메뉴 건너뛰기




Volumn 406, Issue 2, 2011, Pages 285-312

The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein

Author keywords

asymmetric phosphate neutralization; chiral methylphosphonate; electrostatic interactions; protein DNA recognition; restriction endonuclease

Indexed keywords

DNA BINDING PROTEIN; ENDONUCLEASE; OLIGODEOXYNUCLEOTIDE; PHOSPHATE;

EID: 79251594507     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.12.012     Document Type: Article
Times cited : (15)

References (106)
  • 1
    • 0025914242 scopus 로고
    • Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
    • Schultz S.C., Shields G.C., and Steitz T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90° Science 253 1991 1001 1007
    • (1991) Science , vol.253 , pp. 1001-1007
    • Schultz, S.C.1    Shields, G.C.2    Steitz, T.A.3
  • 2
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim Y., Geiger J.H., Hahn S., and Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex Nature 365 1993 512 520
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 3
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of a TATA element
    • Kim J.L., Nikolov D.B., and Burley S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element Nature 365 1993 520 527
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 4
    • 0028922082 scopus 로고
    • The regulation of transcription initiation by integration host factor
    • Goosen N., and Van de Putte P. The regulation of transcription initiation by integration host factor Mol. Microbiol. 16 1995 1 7
    • (1995) Mol. Microbiol. , vol.16 , pp. 1-7
    • Goosen, N.1    Van De Putte, P.2
  • 6
    • 0029131298 scopus 로고
    • Structural basis for DNA bending by the architectural transcription factor LEF-1
    • Love J.J., Li X., Case D.A., Giese K., Grosschedl R., and Wright P.E. Structural basis for DNA bending by the architectural transcription factor LEF-1 Nature 376 1995 791 795
    • (1995) Nature , vol.376 , pp. 791-795
    • Love, J.J.1    Li, X.2    Case, D.A.3    Giese, K.4    Grosschedl, R.5    Wright, P.E.6
  • 7
    • 1842505115 scopus 로고    scopus 로고
    • Crystal structure of the excisionase-DNA complex from bacteriophage lambda
    • Sam M.D., Cascio D., Johnson R.C., and Clubb R.T. Crystal structure of the excisionase-DNA complex from bacteriophage lambda J. Mol. Biol. 338 2004 229 240
    • (2004) J. Mol. Biol. , vol.338 , pp. 229-240
    • Sam, M.D.1    Cascio, D.2    Johnson, R.C.3    Clubb, R.T.4
  • 8
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 Å resolution
    • Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 9
    • 33750527566 scopus 로고    scopus 로고
    • The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
    • Luijsterburg M.S., Noom M.C., Wuite G.J., and Dame R.T. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective J. Struct. Biol. 156 2006 262 272
    • (2006) J. Struct. Biol. , vol.156 , pp. 262-272
    • Luijsterburg, M.S.1    Noom, M.C.2    Wuite, G.J.3    Dame, R.T.4
  • 10
    • 0034705029 scopus 로고    scopus 로고
    • Crystallographic snapshots along a protein-induced DNA-bending pathway
    • Horton N.C., and Perona J.J. Crystallographic snapshots along a protein-induced DNA-bending pathway Proc. Natl Acad. Sci. USA 97 2000 5729 5734
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 5729-5734
    • Horton, N.C.1    Perona, J.J.2
  • 11
    • 0027159254 scopus 로고
    • The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
    • Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R.S., and Heathman S.P. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments EMBO J. 12 1993 1781 1795
    • (1993) EMBO J. , vol.12 , pp. 1781-1795
    • Winkler, F.K.1    Banner, D.W.2    Oefner, C.3    Tsernoglou, D.4    Brown, R.S.5    Heathman, S.P.6
  • 12
    • 0032584223 scopus 로고    scopus 로고
    • How Cro and lambda-repressor distinguish between operators: The structural basis underlying a genetic switch
    • Albright R.A., and Matthews B.W. How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch Proc. Natl Acad. Sci. USA 95 1998 3431 3436
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 3431-3436
    • Albright, R.A.1    Matthews, B.W.2
  • 13
    • 0030736323 scopus 로고    scopus 로고
    • Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
    • Jen-Jacobson L. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state Biopolymers 44 1997 153 180
    • (1997) Biopolymers , vol.44 , pp. 153-180
    • Jen-Jacobson, L.1
  • 14
    • 85015087906 scopus 로고    scopus 로고
    • Ten years of tension: Single-molecule DNA mechanics
    • Bustamante C., Bryant Z., and Smith S.B. Ten years of tension: single-molecule DNA mechanics Nature 421 2003 423 427
    • (2003) Nature , vol.421 , pp. 423-427
    • Bustamante, C.1    Bryant, Z.2    Smith, S.B.3
  • 16
    • 0020134871 scopus 로고
    • Flow birefringence of T7 phage DNA: Dependence on salt concentration
    • Cairney K.L., and Harrington R.E. Flow birefringence of T7 phage DNA: dependence on salt concentration Biopolymers 21 1982 923 934
    • (1982) Biopolymers , vol.21 , pp. 923-934
    • Cairney, K.L.1    Harrington, R.E.2
  • 17
    • 0025911729 scopus 로고
    • Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations
    • Porschke D. Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations Biophys. Chem. 40 1991 169 179
    • (1991) Biophys. Chem. , vol.40 , pp. 169-179
    • Porschke, D.1
  • 18
    • 0026253887 scopus 로고
    • + on the persistence length and excluded volume of T7 bacteriophage DNA
    • + on the persistence length and excluded volume of T7 bacteriophage DNA Biopolymers 31 1991 1559 1564
    • (1991) Biopolymers , vol.31 , pp. 1559-1564
    • Sobel, E.S.1    Harpst, J.A.2
  • 20
    • 0024519056 scopus 로고
    • An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups
    • Manning G.S., Ebralidse K.K., Mirzabekov A.D., and Rich A. An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups J. Biomol. Struct. Dyn. 6 1989 877 889
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 877-889
    • Manning, G.S.1    Ebralidse, K.K.2    Mirzabekov, A.D.3    Rich, A.4
  • 22
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier T.E., and Widom J. Spontaneous sharp bending of double-stranded DNA Mol. Cell 14 2004 355 362
    • (2004) Mol. Cell , vol.14 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 23
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W.K., Gorin A.A., Lu X.J., Hock L.M., and Zhurkin V.B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl. Acad. Sci. USA 95 1998 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
  • 24
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin A.A., Zhurkin V.B., and Olson W.K. B-DNA twisting correlates with base-pair morphology J. Mol. Biol. 247 1995 34 48
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 25
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia J. Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl Acad. Sci. USA 95 1998 1460 1465
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1460-1465
    • Santalucia Jr., J.1
  • 26
    • 0027213193 scopus 로고
    • On the stability of nucleic acid structures in solution: Enthalpy-entropy compensations, internal rotations and reversibility
    • Searle M.S., and Williams D.H. On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility Nucleic Acids Res. 21 1993 2051 2056
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2051-2056
    • Searle, M.S.1    Williams, D.H.2
  • 27
  • 28
    • 0025008815 scopus 로고
    • Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein
    • Zinkel S.S., and Crothers D.M. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein Biopolymers 29 1990 29 38
    • (1990) Biopolymers , vol.29 , pp. 29-38
    • Zinkel, S.S.1    Crothers, D.M.2
  • 29
    • 0028956314 scopus 로고
    • Visualization of TBP oligomers binding and bending the HIV-1 and adeno promoters
    • Griffith J.D., Makhov A., Zawel L., and Reinberg D. Visualization of TBP oligomers binding and bending the HIV-1 and adeno promoters J. Mol. Biol. 246 1995 576 584
    • (1995) J. Mol. Biol. , vol.246 , pp. 576-584
    • Griffith, J.D.1    Makhov, A.2    Zawel, L.3    Reinberg, D.4
  • 30
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
    • Rice P.A., Yang S.W., Mizuuchi K., and Nash H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn Cell 87 1996 1295 1306
    • (1996) Cell , vol.87 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.W.2    Mizuuchi, K.3    Nash, H.A.4
  • 32
    • 0029895487 scopus 로고    scopus 로고
    • The low dielectric interior of proteins is sufficient to cause major structural changes in DNA on association
    • Elcock A.H., and McCammon J.A. The low dielectric interior of proteins is sufficient to cause major structural changes in DNA on association J. Am. Chem. Soc. 118 1996 3787 3788
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3787-3788
    • Elcock, A.H.1    McCammon, J.A.2
  • 33
    • 0001743558 scopus 로고
    • Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending
    • Mirzabekov A.D., and Rich A. Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending Proc. Natl. Acad. Sci. USA 76 1979 1118 1121
    • (1979) Proc. Natl. Acad. Sci. USA , vol.76 , pp. 1118-1121
    • Mirzabekov, A.D.1    Rich, A.2
  • 34
    • 0030803385 scopus 로고    scopus 로고
    • Electrostatic mechanism for DNA bending by bZIP proteins
    • Paolella D.N., Liu Y., Fabian M.A., and Schepartz A. Electrostatic mechanism for DNA bending by bZIP proteins Biochemistry 36 1997 10033 10038
    • (1997) Biochemistry , vol.36 , pp. 10033-10038
    • Paolella, D.N.1    Liu, Y.2    Fabian, M.A.3    Schepartz, A.4
  • 35
    • 0030743625 scopus 로고    scopus 로고
    • The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA
    • Metallo S.J., Paolella D.N., and Schepartz A. The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA Nucleic Acids Res. 25 1997 2967 2972
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2967-2972
    • Metallo, S.J.1    Paolella, D.N.2    Schepartz, A.3
  • 37
    • 0345097650 scopus 로고    scopus 로고
    • Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp?
    • Manning G.S. Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp? J. Am. Chem. Soc. 125 2003 15087 15092
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 15087-15092
    • Manning, G.S.1
  • 38
    • 0028597967 scopus 로고
    • DNA bending by asymmetric phosphate neutralization
    • Strauss J.K., and Maher L.J. III DNA bending by asymmetric phosphate neutralization Science 266 1994 1829 1834
    • (1994) Science , vol.266 , pp. 1829-1834
    • Strauss, J.K.1    Iii, J.M.L.2
  • 39
    • 0036567549 scopus 로고    scopus 로고
    • Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein
    • Hardwidge P.R., Zimmerman J.M., and Maher L.J. III Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein Nucleic Acids Res. 30 2002 1879 1885
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1879-1885
    • Hardwidge, P.R.1    Zimmerman, J.M.2    Iii, J.M.L.3
  • 40
    • 0033526040 scopus 로고    scopus 로고
    • The role of DNA-protein salt bridges in molecular recognition: A model study
    • Gurlie R., Duong T.H., and Zakrzewska K. The role of DNA-protein salt bridges in molecular recognition: a model study Biopolymers 49 1999 313 327
    • (1999) Biopolymers , vol.49 , pp. 313-327
    • Gurlie, R.1    Duong, T.H.2    Zakrzewska, K.3
  • 41
    • 0035626714 scopus 로고    scopus 로고
    • Protein-induced DNA bending: The role of phosphate neutralization
    • Zakrzewska K., and Gurlie R. Protein-induced DNA bending: the role of phosphate neutralization Theor. Chem. Acc. 106 2001 8
    • (2001) Theor. Chem. Acc. , vol.106 , pp. 8
    • Zakrzewska, K.1    Gurlie, R.2
  • 44
    • 0037129935 scopus 로고    scopus 로고
    • DNA bending by bZIP charge variants: A unified study using electrophoretic phasing and fluorescence resonance energy transfer
    • Hardwidge P.R., Wu J., Williams S.L., Parkhurst K.M., Parkhurst L.J., and Maher L.J. III DNA bending by bZIP charge variants: a unified study using electrophoretic phasing and fluorescence resonance energy transfer Biochemistry 41 2002 7732 7742
    • (2002) Biochemistry , vol.41 , pp. 7732-7742
    • Hardwidge, P.R.1    Wu, J.2    Williams, S.L.3    Parkhurst, K.M.4    Parkhurst, L.J.5    Iii, J.M.L.6
  • 45
    • 0030837545 scopus 로고    scopus 로고
    • DNA bending by GCN4 mutants bearing cationic residues
    • Strauss-Soukup J.K., and Maher L.J. III DNA bending by GCN4 mutants bearing cationic residues Biochemistry 36 1997 7
    • (1997) Biochemistry , vol.36 , pp. 7
    • Strauss-Soukup, J.K.1    Iii, J.M.L.2
  • 46
    • 0038713265 scopus 로고    scopus 로고
    • Reflections on apparent DNA bending by charge variants of bZIP proteins
    • Hardwidge P.R., Parkhurst K.M., Parkhurst L.J., and Maher L.J. III Reflections on apparent DNA bending by charge variants of bZIP proteins Biopolymers 69 2003 110 117
    • (2003) Biopolymers , vol.69 , pp. 110-117
    • Hardwidge, P.R.1    Parkhurst, K.M.2    Parkhurst, L.J.3    Iii, J.M.L.4
  • 47
    • 0032972857 scopus 로고    scopus 로고
    • Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
    • Martin A.M., Sam M.D., Reich N.O., and Perona J.J. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease Nat. Struct. Biol. 6 1999 269 277
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 269-277
    • Martin, A.M.1    Sam, M.D.2    Reich, N.O.3    Perona, J.J.4
  • 48
    • 0035812654 scopus 로고    scopus 로고
    • Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: A comparative analysis of T-A and A-T steps within A-tracts
    • Mack D.R., Chiu T.K., and Dickerson R.E. Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts J. Mol. Biol. 312 2001 1037 1049
    • (2001) J. Mol. Biol. , vol.312 , pp. 1037-1049
    • MacK, D.R.1    Chiu, T.K.2    Dickerson, R.E.3
  • 49
    • 0033200072 scopus 로고    scopus 로고
    • Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: A catalytic role for a main chain carbonyl group
    • Thomas M.P., Brady R.L., Halford S.E., Sessions R.B., and Baldwin G.S. Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group Nucleic Acids Res. 27 1999 3438 3445
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3438-3445
    • Thomas, M.P.1    Brady, R.L.2    Halford, S.E.3    Sessions, R.B.4    Baldwin, G.S.5
  • 52
    • 33749039501 scopus 로고    scopus 로고
    • Positively charged C-terminal subdomains of EcoRV endonuclease: Contributions to DNA binding, bending, and cleavage
    • Hiller D.A., and Perona J.J. Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage Biochemistry 45 2006 11453 11463
    • (2006) Biochemistry , vol.45 , pp. 11453-11463
    • Hiller, D.A.1    Perona, J.J.2
  • 53
    • 0028988416 scopus 로고
    • 2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Å resolution
    • 2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution Biochemistry 34 1995 683 696
    • (1995) Biochemistry , vol.34 , pp. 683-696
    • Kostrewa, D.1    Winkler, F.K.2
  • 54
    • 0034435652 scopus 로고    scopus 로고
    • Structural and thermodynamic strategies for site-specific DNA binding proteins
    • Jen-Jacobson L., Engler L.E., and Jacobson L.A. Structural and thermodynamic strategies for site-specific DNA binding proteins Structure 8 2000 1015 1023
    • (2000) Structure , vol.8 , pp. 1015-1023
    • Jen-Jacobson, L.1    Engler, L.E.2    Jacobson, L.A.3
  • 55
    • 0036708467 scopus 로고    scopus 로고
    • Relationship between ion pair geometries and electrostatic strengths in proteins
    • Kumar S., and Nussinov R. Relationship between ion pair geometries and electrostatic strengths in proteins Biophys. J. 83 2002 1595 1612
    • (2002) Biophys. J. , vol.83 , pp. 1595-1612
    • Kumar, S.1    Nussinov, R.2
  • 56
    • 76249089135 scopus 로고    scopus 로고
    • Electrostatic solvation energy for two oppositely charged ions
    • Gong H., and Freed K.F. Electrostatic solvation energy for two oppositely charged ions Biophys. J. 98 2010 470 477
    • (2010) Biophys. J. , vol.98 , pp. 470-477
    • Gong, H.1    Freed, K.F.2
  • 57
    • 0037102493 scopus 로고    scopus 로고
    • Effect of a neutralized phosphate backbone on the minor groove of B-DNA: Molecular dynamics simulation studies
    • Hamelberg D., Williams L.D., and Wilson W.D. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies Nucleic Acids Res. 30 2002 3615 3623
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3615-3623
    • Hamelberg, D.1    Williams, L.D.2    Wilson, W.D.3
  • 58
    • 0021100807 scopus 로고
    • 2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study
    • 2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study Nucleic Acids Res. 11 1983 2801 2814
    • (1983) Nucleic Acids Res. , vol.11 , pp. 2801-2814
    • Chacko, K.K.1    Lindner, K.2    Saenger, W.3    Miller, P.S.4
  • 59
    • 0028934112 scopus 로고
    • Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions
    • Vipond I.B., and Halford S.E. Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions Biochemistry 34 1995 1113 1119
    • (1995) Biochemistry , vol.34 , pp. 1113-1119
    • Vipond, I.B.1    Halford, S.E.2
  • 60
    • 0031591392 scopus 로고    scopus 로고
    • Specific binding by EcoRV endonuclease to its DNA recognition site GATATC
    • Engler L.E., Welch K.K., and Jen-Jacobson L. Specific binding by EcoRV endonuclease to its DNA recognition site GATATC J. Mol. Biol. 269 1997 82 101
    • (1997) J. Mol. Biol. , vol.269 , pp. 82-101
    • Engler, L.E.1    Welch, K.K.2    Jen-Jacobson, L.3
  • 61
    • 0033614808 scopus 로고    scopus 로고
    • Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease
    • Martin A.M., Horton N.C., Lusetti S., Reich N.O., and Perona J.J. Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease Biochemistry 38 1999 8430 8439
    • (1999) Biochemistry , vol.38 , pp. 8430-8439
    • Martin, A.M.1    Horton, N.C.2    Lusetti, S.3    Reich, N.O.4    Perona, J.J.5
  • 62
    • 0032506110 scopus 로고    scopus 로고
    • Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases
    • Horton N.C., Newberry K.J., and Perona J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases Proc. Natl Acad. Sci. USA 95 1998 13489 13494
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 13489-13494
    • Horton, N.C.1    Newberry, K.J.2    Perona, J.J.3
  • 63
    • 0031576347 scopus 로고    scopus 로고
    • Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis
    • Perona J.J., and Martin A.M. Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis J. Mol. Biol. 273 1997 207 225
    • (1997) J. Mol. Biol. , vol.273 , pp. 207-225
    • Perona, J.J.1    Martin, A.M.2
  • 64
    • 0026323912 scopus 로고
    • Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between protein and helical DNA
    • Record M.T. Jr, Ha J.H., and Fisher M.A. Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between protein and helical DNA Methods Enzymol. 208 1991 291 343
    • (1991) Methods Enzymol. , vol.208 , pp. 291-343
    • Record, M.T.1    Ha, J.H.2    Fisher, M.A.3
  • 65
    • 4243067681 scopus 로고    scopus 로고
    • Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests
    • Hendsch Z.S., Jonsson T., Sauer R.T., and Tidor B. Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests Biochemistry 35 1996 7621 7625
    • (1996) Biochemistry , vol.35 , pp. 7621-7625
    • Hendsch, Z.S.1    Jonsson, T.2    Sauer, R.T.3    Tidor, B.4
  • 66
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Q. Rev. Biophys. 11 1978 179 246
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 68
    • 67649883207 scopus 로고    scopus 로고
    • Local and global effects of strong DNA bending induced during molecular dynamics simulations
    • Curuksu J., Zacharias M., Lavery R., and Zakrzewska K. Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res. 37 2009 3766 3773
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3766-3773
    • Curuksu, J.1    Zacharias, M.2    Lavery, R.3    Zakrzewska, K.4
  • 69
    • 70350434060 scopus 로고    scopus 로고
    • Role of water and effects of small ions in site-specific protein-DNA interactions
    • Jen-Jacobson L., and Jacobson L.A. Role of water and effects of small ions in site-specific protein-DNA interactions P.A. Rice, C.C. Correll, Protein-Nucleic Acid Interactions: Structural Biology 2008 Royal Society of Chemistry Press Cambridge, UK 14 37
    • (2008) Protein-Nucleic Acid Interactions: Structural Biology , pp. 14-37
    • Jen-Jacobson, L.1    Jacobson, L.A.2
  • 70
    • 0026687952 scopus 로고
    • Fluorescence resonance energy transfer and nucleic acids
    • Clegg R.M. Fluorescence resonance energy transfer and nucleic acids Methods Enzymol. 211 1992 353 388
    • (1992) Methods Enzymol. , vol.211 , pp. 353-388
    • Clegg, R.M.1
  • 71
    • 0346220020 scopus 로고    scopus 로고
    • Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence
    • Hiller D.A., Fogg J.M., Martin A.M., Beechem J.M., Reich N.O., and Perona J.J. Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence Biochemistry 42 2003 14375 14385
    • (2003) Biochemistry , vol.42 , pp. 14375-14385
    • Hiller, D.A.1    Fogg, J.M.2    Martin, A.M.3    Beechem, J.M.4    Reich, N.O.5    Perona, J.J.6
  • 72
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids: 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions
    • Winter R.B., Berg O.G., and von Hippel P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids: 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions Biochemistry 20 1981 6961 6977
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1    Berg, O.G.2    Von Hippel, P.H.3
  • 73
    • 0019823390 scopus 로고
    • Quantitative analysis of drug-receptor interactions: I. Determination of kinetic and equilibrium properties
    • Weiland G.A., and Molinoff P.B. Quantitative analysis of drug-receptor interactions: I. Determination of kinetic and equilibrium properties Life Sci. 29 1981 313 330
    • (1981) Life Sci. , vol.29 , pp. 313-330
    • Weiland, G.A.1    Molinoff, P.B.2
  • 74
    • 0021341905 scopus 로고
    • Kinetics of interaction of N epsilon-fluorescein isothiocyanate-lysine- 23-cobra alpha-toxin with the acetylcholine receptor
    • Cheung A.T., Johnson D.A., and Taylor P. Kinetics of interaction of N epsilon-fluorescein isothiocyanate-lysine-23-cobra alpha-toxin with the acetylcholine receptor Biophys. J. 45 1984 447 454
    • (1984) Biophys. J. , vol.45 , pp. 447-454
    • Cheung, A.T.1    Johnson, D.A.2    Taylor, P.3
  • 75
    • 0037076536 scopus 로고    scopus 로고
    • Stopped-flow studies of the kinetics of single-stranded DNA binding and wrapping around the Escherichia coli SSB tetramer
    • Kozlov A.G., and Lohman T.M. Stopped-flow studies of the kinetics of single-stranded DNA binding and wrapping around the Escherichia coli SSB tetramer Biochemistry 41 2002 6032 6044
    • (2002) Biochemistry , vol.41 , pp. 6032-6044
    • Kozlov, A.G.1    Lohman, T.M.2
  • 76
    • 65549171477 scopus 로고    scopus 로고
    • An end to 40 years of mistakes in DNA-protein association kinetics?
    • Halford S.E. An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 37 2009 343 348
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 343-348
    • Halford, S.E.1
  • 77
    • 0018074213 scopus 로고
    • Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions
    • Lohman T.M., DeHaseth P.L., and Record M.T. Jr Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions Biophys. Chem. 8 1978 281 294
    • (1978) Biophys. Chem. , vol.8 , pp. 281-294
    • Lohman, T.M.1    Dehaseth, P.L.2    Record Jr., M.T.3
  • 78
    • 0022573212 scopus 로고
    • Kinetics of protein-nucleic acid interactions: Use of salt effects to probe mechanisms of interaction
    • Lohman T.M. Kinetics of protein-nucleic acid interactions: use of salt effects to probe mechanisms of interaction CRC Crit. Rev. Biochem. 19 1985 191 245
    • (1985) CRC Crit. Rev. Biochem. , vol.19 , pp. 191-245
    • Lohman, T.M.1
  • 81
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas F., Sponer J., Langowski J., and Cheatham T.E. III DNA basepair step deformability inferred from molecular dynamics simulations Biophys. J. 85 2003 2872 2883
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Iii, E.C.T.4
  • 82
    • 77955267122 scopus 로고    scopus 로고
    • Mechanism of DNA recognition by the restriction enzyme EcoRV
    • Zahran M., Daidone I., Smith J.C., and Imhof P. Mechanism of DNA recognition by the restriction enzyme EcoRV J. Mol. Biol. 401 2010 415 432
    • (2010) J. Mol. Biol. , vol.401 , pp. 415-432
    • Zahran, M.1    Daidone, I.2    Smith, J.C.3    Imhof, P.4
  • 85
    • 0024531901 scopus 로고
    • Facilitated target location in biological system
    • von Hippel P.H., and Berg O.G. Facilitated target location in biological system J. Biol. Chem. 264 1989 675 678
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 86
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • Halford S.E., and Marko J.F. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32 2004 3040 3052
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 87
    • 2642527026 scopus 로고    scopus 로고
    • DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites
    • Horton N.C., and Perona J.J. DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites Biochemistry 43 2004 6841 6857
    • (2004) Biochemistry , vol.43 , pp. 6841-6857
    • Horton, N.C.1    Perona, J.J.2
  • 90
    • 0026487068 scopus 로고
    • Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex
    • Lesser D.R., Grajkowski A., Kurpiewski M.R., Koziolkiewicz M., Stec W.J., and Jen-Jacobson L. Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex J. Biol. Chem. 267 1992 24810 24818
    • (1992) J. Biol. Chem. , vol.267 , pp. 24810-24818
    • Lesser, D.R.1    Grajkowski, A.2    Kurpiewski, M.R.3    Koziolkiewicz, M.4    Stec, W.J.5    Jen-Jacobson, L.6
  • 91
    • 0014721907 scopus 로고
    • Oligonucleotide interactions: IV. Conformational differences between deoxy- and ribodinucleoside phosphates
    • Warshaw M.M., and Cantor C.R. Oligonucleotide interactions: IV. Conformational differences between deoxy- and ribodinucleoside phosphates Biopolymers 9 1970 1079 1103
    • (1970) Biopolymers , vol.9 , pp. 1079-1103
    • Warshaw, M.M.1    Cantor, C.R.2
  • 92
    • 0024290403 scopus 로고
    • Influence of dangling thymidine residues on the stability and structure of two DNA duplexes
    • Senior M., Jones R.A., and Breslauer K.J. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes Biochemistry 27 1988 3879 3885
    • (1988) Biochemistry , vol.27 , pp. 3879-3885
    • Senior, M.1    Jones, R.A.2    Breslauer, K.J.3
  • 93
    • 0022474733 scopus 로고
    • The enfolding arms of EcoRI endonuclease: Role in DNA binding and cleavage
    • Jen-Jacobson L., Lesser D., and Kurpiewski M. The enfolding arms of EcoRI endonuclease: role in DNA binding and cleavage Cell 45 1986 619 629
    • (1986) Cell , vol.45 , pp. 619-629
    • Jen-Jacobson, L.1    Lesser, D.2    Kurpiewski, M.3
  • 94
    • 0025203657 scopus 로고
    • The energetic basis of specificity in the EcoRI endonuclease-DNA interaction
    • Lesser D.R., Kurpiewski M.R., and Jen-Jacobson L. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction Science 250 1990 776 786
    • (1990) Science , vol.250 , pp. 776-786
    • Lesser, D.R.1    Kurpiewski, M.R.2    Jen-Jacobson, L.3
  • 96
    • 0014945567 scopus 로고
    • The lac repressor-operator interaction: 3. Kinetic studies
    • Riggs A.D., Bourgeois S., and Cohn M. The lac repressor-operator interaction: 3. Kinetic studies J. Mol. Biol. 53 1970 401 417
    • (1970) J. Mol. Biol. , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeois, S.2    Cohn, M.3
  • 97
    • 0029053412 scopus 로고
    • Interpreting complex binding kinetics from optical biosensors: A comparison of analysis by linearization, the integrated rate equation and numerical integration
    • Morton T.A., Myszka D.G., and Chaiken I.M. Interpreting complex binding kinetics from optical biosensors: a comparison of analysis by linearization, the integrated rate equation and numerical integration Anal. Biochem. 227 1995 176 185
    • (1995) Anal. Biochem. , vol.227 , pp. 176-185
    • Morton, T.A.1    Myszka, D.G.2    Chaiken, I.M.3
  • 100
    • 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., and Ferguson D.M. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5    Ferguson, D.M.6
  • 101
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 102
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Rykeart J.P., Ciccotti G., and Brenderson H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Rykeart, J.P.1    Ciccotti, G.2    Brenderson, H.J.C.3
  • 105
    • 0029737547 scopus 로고    scopus 로고
    • Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5′ end of oligonucleotides: Multiple conformers of single-stranded and double-stranded dye-DNA complexes
    • Vamosi G., Gohlke C., and Clegg R.M. Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5′ end of oligonucleotides: multiple conformers of single-stranded and double-stranded dye-DNA complexes Biophys. J. 71 1996 972 994
    • (1996) Biophys. J. , vol.71 , pp. 972-994
    • Vamosi, G.1    Gohlke, C.2    Clegg, R.M.3
  • 106
    • 0033554438 scopus 로고    scopus 로고
    • DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer
    • Lorenz M., Hillisch A., Payet D., Buttinelli M., Travers A., and Diekmann S. DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer Biochemistry 38 1999 12150 12158
    • (1999) Biochemistry , vol.38 , pp. 12150-12158
    • Lorenz, M.1    Hillisch, A.2    Payet, D.3    Buttinelli, M.4    Travers, A.5    Diekmann, S.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.