. S. Fujimoto. 1999. Dynamic twisting correlations in a model DNA with uniform torsion elastic constant. Biopolymers. 49:355-359.
    • (1999) Biopolymers , vol.49 , pp. 355-359
    • Schurr, J.M.1    Fujimoto, B.S.2
  • 45
    • 0021022977 scopus 로고
    • Energetics of DNA twisting. I. Relation between twist and cyclization probability
    • Shore, D., and R. L. Baldwin. 1983. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170:957-981.
    • (1983) J. Mol. Biol. , vol.170 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 46
    • 0022691672 scopus 로고
    • The flexibility of nucleic acids: SIR, a novel approach to the variation of polymer geometry in constraint systems
    • Sklenar, H., R. Lavery, and B. Pullman. 1986. The flexibility of nucleic acids: SIR, a novel approach to the variation of polymer geometry in constraint systems. J. Biomol. Struct. Dyn. 3:967-987.
    • (1986) J. Biomol. Struct. Dyn. , vol.3 , pp. 967-987
    • Sklenar, H.1    Lavery, R.2    Pullman, B.3
  • 47
    • 0025355712 scopus 로고
    • Application of the method of phage T4 DNA figase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat
    • Taylor, W. H., and P. J. Hagerman. 1990. Application of the method of phage T4 DNA figase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol Biol. 212:363-376.
    • (1990) J. Mol Biol. , vol.212 , pp. 363-376
    • Taylor, W.H.1    Hagerman, P.J.2
  • 49
    • 0029744135 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and iterative relaxation matrix approach
    • 2 by two-dimensional NMR and iterative relaxation matrix approach. Biochemistry. 35:9677-9689.
    • (1996) Biochemistry , vol.35 , pp. 9677-9689
    • Wu, M.1    Turner, D.H.2
  • 50
    • 0028969693 scopus 로고
    • Bulge-induced bends in RNA: Quantification by transient electric birefringence
    • Zacharias, M., and P. J. Hagerman. 1995. Bulge-induced bends in RNA: quantification by transient electric birefringence. J. Mol. Biol. 247:486-500.
    • (1995) J. Mol. Biol. , vol.247 , pp. 486-500
    • Zacharias, M.1    Hagerman, P.J.2
  • 51
    • 0030735002 scopus 로고    scopus 로고
    • Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions
    • Zacharias, M., and H. Sklenar. 1997. Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions. Biophys. J. 73:2990-3003.
    • (1997) Biophys. J. , vol.73 , pp. 2990-3003
    • Zacharias, M.1    Sklenar, H.2
  • 52
    • 0001147249 scopus 로고    scopus 로고
    • Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to a minor-groove DNA binding ligand
    • Zacharias, M., and H. Sklenar. 1999a. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: application to a minor-groove DNA binding ligand. J. Comput. Chem. 20:287-300.
    • (1999) J. Comput. Chem. , vol.20 , pp. 287-300
    • Zacharias, M.1    Sklenar, H.2
  • 53
    • 0033523082 scopus 로고    scopus 로고
    • Conformational analysis of single-base bulge structures in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model
    • Zacharias, M., and H. Sklenar. 1999b. Conformational analysis of single-base bulge structures 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    Sklenar, H.2


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