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Volumn 156, Issue 1, 2011, Pages 79-87

Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes

Author keywords

Binding; Counterion condensation theory; Debye H ckel equation; Electrostatics; Generalized Born model; Poisson Boltzmann equation

Indexed keywords

ARTICLE; COMPARATIVE STUDY; CONCENTRATION (PARAMETERS); DEBYE HUCKEL EQUATION; DNA BINDING MOTIF; GENE MUTATION; GENERALIZED BORN MODEL; MATHEMATICAL PARAMETERS; OSMOTIC PRESSURE; POISSON BOLTZMANN EQUATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN RNA BINDING; SALT CONCENTRATION; STATIC ELECTRICITY;

EID: 79955888291     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.02.010     Document Type: Article
Times cited : (12)

References (89)
  • 1
    • 0026730188 scopus 로고
    • Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
    • D.P. Mascotti, T.M. Lohman, Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan, Biochemistry 31 (1992) 8932-8946.
    • (1992) Biochemistry , vol.31 , pp. 8932-8946
    • Mascotti, D.P.1    Lohman, T.M.2
  • 2
    • 0027379588 scopus 로고
    • Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition
    • DOI 10.1021/bi00091a006
    • D.P. Mascotti, T.M. Lohman, Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition, Biochemistry 32 (1993) 10568-10579. (Pubitemid 23327788)
    • (1993) Biochemistry , vol.32 , Issue.40 , pp. 10568-10579
    • Mascotti, D.P.1    Lohman, T.M.2
  • 3
    • 0030920231 scopus 로고    scopus 로고
    • Thermodynamics of oligoarginines binding to RNA and DNA
    • DOI 10.1021/bi970272n
    • D.P. Mascotti, T.M. Lohman, Thermodynamics of Oligoarginines binding to RNA and DNA, Biochemistry 36 (1997) 7272-7279. (Pubitemid 27258144)
    • (1997) Biochemistry , vol.36 , Issue.23 , pp. 7272-7279
    • Mascotti, D.P.1    Lohman, T.M.2
  • 4
    • 39149124468 scopus 로고    scopus 로고
    • Interplay of ion binding and attraction in DNA condensed by multivalent cations
    • DOI 10.1093/nar/gkm1038
    • B.A. Todd, D.C. Rau, Interplay of ion binding and attraction in DNA condensed by multivalent cations, Nucleic Acids Res. 36 (2008) 501-510. (Pubitemid 351250441)
    • (2008) Nucleic Acids Research , vol.36 , Issue.2 , pp. 501-510
    • Todd, B.A.1    Rau, D.C.2
  • 5
    • 60649106752 scopus 로고    scopus 로고
    • RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne
    • M.M. Islam, P. Pandya, S. Kumar, G.S. Kumar, RNA targeting through binding of small molecules: studies on t-RNA binding by the cytotoxic protoberberine alkaloid coralyne, Mol. Biosyst. 5 (2009) 244-254.
    • (2009) Mol. Biosyst. , vol.5 , pp. 244-254
    • Islam, M.M.1    Pandya, P.2    Kumar, S.3    Kumar, G.S.4
  • 6
    • 61949239352 scopus 로고    scopus 로고
    • Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides, J
    • M.M. Islam, S.R. Chowdhury, G.S. Kumar, Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides, J. Phys. Chem. B 113 (2009) 1210-1224.
    • (2009) Phys. Chem. B , vol.113 , pp. 1210-1224
    • Islam, M.M.1    Chowdhury, S.R.2    Kumar, G.S.3
  • 7
    • 0037129948 scopus 로고    scopus 로고
    • Thermodynamics of aminoglycoside-rRNA recognition: The binding of neomycin-class aminoglycosides to the A site of 16S rRNA
    • DOI 10.1021/bi020130f
    • M. Kaul, D.S. Pilch, Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16S rRNA, Biochemistry 41 (2002) 7695-7706. (Pubitemid 34627797)
    • (2002) Biochemistry , vol.41 , Issue.24 , pp. 7695-7706
    • Kaul, M.1    Pilch, D.S.2
  • 8
    • 77449117999 scopus 로고    scopus 로고
    • Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB
    • A. Paleskava, A.L. Konevega, M.V. Rodnina, Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB, J. Biol. Chem. 285 (2010) 3014-3020.
    • (2010) J. Biol. Chem. , vol.285 , pp. 3014-3020
    • Paleskava, A.1    Konevega, A.L.2    Rodnina, M.V.3
  • 9
    • 77953106274 scopus 로고    scopus 로고
    • Coevolution of Drosophila snf protein and its snRNA targets
    • S.G. Williams, K.B. Hall, Coevolution of Drosophila snf protein and its snRNA targets, Biochemistry 49 (2010) 4571-4582.
    • (2010) Biochemistry , vol.49 , pp. 4571-4582
    • Williams, S.G.1    Hall, K.B.2
  • 10
    • 75349085366 scopus 로고    scopus 로고
    • A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation
    • N. Korolev, N.V. Berezhnoy, K.D. Eom, J.P. Tam, L. Nordenskiold, A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation, Nucleic Acids Res. 37 (2009) 7137-7150.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 7137-7150
    • Korolev, N.1    Berezhnoy, N.V.2    Eom, K.D.3    Tam, J.P.4    Nordenskiold, L.5
  • 11
    • 77749253818 scopus 로고    scopus 로고
    • An RNA aptamer with high affinity and broad specificity for zinc finger proteins
    • T.C. Weiss, G.G. Zhai, S.S. Bhatia, P.J. Romaniuk, An RNA aptamer with high affinity and broad specificity for zinc finger proteins, Biochemistry 49 (2010) 2732-2740.
    • (2010) Biochemistry , vol.49 , pp. 2732-2740
    • Weiss, T.C.1    Zhai, G.G.2    Bhatia, S.S.3    Romaniuk, P.J.4
  • 12
    • 77951674873 scopus 로고    scopus 로고
    • Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA
    • S.S. Athavale, W. Ouyang, M.P. McPike, B.S. Hudson, P.N. Borer, Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA, Biochemistry 49 (2010) 3525-3533.
    • (2010) Biochemistry , vol.49 , pp. 3525-3533
    • Athavale, S.S.1    Ouyang, W.2    McPike, M.P.3    Hudson, B.S.4    Borer, P.N.5
  • 13
    • 77951023778 scopus 로고    scopus 로고
    • Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices
    • H. Xi, S. Kumar, L. Dosen-Micovic, D.P. Arya, Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices, Biochimie (2010) 514-529.
    • (2010) Biochimie , pp. 514-529
    • Xi, H.1    Kumar, S.2    Dosen-Micovic, L.3    Arya, D.P.4
  • 14
    • 0029782652 scopus 로고    scopus 로고
    • Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR
    • DOI 10.1021/bi9607259
    • P.C. Bevilacqua, T.R. Cech, Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR, Biochemistry 35 (1996) 9983-9994. (Pubitemid 26269913)
    • (1996) Biochemistry , vol.35 , Issue.31 , pp. 9983-9994
    • Bevilacqua, P.C.1    Cech, T.R.2
  • 15
    • 77956064643 scopus 로고    scopus 로고
    • Thermodynamics of peptide - RNA recognition: The binding of a Tat peptide to TAR RNA
    • H. Suryawanshi, H. Sabharwal, S. Maiti, Thermodynamics of peptide - RNA recognition: the binding of a Tat peptide to TAR RNA, J. Phys. Chem. B 114 (2010) 11155-11163.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 11155-11163
    • Suryawanshi, H.1    Sabharwal, H.2    Maiti, S.3
  • 16
    • 70349422115 scopus 로고    scopus 로고
    • Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions
    • S.H. Mishra, A.M. Spring, M.W. Germann, Thermodynamic profiling of HIV RREIIB RNA-zinc finger interactions, J. Mol. Biol. 393 (2009) 369-382.
    • (2009) J. Mol. Biol. , vol.393 , pp. 369-382
    • Mishra, S.H.1    Spring, A.M.2    Germann, M.W.3
  • 17
    • 0031776135 scopus 로고    scopus 로고
    • Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
    • M.T. Record Jr., W. Zhang, C.F. Anderson, Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts, Adv. Protein Chem. 51 (1998) 281-353.
    • (1998) Adv. Protein Chem. , vol.51 , pp. 281-353
    • Record Jr., M.T.1    Zhang, W.2    Anderson, C.F.3
  • 18
    • 0028246710 scopus 로고
    • Salt effects on ligand-DNA binding: Minor groove binding antibiotics
    • V.K. Misra, K.A. Sharp, R.A. Friedman, B. Honig, Salt effects on ligand-DNA binding: minor groove binding antibiotics, J. Mol. Biol. 238 (1994) 245-263.
    • (1994) J. Mol. Biol. , vol.238 , pp. 245-263
    • Misra, V.K.1    Sharp, K.A.2    Friedman, R.A.3    Honig, B.4
  • 19
    • 0028239626 scopus 로고
    • Salt effects on protein- DNA interactions: The λ cI repressor and EcoRI endonuclease
    • V.K. Misra, J.L. Hecht, K.A. Sharp, R.A. Friedman, B. Honig, Salt effects on protein- DNA interactions: the λ cI repressor and EcoRI endonuclease, J. Mol. Biol. 238 (1994) 264-280.
    • (1994) J. Mol. Biol. , vol.238 , pp. 264-280
    • Misra, V.K.1    Hecht, J.L.2    Sharp, K.A.3    Friedman, R.A.4    Honig, B.5
  • 20
    • 0026619551 scopus 로고
    • Poisson-Boltzmann analysis of the λ repressor-operator interaction
    • M. Zacharias, B.A. Luty, M.E. Davis, J.A. McCammon, Poisson-Boltzmann analysis of the λ repressor-operator interaction, Biophys. J. 63 (1992) 1280-1285.
    • (1992) Biophys. J. , vol.63 , pp. 1280-1285
    • Zacharias, M.1    Luty, B.A.2    Davis, M.E.3    McCammon, J.A.4
  • 21
    • 0029047968 scopus 로고
    • On the magnitude of the electrostatic contribution to ligand-DNA interactions
    • V.K. Misra, B. Honig, On the magnitude of the electrostatic contribution to ligand-DNA interactions, Proc. Natl Acad. Sci. U.S.A. 92 (1995) 4691-4695.
    • (1995) Proc. Natl Acad. Sci. U.S.A. , vol.92 , pp. 4691-4695
    • Misra, V.K.1    Honig, B.2
  • 22
    • 67650542563 scopus 로고    scopus 로고
    • Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors
    • J.M. Blose, D.J. Proctor, N. Veeraraghavan, V.K. Misra, P.C. Bevilacqua, Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors, J. Am. Chem. Soc. 131 (2009) 8474-8484.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 8474-8484
    • Blose, J.M.1    Proctor, D.J.2    Veeraraghavan, N.3    Misra, V.K.4    Bevilacqua, P.C.5
  • 23
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • G.S. Manning, The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides, Q. Rev. Biophys. 11 (1978) 179-246. (Pubitemid 8373665)
    • (1978) Quarterly Reviews of Biophysics , vol.11 , Issue.2 , pp. 179-246
    • Manning, G.S.1
  • 24
    • 0030572245 scopus 로고    scopus 로고
    • Macroion attraction due to electrostatic correlation between screening counterions. 1. Mobile surface-adsorbed ions and diffuse ion cloud
    • I. Rouzina, V.A. Bloomfield, Macroion attraction due to electrostatic correlation between screening counterions. 1. Mobile surface-adsorbed ions and diffuse ion cloud, J. Phys. Chem. 100 (1996) 9977-9989.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9977-9989
    • Rouzina, I.1    Bloomfield, V.A.2
  • 25
    • 0007425498 scopus 로고    scopus 로고
    • Competitive electrostatic binding of charged ligands to polyelectrolytes: Planar and cylindrical geometries
    • I. Rouzina, V.A. Bloomfield, Competitive electrostatic binding of charged ligands to polyelectrolytes: planar and cylindrical geometries, J. Phys. Chem. 100 (1996) 4292-4304.
    • (1996) J. Phys. Chem. , vol.100 , pp. 4292-4304
    • Rouzina, I.1    Bloomfield, V.A.2
  • 26
    • 0023972836 scopus 로고
    • Binding of positively charged ligands to DNA. Effects of ionic strength, ligand charge and size
    • A.V. Sivolob, S.N. Khrapunov, Binding of positively charged ligands to DNA. Effects of ionic strength, ligand charge and size, Mol. Biol. 22 (1988) 414-422.
    • (1988) Mol. Biol. , vol.22 , pp. 414-422
    • Sivolob, A.V.1    Khrapunov, S.N.2
  • 27
    • 0029816432 scopus 로고    scopus 로고
    • Binding of ionic ligands to polyelectrolytes
    • D. Stigter, K.A. Dill, Binding of ionic ligands to polyelectrolytes, Biophys. J. 71 (1996) 2064-2074. (Pubitemid 26325985)
    • (1996) Biophysical Journal , vol.71 , Issue.4 , pp. 2064-2074
    • Stigter, D.1    Dill, K.A.2
  • 28
    • 44849122543 scopus 로고    scopus 로고
    • Recent progress in numerical methods for the Poisson-Boltzmann Equation in biophysical applications
    • B.Z. Lu, Y.C. Zhou, M.J. Holst, J.A. McCammon, Recent progress in numerical methods for the Poisson-Boltzmann Equation in biophysical applications, Commun Comput Phys. 3 (2008) 973-1009.
    • (2008) Commun Comput Phys. , vol.3 , pp. 973-1009
    • Lu, B.Z.1    Zhou, Y.C.2    Holst, M.J.3    McCammon, J.A.4
  • 29
    • 2342454337 scopus 로고    scopus 로고
    • Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
    • A.H. Boschitsch, M.O. Fenley, Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation, J. Comput. Chem. 25 (2004) 935-955.
    • (2004) J. Comput. Chem. , vol.25 , pp. 935-955
    • Boschitsch, A.H.1    Fenley, M.O.2
  • 30
    • 77955695135 scopus 로고    scopus 로고
    • Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach
    • M.O. Fenley, R.C. Harris, B. Jayaram, A.H. Boschitsch, Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach, Biophys. J. (2010) 879-886.
    • (2010) Biophys. J. , pp. 879-886
    • Fenley, M.O.1    Harris, R.C.2    Jayaram, B.3    Boschitsch, A.H.4
  • 32
    • 44349096354 scopus 로고    scopus 로고
    • Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations
    • DOI 10.1002/prot.21878
    • T. Murtola, I. Vattulainen, E. Falck, Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations, Proteins 71 (2008) 1995-2011. (Pubitemid 351732951)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.4 , pp. 1995-2011
    • Murtola, T.1    Vattulainen, I.2    Falck, E.3
  • 33
    • 44849123749 scopus 로고    scopus 로고
    • The role of anionic protein residues on the salt dependence of the binding of aminoacyl-tRNA: Synthetases to tRNA: A Poisson-Boltzmann analysis
    • J.H. Bredenberg, A.H. Boschitsch, M.O. Fenley, The role of anionic protein residues on the salt dependence of the binding of aminoacyl-tRNA: synthetases to tRNA: a Poisson-Boltzmann analysis, Commun. Comput. Phys. 3 (2008) 1051-1070.
    • (2008) Commun. Comput. Phys. , vol.3 , pp. 1051-1070
    • Bredenberg, J.H.1    Boschitsch, A.H.2    Fenley, M.O.3
  • 35
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • W.C. Still, A. Tempczyk, R.C. Hawley, T. Hendrickson, Semianalytical treatment of solvation for molecular mechanics and dynamics, J. Am. Chem. Soc. 112 (1990) 6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 36
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • D. Bashford, D.A. Case, Generalized born models of macromolecular solvation effects, Annu. Rev. Phys. Chem. 51 (2000) 129-152.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 37
    • 0033468737 scopus 로고    scopus 로고
    • Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
    • J. Srinivasan, M.W. Trevathan, P. Beroza, D.A. Case, Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects, Theor. Chem. Acc. 101 (1999) 426-434.
    • (1999) Theor. Chem. Acc. , vol.101 , pp. 426-434
    • Srinivasan, J.1    Trevathan, M.W.2    Beroza, P.3    Case, D.A.4
  • 39
    • 0034598941 scopus 로고    scopus 로고
    • Thermodynamics of DNA binding and condensation: Isothermal titration calorimetry and electrostatic mechanism
    • D. Matulis, I. Rouzina, V.A. Bloomfield, Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism, J. Mol. Biol. 296 (2000) 1053-1063.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1053-1063
    • Matulis, D.1    Rouzina, I.2    Bloomfield, V.A.3
  • 40
    • 0038499698 scopus 로고    scopus 로고
    • Electrostatic interactions in a peptide-RNA complex
    • C. García-García, D.E. Draper, Electrostatic interactions in a peptide-RNA complex, J. Mol. Biol. 331 (2003) 75-88.
    • (2003) J. Mol. Biol. , vol.331 , pp. 75-88
    • García-García, C.1    Draper, D.E.2
  • 42
    • 0345733992 scopus 로고    scopus 로고
    • Differential Modes of Recognition in N Peptide-BoxB Complexes
    • DOI 10.1021/bi0351312
    • R.J. Austin, T. Xia, J. Ren, T.T. Takahashi, R.W. Roberts, Differential modes of recognition in N peptide-BoxB complexes, Biochemistry 42 (2003) 14957-14967. (Pubitemid 37553526)
    • (2003) Biochemistry , vol.42 , Issue.50 , pp. 14957-14967
    • Austin, R.J.1    Xia, T.2    Ren, J.3    Takahashi, T.T.4    Roberts, R.W.5
  • 43
    • 77954724146 scopus 로고    scopus 로고
    • Acridine-N peptide conjugates display enhanced affinity and specificity for boxB RNA targets
    • X. Qi, T. Xia, R.W. Roberts, Acridine-N peptide conjugates display enhanced affinity and specificity for boxB RNA targets, Biochemistry 49 (2010) 5782-5789.
    • (2010) Biochemistry , vol.49 , pp. 5782-5789
    • Qi, X.1    Xia, T.2    Roberts, R.W.3
  • 46
    • 0022434014 scopus 로고
    • Direct determination of the association constant between elongation factor Tu. GTP and aminoacyl-tRNA using fluorescence
    • J.K. Abrahamson, T.M. Laue, D.L. Miller, A.E. Johnson, Direct determination of the association constant between elongation factor Tu. GTP and aminoacyl-tRNA using fluorescence, Biochemistry 24 (1985) 692-700.
    • (1985) Biochemistry , vol.24 , pp. 692-700
    • Abrahamson, J.K.1    Laue, T.M.2    Miller, D.L.3    Johnson, A.E.4
  • 47
    • 33745823525 scopus 로고    scopus 로고
    • Interactions of cationic ligands and proteins with small nucleic acids: Analytic treatment of the large Coulombic end effect on binding free energy as a function of salt concentration
    • DOI 10.1021/bi0520434
    • I.A. Shkel, J.D. Ballin, M.T. Record Jr., Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large Coulombic end effect on binding free energy as a function of salt concentration, Biochemistry 45 (2006) 8411-8426. (Pubitemid 44036547)
    • (2006) Biochemistry , vol.45 , Issue.27 , pp. 8411-8426
    • Shkel, I.A.1    Ballin, J.D.2    Record Jr., M.T.3
  • 48
    • 0036600872 scopus 로고    scopus 로고
    • Protein surface salt bridges and paths for DNA wrapping
    • DOI 10.1016/S0959-440X(02)00326-3
    • R.M. Saecker, M.T. Record Jr., Protein surface salt bridges and paths for DNA wrapping, Curr. Opin. Struct. Biol. 12 (2002) 311-319. (Pubitemid 34804612)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.3 , pp. 311-319
    • Saecker, R.M.1    Record, J.M.T.2
  • 49
    • 77952592558 scopus 로고    scopus 로고
    • Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate
    • W.S. Kontur, M.W. Capp, T.J. Gries, R.M. Saecker, M.T. Record Jr., Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate, Biochemistry 49 (2010) 4361-4373.
    • (2010) Biochemistry , vol.49 , pp. 4361-4373
    • Kontur, W.S.1    Capp, M.W.2    Gries, T.J.3    Saecker, R.M.4    Record Jr., M.T.5
  • 50
    • 39649115803 scopus 로고    scopus 로고
    • Formation of a wrapped DNA-protein interface: Experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H'DNA
    • K.A. Vander Meulen, R.M. Saecker, M.T. Record Jr., Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H'DNA, J. Mol. Biol. 377 (2008) 9-27.
    • (2008) J. Mol. Biol. , vol.377 , pp. 9-27
    • Vander Meulen, K.A.1    Saecker, R.M.2    Record Jr., M.T.3
  • 51
    • 44849130978 scopus 로고    scopus 로고
    • Salt dependent association of novel mutants of TATA-binding proteins to DNA: Predictions from theory and experiments
    • J.H. Bredenberg, M.O. Fenley, Salt dependent association of novel mutants of TATA-binding proteins to DNA: predictions from theory and experiments, Commun. Comput. Phys. 3 (2008) 1132-1153.
    • (2008) Commun. Comput. Phys. , vol.3 , pp. 1132-1153
    • Bredenberg, J.H.1    Fenley, M.O.2
  • 52
    • 0037076079 scopus 로고    scopus 로고
    • Fast boundary element method for the linear Poisson-Boltzmann equation
    • A.H. Boschitsch, M.O. Fenley, H.X. Zhou, Fast boundary element method for the linear Poisson-Boltzmann equation, J. Phys. Chem. 106 (2002) 2741-2754.
    • (2002) J. Phys. Chem. , vol.106 , pp. 2741-2754
    • Boschitsch, A.H.1    Fenley, M.O.2    Zhou, H.X.3
  • 53
    • 44849086045 scopus 로고    scopus 로고
    • Modeling salt dependence of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation
    • K. Talley, P. Kundrotas, E. Alexov, Modeling salt dependence of protein-protein association: linear vs non-linear Poisson-Boltzmann equation, Commun. Comput. Phys. 3 (2008) 1071-1086.
    • (2008) Commun. Comput. Phys. , vol.3 , pp. 1071-1086
    • Talley, K.1    Kundrotas, P.2    Alexov, E.3
  • 54
    • 50149114096 scopus 로고    scopus 로고
    • Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate
    • M.J. Plantinga, A.V. Korennykh, J.A. Piccirilli, C.C. Correll, Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate, Biochemistry 47 (2008) 8912-8918.
    • (2008) Biochemistry , vol.47 , pp. 8912-8918
    • Plantinga, M.J.1    Korennykh, A.V.2    Piccirilli, J.A.3    Correll, C.C.4
  • 55
    • 0034695428 scopus 로고    scopus 로고
    • Contributions of basic residues to ribosomal protein L11 recognition of RNA
    • D. GuhaThakurta, D.E. Draper, Contributions of basic residues to ribosomal protein L11 recognition of RNA, J. Mol. Biol. 295 (2000) 569-580.
    • (2000) J. Mol. Biol. , vol.295 , pp. 569-580
    • GuhaThakurta, D.1    Draper, D.E.2
  • 56
    • 31544473809 scopus 로고    scopus 로고
    • The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
    • DOI 10.1093/nar/gkj436
    • M.J. Law, M.E. Linde, E.J. Chambers, C. Oubridge, P.S. Katsamba, L. Nilsson, I.S. Haworth, I.A. Laird-Offringa, The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA, Nucleic Acids Res. 34 (2006) 275-285. (Pubitemid 43160050)
    • (2006) Nucleic Acids Research , vol.34 , Issue.1 , pp. 275-285
    • Law, M.J.1    Linde, M.E.2    Chambers, E.J.3    Oubridge, C.4    Katsamba, P.S.5    Nilsson, L.6    Haworth, I.S.7    Laird-Offringa, I.A.8
  • 57
    • 45849099824 scopus 로고    scopus 로고
    • Salt-mediated electrostatics in the association of TATA binding proteins to DNA: A combined molecular mechanics/ Poisson-Boltzmann study
    • J.H. Bredenberg, C. Russo, M.O. Fenley, Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/ Poisson-Boltzmann study, Biophys. J. 94 (2008) 4634-4645.
    • (2008) Biophys. J. , vol.94 , pp. 4634-4645
    • Bredenberg, J.H.1    Russo, C.2    Fenley, M.O.3
  • 58
    • 73349099987 scopus 로고    scopus 로고
    • Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations
    • R.P. Bahadur, S. Kannan, M. Zacharias, Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations, Biophys. J. 97 (2009) 3139-3149.
    • (2009) Biophys. J. , vol.97 , pp. 3139-3149
    • Bahadur, R.P.1    Kannan, S.2    Zacharias, M.3
  • 59
    • 2242469712 scopus 로고    scopus 로고
    • Structure of the HIV-1 nucleocapsid protein bound to the SL3 Ψ-RNA recognition element
    • DOI 10.1126/science.279.5349.384
    • R.N. De Guzman, Z.R. Wu, C.C. Stalling, L. Pappalardo, P.N. Borer, M.F. Summers, Structure of the HIV-1 nucleocapsid protein bound to the SL3 Ψ-RNA recognition element, Science 279 (1998) 384-388. (Pubitemid 28063374)
    • (1998) Science , vol.279 , Issue.5349 , pp. 384-388
    • De Guzman, R.N.1    Wu, Z.R.2    Stalling, C.C.3    Pappalardo, L.4    Borer, P.N.5    Summers, M.F.6
  • 60
    • 0031916834 scopus 로고    scopus 로고
    • Solution structure of P22 transcriptional antitermination N peptide-box B RNA complex
    • DOI 10.1038/nsb0398-203
    • Z. Cai, A. Gorin, R. Frederick, X. Ye, W. Hu, A. Majumdar, A. Kettani, D.J. Patel, Solution structure of P22 transcriptional antitermination N peptide-box B RNA complex, Nat. Struct. Mol. Biol. 5 (1998) 203-212. (Pubitemid 28113752)
    • (1998) Nature Structural Biology , vol.5 , Issue.3 , pp. 203-212
    • Cai, Z.1    Gorin, A.2    Frederick, R.3    Ye, X.4    Hu, W.5    Majumdar, A.6    Kettani, A.7    Patel, D.J.8
  • 61
    • 0029613238 scopus 로고
    • Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex
    • X. Ye, R.A. Kumar, D.J. Patel, Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex, Chem. Biol. 2 (1995) 827-840.
    • (1995) Chem. Biol. , vol.2 , pp. 827-840
    • Ye, X.1    Kumar, R.A.2    Patel, D.J.3
  • 62
    • 0033572743 scopus 로고    scopus 로고
    • Anchoring an extended HTLV-1 rex peptide within an RNA major groove containing junctional base triples
    • DOI 10.1016/S0969-2126(00)88337-9
    • F. Jiang, A. Gorin, W. Hu, A. Majumdar, S. Baskerville, W. Xu, A. Ellington, D.J. Patel, Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples, Structure 7 (1999) 1461-1472. (Pubitemid 30007232)
    • (1999) Structure , vol.7 , Issue.12 , pp. 1461-1472
    • Jiang, F.1    Gorin, A.2    Hu, W.3    Majumdar, A.4    Baskerville, S.5    Xu, W.6    Ellington, A.7    Patel, D.J.8
  • 64
    • 0035943613 scopus 로고    scopus 로고
    • The structure of the coliphage HK022 Nun protein-λ-phage boxB RNA complex
    • C. Faber, M. Schärpf, T. Becker, H. Sticht, P. Rösch, The structure of the coliphage HK022 Nun protein-λ-phage boxB RNA complex, J. Biol. Chem. 276 (2001) 32064-32070.
    • (2001) J. Biol. Chem. , vol.276 , pp. 32064-32070
    • Faber, C.1    Schärpf, M.2    Becker, T.3    Sticht, H.4    Rösch, P.5
  • 65
    • 0035019574 scopus 로고    scopus 로고
    • Structural characterization of the complex of the Rev response element RNA with a selected peptide
    • Q. Zhang, K. Harada, H.S. Cho, A.D. Frankel, D.E. Wemmer, Structural characterization of the complex of the Rev response element RNA with a selected peptide, Chem. Biol. 8 (2001) 511-520.
    • (2001) Chem. Biol. , vol.8 , pp. 511-520
    • Zhang, Q.1    Harada, K.2    Cho, H.S.3    Frankel, A.D.4    Wemmer, D.E.5
  • 66
    • 0028858599 scopus 로고
    • Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
    • J.D. Puglisi, L. Chen, S. Blanchard, A.D. Frankel, Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex, Science 270 (1995) 1200-1203.
    • (1995) Science , vol.270 , pp. 1200-1203
    • Puglisi, J.D.1    Chen, L.2    Blanchard, S.3    Frankel, A.D.4
  • 67
    • 0038813728 scopus 로고    scopus 로고
    • Structural mimicry in the phage φ21 N peptide-boxB RNA complex
    • DOI 10.1261/rna.2189203
    • C.D. Cilley, J.R. Williamson, Structural mimicry in the phage φ21 N peptide-boxB RNA complex, RNA. 9 (2003) 663-676. (Pubitemid 36618195)
    • (2003) RNA , vol.9 , Issue.6 , pp. 663-676
    • Cilley, C.D.1    Williamson, J.R.2
  • 69
    • 24944500398 scopus 로고    scopus 로고
    • TAR RNA recognition by a cyclic peptidomimetic of Tat protein
    • DOI 10.1021/bi0510532
    • T.C. Leeper, Z. Athanassiou, R.L. Dias, J.A. Robinson, G. Varani, TAR RNA recognition by a cyclic peptidomimetic of Tat protein, Biochemistry 44 (2005) 12362-12372. (Pubitemid 41324328)
    • (2005) Biochemistry , vol.44 , Issue.37 , pp. 12362-12372
    • Leeper, T.C.1    Athanassiou, Z.2    Dias, R.L.A.3    Robinson, J.A.4    Varani, G.5
  • 71
    • 0000641399 scopus 로고    scopus 로고
    • Antitermination in bacteriophage: The structure of the N36 peptide-boxB RNA complex
    • M. Schärpf, H. Sticht, K. Schweimer, M. Boehm, S. Hoffmann, P. Rösch, Antitermination in bacteriophage: the structure of the N36 peptide-boxB RNA complex, FEBS J. 267 (2000) 2397-2408.
    • (2000) FEBS J. , vol.267 , pp. 2397-2408
    • Schärpf, M.1    Sticht, H.2    Schweimer, K.3    Boehm, M.4    Hoffmann, S.5    Rösch, P.6
  • 72
    • 0030475417 scopus 로고    scopus 로고
    • Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex
    • DOI 10.1038/nsb1296-1026
    • X. Ye, A. Gorin, A.D. Ellington, D.J. Patel, Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex, Nat. Struct. Mol. Biol. 3 (1996) 1026-1033. (Pubitemid 27014631)
    • (1996) Nature Structural Biology , vol.3 , Issue.12 , pp. 1026-1033
    • Ye, X.1    Gorin, A.2    Ellington, A.D.3    Patel, D.J.4
  • 74
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, N.A. Baker, PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations, Nucleic Acids Res. 32 (2004) W665-W667.
    • (2004) Nucleic Acids Res. , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 77
    • 0029068766 scopus 로고    scopus 로고
    • Polyelectrolyte electrostatics: Salt dependence, entropic, and enthalpic contributions to free energy in nonlinear Poisson-Boltzmann model
    • K.A. Sharp, Polyelectrolyte electrostatics: salt dependence, entropic, and enthalpic contributions to free energy in nonlinear Poisson-Boltzmann model, Biopolymers 36 (2005) 227-243.
    • (2005) Biopolymers , vol.36 , pp. 227-243
    • Sharp, K.A.1
  • 79
    • 0034510099 scopus 로고    scopus 로고
    • Ion distributions in a cylindrical capillary as seen by the modified Poisson-Boltzmann theory and Monte Carlo simulations
    • B. Hribar, V. Vlachy, L.B. Bhuiyan, C.W. Outhwaite, Ion distributions in a cylindrical capillary as seen by the modified Poisson-Boltzmann theory and Monte Carlo simulations, J. Phys. Chem. B 104 (2000) 11522-11527.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 11522-11527
    • Hribar, B.1    Vlachy, V.2    Bhuiyan, L.B.3    Outhwaite, C.W.4
  • 80
    • 0036857758 scopus 로고    scopus 로고
    • Electrostatic correlations: From plasma to biology
    • Y. Levin, Electrostatic correlations: from plasma to biology, Rep. Prog. Phys. 65 (2002) 1577-1632.
    • (2002) Rep. Prog. Phys. , vol.65 , pp. 1577-1632
    • Levin, Y.1
  • 81
    • 0001552389 scopus 로고    scopus 로고
    • Electrostatistics of counter-ions at and between planar chargedwalls: From Poisson-Boltzmann to the strong-coupling theory
    • R.R.Netz, Electrostatistics of counter-ions at and between planar chargedwalls: from Poisson-Boltzmann to the strong-coupling theory, Eur. Phys. J. E 5 (2001) 557-574.
    • (2001) Eur. Phys. J. E , vol.5 , pp. 557-574
    • Netz, R.R.1
  • 82
    • 0033558393 scopus 로고    scopus 로고
    • Field theory for charged fluids and colloids
    • R.R. Netz, H. Orland, Field theory for charged fluids and colloids, Europhys. Lett. 45 (1999) 726-732.
    • (1999) Europhys. Lett. , vol.45 , pp. 726-732
    • Netz, R.R.1    Orland, H.2
  • 83
    • 0001020827 scopus 로고    scopus 로고
    • Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions
    • R.R. Netz, H. Orland, Beyond Poisson-Boltzmann: fluctuation effects and correlation functions, Eur. Phys. J. E 1 (2000) 203-214.
    • (2000) Eur. Phys. J. E , vol.1 , pp. 203-214
    • Netz, R.R.1    Orland, H.2
  • 84
    • 0000237456 scopus 로고
    • A simple analysis of ion-ion correlation in polyelectrolyte solutions
    • R. Penfold, S. Nordholm, B. Jönsson, C.E. Woodward, A simple analysis of ion-ion correlation in polyelectrolyte solutions, J. Chem. Phys. 92 (1990) 1915-1922.
    • (1990) J. Chem. Phys. , vol.92 , pp. 1915-1922
    • Penfold, R.1    Nordholm, S.2    Jönsson, B.3    Woodward, C.E.4
  • 85
    • 34247871418 scopus 로고    scopus 로고
    • 2+ solution
    • DOI 10.1529/biophysj.106.100388
    • Z. Tan, S. Chen, RNA helix stability in mixed Na+/Mg2+ solution, Biophys. J. 92 (2007) 3615-3632. (Pubitemid 46698651)
    • (2007) Biophysical Journal , vol.92 , Issue.10 , pp. 3615-3632
    • Tan, Z.-J.1    Chen, S.-J.2
  • 86
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: Conformational statistics, folding kinetics, and ion electrostatics
    • S. Chen, RNA folding: conformational statistics, folding kinetics, and ion electrostatics, Annu. Rev. Biophys. 37 (2008) 197-214.
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 197-214
    • Chen, S.1
  • 87
    • 0017667044 scopus 로고
    • Interpretation of monovalent and divalent cation effects on the lac repressor operator interaction
    • M.T. Record Jr., P.L. DeHaseth, T.M. Lohman, Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction, Biochemistry 16 (1977) 4791-4796. (Pubitemid 8220967)
    • (1977) Biochemistry , vol.16 , Issue.22 , pp. 4791-4796
    • Record Jr., M.T.1    DeHaseth, P.L.2    Lohman, T.M.3
  • 88
    • 0019330787 scopus 로고
    • Pentalysine-deoxyribonucleic acid interactions: A model for the general effects of ion concentrations on the interactions of proteins with nucleic acids
    • T.M. Lohman, P.L. DeHaseth, M.T. Record Jr., Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids, Biochemistry 19 (1980) 3522-3530.
    • (1980) Biochemistry , vol.19 , pp. 3522-3530
    • Lohman, T.M.1    DeHaseth, P.L.2    Record Jr., M.T.3


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