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Volumn 7, Issue , 2007, Pages

Energetics of the protein-DNA-water interaction

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA; DNA BASE; DNA BINDING PROTEIN; HYDROGEN; NUCLEOTIDE; OCTANOL; PROTEIN; WATER;

EID: 33846894984     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-7-4     Document Type: Article
Times cited : (56)

References (132)
  • 1
    • 0026686973 scopus 로고
    • DNA curving and bending in protein-DNA recognition
    • 10.1111/j.1365. 1333034
    • DNA curving and bending in protein-DNA recognition. RE Harrington, Mol Microbiol 1992 6 2549 2555 10.1111/j.1365-2958.1992.tb01431.x 1333034
    • (1992) Mol Microbiol , vol.6 , pp. 2549-2555
    • Harrington, R.E.1
  • 2
    • 0024294636 scopus 로고
    • Protein-DNA interaction. No code for recognition
    • 10.1038/335294a0. 3419498
    • Protein-DNA interaction. No code for recognition. BW Matthews, Nature 1988 335 294 295 10.1038/335294a0 3419498
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.W.1
  • 3
    • 0027328347 scopus 로고
    • Protein-DNA complexes: The cost of recognition
    • 8356038. 10.1073/pnas.90.16.7429
    • Protein-DNA complexes: the cost of recognition. DE Draper, Proc Natl Acad Sci U S A 1993 90 7429 7430 8356038 10.1073/pnas.90.16.7429
    • (1993) Proc Natl Acad Sci U S a , vol.90 , pp. 7429-7430
    • Draper, D.E.1
  • 4
    • 0021196998 scopus 로고
    • Protein-DNA recognition
    • 10.1146/annurev.bi.53.070184.001453. 6236744
    • Protein-DNA recognition. CO Pabo RT Sauer, Annu Rev Biochem 1984 53 293 321 10.1146/annurev.bi.53.070184.001453 6236744
    • (1984) Annu Rev Biochem , vol.53 , pp. 293-321
    • Pabo, C.O.1    Sauer, R.T.2
  • 5
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • 9580679. 10.1093/nar/26.10.2306
    • Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Y Mandel-Gutfreund H Margalit, Nucleic Acids Res 1998 26 2306 2312 9580679 10.1093/nar/26.10.2306
    • (1998) Nucleic Acids Res , vol.26 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 6
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • 10.1006/jmbi.2000.3918. 10966773
    • Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? CO Pabo L Nekludova, J Mol Biol 2000 301 597 624 10.1006/jmbi.2000.3918 10966773
    • (2000) J Mol Biol , vol.301 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 7
    • 0036013781 scopus 로고    scopus 로고
    • Is there a code for protein-DNA recognition? Probab(ilistical)ly
    • 10.1002/bies.10073. 12001270
    • Is there a code for protein-DNA recognition? Probab(ilistical)ly. PV Benos AS Lapedes GD Stormo, Bioessays 2002 24 466 475 10.1002/bies.10073 12001270
    • (2002) Bioessays , vol.24 , pp. 466-475
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 8
    • 0024284648 scopus 로고
    • Structure of the lambda complex at 2.5 a resolution: Details of the repressor-operator interactions
    • 10.1126/science.3187530. 3187530
    • Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. SR Jordan CO Pabo, Science 1988 242 893 899 10.1126/science.3187530 3187530
    • (1988) Science , vol.242 , pp. 893-899
    • Jordan, S.R.1    Pabo, C.O.2
  • 9
    • 0025009802 scopus 로고
    • Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex
    • 2146682. 10.1073/pnas.87.20.8165
    • Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. RG Brennan SL Roderick Y Takeda BW Matthews, Proc Natl Acad Sci U S A 1990 87 8165 8169 2146682 10.1073/pnas.87.20.8165
    • (1990) Proc Natl Acad Sci U S a , vol.87 , pp. 8165-8169
    • Brennan, R.G.1    Roderick, S.L.2    Takeda, Y.3    Matthews, B.W.4
  • 10
    • 0025914242 scopus 로고
    • Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
    • 10.1126/science.1653449. 1653449
    • Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. SC Schultz GC Shields TA Steitz, Science 1991 253 1001 1007 10.1126/science. 1653449 1653449
    • (1991) Science , vol.253 , pp. 1001-1007
    • Schultz, S.C.1    Shields, G.C.2    Steitz, T.A.3
  • 11
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • 10.1006/jmbi.1995.0559. 7563096
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. Y Mandel-Gutfreund O Schueler H Margalit, J Mol Biol 1995 253 370 382 10.1006/jmbi.1995.0559 7563096
    • (1995) J Mol Biol , vol.253 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 12
    • 0026682657 scopus 로고
    • Transcription factors: Structural families and principles of DNA recognition
    • 10.1146/annurev.bi.61.070192.005201. 1497306
    • Transcription factors: structural families and principles of DNA recognition. CO Pabo RT Sauer, Annu Rev Biochem 1992 61 1053 1095 10.1146/annurev.bi.61.070192.005201 1497306
    • (1992) Annu Rev Biochem , vol.61 , pp. 1053-1095
    • Pabo, C.O.1    Sauer, R.T.2
  • 13
    • 0033526040 scopus 로고    scopus 로고
    • The role of DNA-protein salt bridges in molecular recognition: A model study
    • 10.1002/(SICI)1097-0282(19990405)49:4<313::AID-BIP6>3.0.CO;2. 10079770
    • The role of DNA-protein salt bridges in molecular recognition: a model study. R Gurlie TH Duong K Zakrzewska, Biopolymers 1999 49 313 327 10.1002/(SICI)1097-0282(19990405)49:4<313::AID-BIP6>3.0.CO;2-0 10079770
    • (1999) Biopolymers , vol.49-50 , pp. 313-327
    • Gurlie, R.1    Duong, T.H.2    Zakrzewska, K.3
  • 14
    • 0034049693 scopus 로고    scopus 로고
    • Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition
    • 10.1046/j.1365. 10886361
    • Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition. M Oda H Nakamura, Genes Cells 2000 5 319 326 10.1046/j.1365-2443.2000.00335.x 10886361
    • (2000) Genes Cells , vol.5 , pp. 319-326
    • Oda, M.1    Nakamura, H.2
  • 15
    • 0031047683 scopus 로고    scopus 로고
    • The role of water in protein-DNA interactions
    • 10.1016/S0959-440X(97)80016. 9032063
    • The role of water in protein-DNA interactions. JW Schwabe, Curr Opin Struct Biol 1997 7 126 134 10.1016/S0959-440X(97)80016-4 9032063
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 126-134
    • Schwabe, J.W.1
  • 16
    • 3042596869 scopus 로고    scopus 로고
    • The role of water in protein-DNA recognition
    • 10.1146/annurev.biophys.33.110502.140414. 15139817
    • The role of water in protein-DNA recognition. B Jayaram T Jain, Annu Rev Biophys Biomol Struct 2004 33 343 361 10.1146/annurev.biophys.33.110502.140414 15139817
    • (2004) Annu Rev Biophys Biomol Struct , vol.33 , pp. 343-361
    • Jayaram, B.1    Jain, T.2
  • 17
    • 0035965868 scopus 로고    scopus 로고
    • Heat does not come in different colours: Entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions
    • 10.1016/S0301-4622(01)00222. 11804727
    • Heat does not come in different colours: entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions. A Cooper CM Johnson JH Lakey M Nollmann, Biophys Chem 2001 93 215 230 10.1016/S0301-4622(01)00222-8 11804727
    • (2001) Biophys Chem , vol.93 , pp. 215-230
    • Cooper, A.1    Johnson, C.M.2    Lakey, J.H.3    Nollmann, M.4
  • 18
    • 14744268745 scopus 로고    scopus 로고
    • Heat capacity effects in protein folding and ligand binding: A re-evaluation of the role of water in biomolecular thermodynamics
    • 10.1016/j.bpc.2004.12.011. 15752588
    • Heat capacity effects in protein folding and ligand binding: a re-evaluation of the role of water in biomolecular thermodynamics. A Cooper, Biophys Chem 2005 115 89 97 10.1016/j.bpc.2004.12.011 15752588
    • (2005) Biophys Chem , vol.115 , pp. 89-97
    • Cooper, A.1
  • 19
    • 0029130871 scopus 로고
    • Macromolecules and water: Probing with osmotic stress
    • 8538466
    • Macromolecules and water: probing with osmotic stress. VA Parsegian RP Rand DC Rau, Methods Enzymol 1995 259 43 94 8538466
    • (1995) Methods Enzymol , vol.259 , pp. 43-94
    • Parsegian, V.A.1    Rand, R.P.2    Rau, D.C.3
  • 20
    • 0028961741 scopus 로고
    • Water release associated with specific binding of gal repressor
    • 7720716
    • Water release associated with specific binding of gal repressor. MM Garner DC Rau, Embo J 1995 14 1257 1263 7720716
    • (1995) Embo J , vol.14 , pp. 1257-1263
    • Garner, M.M.1    Rau, D.C.2
  • 21
    • 0035919819 scopus 로고    scopus 로고
    • Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: Separating their roles in specific and non-specific binding
    • 10.1006/jmbi.2001.4781. 11453689
    • Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding. NY Sidorova DC Rau, J Mol Biol 2001 310 801 816 10.1006/jmbi.2001.4781 11453689
    • (2001) J Mol Biol , vol.310 , pp. 801-816
    • Sidorova, N.Y.1    Rau, D.C.2
  • 22
    • 0028360796 scopus 로고
    • Macromolecular crowding and confinement in cells exposed to hypertonicity
    • 8178962
    • Macromolecular crowding and confinement in cells exposed to hypertonicity. MM Garner MB Burg, Am J Physiol 1994 266 C877 892 8178962
    • (1994) Am J Physiol , vol.266 , pp. 877-892
    • Garner, M.M.1    Burg, M.B.2
  • 23
    • 0032311227 scopus 로고    scopus 로고
    • Molecular crowding: Analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion
    • 9750217
    • Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. AP Minton, Methods Enzymol 1998 295 127 149 9750217
    • (1998) Methods Enzymol , vol.295 , pp. 127-149
    • Minton, A.P.1
  • 24
    • 0029995486 scopus 로고    scopus 로고
    • Protein function in the crystal
    • 10.1146/annurev.bb.25.060196.002015. 8800474
    • Protein function in the crystal. A Mozzarelli GL Rossi, Annu Rev Biophys Biomol Struct 1996 25 343 365 10.1146/annurev.bb.25.060196.002015 8800474
    • (1996) Annu Rev Biophys Biomol Struct , vol.25 , pp. 343-365
    • Mozzarelli, A.1    Rossi, G.L.2
  • 25
    • 0002802966 scopus 로고    scopus 로고
    • Functional properties of immobilized proteins
    • Tokio, Gordon and Breach Science Publishers Nalwa HS
    • Functional properties of immobilized proteins. A Mozzarelli S Bettati, Advanced Functional Molecules and Polymers Volume 4 Tokio, Gordon and Breach Science Publishers, Nalwa HS, 2001 4 55 97
    • (2001) Advanced Functional Molecules and Polymers Volume 4 , vol.4 , pp. 55-97
    • Mozzarelli, A.1    Bettati, S.2
  • 26
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • 10.1007/BF00126743. 7964925
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. HJ Bohm, J Comput Aided Mol Des 1994 8 243 256 10.1007/BF00126743 7964925
    • (1994) J Comput Aided Mol des , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 27
    • 0001382020 scopus 로고    scopus 로고
    • Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
    • 10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0.CO;2
    • Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Aqvist, J Comput Chem 1996 17 1587 1597 10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0. CO;2-H
    • (1996) J Comput Chem , vol.17 , pp. 1587-1597
    • Aqvist, J.1
  • 28
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. the development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • 10.1023/A:1007996124545. 9385547
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. MD Eldridge CW Murray TR Auton GV Paolini RP Mee, J Comput Aided Mol Des 1997 11 425 445 10.1023/A:1007996124545 9385547
    • (1997) J Comput Aided Mol des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 29
    • 0037030649 scopus 로고    scopus 로고
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water
    • 10.1021/jm0200299. 12036355
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water. P Cozzini M Fornabaio A Marabotti DJ Abraham GE Kellogg A Mozzarelli, J Med Chem 2002 45 2469 2483 10.1021/jm0200299 12036355
    • (2002) J Med Chem , vol.45 , pp. 2469-2483
    • Cozzini, P.1    Fornabaio, M.2    Marabotti, A.3    Abraham, D.J.4    Kellogg, G.E.5    Mozzarelli, A.6
  • 30
    • 0025203657 scopus 로고
    • The energetic basis of specificity in the Eco RI endonuclease - DNA interaction
    • 10.1126/science.2237428. 2237428
    • The energetic basis of specificity in the Eco RI endonuclease - DNA interaction. DR Lesser MR Kurpiewski L Jen-Jacobson, Science 1990 250 776 786 10.1126/science.2237428 2237428
    • (1990) Science , vol.250 , pp. 776-786
    • Lesser, D.R.1    Kurpiewski, M.R.2    Jen-Jacobson, L.3
  • 31
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • 10.1016/S0022-2836(02)00917. 12419259
    • Probabilistic code for DNA recognition by proteins of the EGR family. PV Benos AS Lapedes GD Stormo, J Mol Biol 2002 323 701 727 10.1016/S0022-2836(02) 00917-8 12419259
    • (2002) J Mol Biol , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 32
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • 10.1016/S0022-2836(02)00571. 12126620
    • Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. NM Luscombe JM Thornton, J Mol Biol 2002 320 991 1009 10.1016/S0022-2836(02)00571-5 12126620
    • (2002) J Mol Biol , vol.320 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 33
    • 0033574510 scopus 로고    scopus 로고
    • Protein-DNA interactions: A structural analysis
    • 10.1006/jmbi.1999.2659. 10222198
    • Protein-DNA interactions: A structural analysis. S Jones P van Heyningen HM Berman JM Thornton, J Mol Biol 1999 287 877 896 10.1006/jmbi.1999.2659 10222198
    • (1999) J Mol Biol , vol.287 , pp. 877-896
    • Jones, S.1    Van Heyningen, P.2    Berman, H.M.3    Thornton, J.M.4
  • 34
    • 0031042082 scopus 로고    scopus 로고
    • Physical basis of a protein-DNA recognition code
    • 10.1016/S0959-440X(97)80015. 9032060
    • Physical basis of a protein-DNA recognition code. Y Choo A Klug, Curr Opin Struct Biol 1997 7 117 125 10.1016/S0959-440X(97)80015-2 9032060
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 117-125
    • Choo, Y.1    Klug, A.2
  • 35
    • 0141954199 scopus 로고    scopus 로고
    • Energetics of sequence-specific protein-DNA association: Computational analysis of integrase Tn916 binding to its target DNA
    • 10.1021/bi026937p. 14529266
    • Energetics of sequence-specific protein-DNA association: computational analysis of integrase Tn916 binding to its target DNA. AA Gorfe I Jelesarov, Biochemistry 2003 42 11568 11576 10.1021/bi026937p 14529266
    • (2003) Biochemistry , vol.42 , pp. 11568-11576
    • Gorfe, A.A.1    Jelesarov, I.2
  • 36
    • 0001101548 scopus 로고    scopus 로고
    • Free Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease-DNA Complex
    • 10.1006/jcph.1998.6173
    • Free Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease-DNA Complex. B Jayaram KJ McConnell SB Dixit DL Beveridge, J Comput Phys 1999 151 333 357 10.1006/jcph.1998.6173
    • (1999) J Comput Phys , vol.151 , pp. 333-357
    • Jayaram, B.1    McConnell, K.J.2    Dixit, S.B.3    Beveridge, D.L.4
  • 37
    • 0037079572 scopus 로고    scopus 로고
    • Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level
    • 10.1002/jcc.10009. 11913374
    • Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. B Jayaram K McConnell SB Dixit A Das DL Beveridge, J Comput Chem 2002 23 1 14 10.1002/jcc.10009 11913374
    • (2002) J Comput Chem , vol.23 , pp. 1-14
    • Jayaram, B.1    McConnell, K.2    Dixit, S.B.3    Das, A.4    Beveridge, D.L.5
  • 38
    • 0019456340 scopus 로고
    • Structure of the cro repressor from bacteriophage lambda and its interaction with DNA
    • 10.1038/290754a0. 6452580
    • Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. WF Anderson DH Ohlendorf Y Takeda BW Matthews, Nature 1981 290 754 758 10.1038/290754a0 6452580
    • (1981) Nature , vol.290 , pp. 754-758
    • Anderson, W.F.1    Ohlendorf, D.H.2    Takeda, Y.3    Matthews, B.W.4
  • 39
    • 0343517556 scopus 로고    scopus 로고
    • Hydrophobicity: Is LogP(o/w) more than the sum of its parts?
    • 10.1016/S0223-5234(00)00167. 10960181
    • Hydrophobicity: is LogP(o/w) more than the sum of its parts? GE Kellogg DJ Abraham, Eur J Med Chem 2000 35 651 661 10.1016/S0223-5234(00)00167-7 10960181
    • (2000) Eur J Med Chem , vol.35 , pp. 651-661
    • Kellogg, G.E.1    Abraham, D.J.2
  • 41
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • 8995351
    • Additivity principles in biochemistry. KA Dill, J Biol Chem 1997 272 701 704 8995351
    • (1997) J Biol Chem , vol.272 , pp. 701-704
    • Dill, K.A.1
  • 42
    • 0141923634 scopus 로고    scopus 로고
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 2. Computational titration and pH effects in molecular models of neuraminidase-inhibitor complexes
    • 10.1021/jm0302593. 14521411
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 2. Computational titration and pH effects in molecular models of neuraminidase-inhibitor complexes. M Fornabaio P Cozzini A Mozzarelli DJ Abraham GE Kellogg, J Med Chem 2003 46 4487 4500 10.1021/jm0302593 14521411
    • (2003) J Med Chem , vol.46 , pp. 4487-4500
    • Fornabaio, M.1    Cozzini, P.2    Mozzarelli, A.3    Abraham, D.J.4    Kellogg, G.E.5
  • 43
    • 4143081344 scopus 로고    scopus 로고
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. the free energy contribution of structural water molecules in HIV-1 protease complexes
    • 10.1021/jm030596b. 15317462
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes. M Fornabaio F Spyrakis A Mozzarelli P Cozzini DJ Abraham GE Kellogg, J Med Chem 2004 47 4507 4516 10.1021/jm030596b 15317462
    • (2004) J Med Chem , vol.47 , pp. 4507-4516
    • Fornabaio, M.1    Spyrakis, F.2    Mozzarelli, A.3    Cozzini, P.4    Abraham, D.J.5    Kellogg, G.E.6
  • 44
    • 33645106609 scopus 로고    scopus 로고
    • Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: Predictive tools for characterizing the roles of water in biomolecules
    • 10.1016/j.jmb.2006.01.053. 16497327
    • Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules. A Amadasi F Spyrakis P Cozzini DJ Abraham GE Kellogg A Mozzarelli, J Mol Biol 2006 358 289 309 10.1016/j.jmb.2006.01.053 16497327
    • (2006) J Mol Biol , vol.358 , pp. 289-309
    • Amadasi, A.1    Spyrakis, F.2    Cozzini, P.3    Abraham, D.J.4    Kellogg, G.E.5    Mozzarelli, A.6
  • 45
    • 0034701042 scopus 로고    scopus 로고
    • Computational methodology for estimating changes in free energies of biomolecular association upon mutation. the importance of bound water in dimer-tetramer assembly for beta 37 mutant hemoglobins
    • 10.1021/bi991724u. 10677211
    • Computational methodology for estimating changes in free energies of biomolecular association upon mutation. The importance of bound water in dimer-tetramer assembly for beta 37 mutant hemoglobins. JC Burnett GE Kellogg DJ Abraham, Biochemistry 2000 39 1622 1633 10.1021/bi991724u 10677211
    • (2000) Biochemistry , vol.39 , pp. 1622-1633
    • Burnett, J.C.1    Kellogg, G.E.2    Abraham, D.J.3
  • 46
    • 0035866237 scopus 로고    scopus 로고
    • Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: Systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins
    • 10.1002/1097-0134(20010215)42:3<355::AID-PROT60>3.0.CO;2. 11151007
    • Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins. JC Burnett P Botti DJ Abraham GE Kellogg, Proteins 2001 42 355 377 10.1002/1097-0134(20010215)42:3<355::AID-PROT60>3.0.CO;2-F 11151007
    • (2001) Proteins , vol.42 , pp. 355-377
    • Burnett, J.C.1    Botti, P.2    Abraham, D.J.3    Kellogg, G.E.4
  • 47
    • 0032531740 scopus 로고    scopus 로고
    • Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides
    • 9753742. 10.1093/nar/26.20.4721
    • Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides. GE Kellogg JN Scarsdale FA Fornari Jr., Nucleic Acids Res 1998 26 4721 4732 9753742 10.1093/nar/26.20.4721
    • (1998) Nucleic Acids Res , vol.26 , pp. 4721-4732
    • Kellogg, G.E.1    Scarsdale, J.N.2    Fornari Jr., F.A.3
  • 48
    • 0043163784 scopus 로고    scopus 로고
    • Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA
    • 12888500. 10.1093/nar/gkg645
    • Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA. DJ Cashman JN Scarsdale GE Kellogg, Nucleic Acids Res 2003 31 4410 4416 12888500 10.1093/nar/gkg645
    • (2003) Nucleic Acids Res , vol.31 , pp. 4410-4416
    • Cashman, D.J.1    Scarsdale, J.N.2    Kellogg, G.E.3
  • 49
    • 1542358019 scopus 로고    scopus 로고
    • A computational model for anthracycline binding to DNA: Tuning groove-binding intercalators for specific sequences
    • 10.1021/jm030529h. 14998326
    • A computational model for anthracycline binding to DNA: tuning groove-binding intercalators for specific sequences. DJ Cashman GE Kellogg, J Med Chem 2004 47 1360 1374 10.1021/jm030529h 14998326
    • (2004) J Med Chem , vol.47 , pp. 1360-1374
    • Cashman, D.J.1    Kellogg, G.E.2
  • 50
    • 0033572790 scopus 로고    scopus 로고
    • Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition
    • 10.1016/S0969-2126(00)88333. 10647173
    • Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. J Janin, Structure 1999 7 R277 279 10.1016/S0969- 2126(00)88333-1 10647173
    • (1999) Structure , vol.7 , pp. 277-279
    • Janin, J.1
  • 51
    • 0035976713 scopus 로고    scopus 로고
    • Do water molecules mediate protein-DNA recognition?
    • 10.1006/jmbi.2001.5154. 11846571
    • Do water molecules mediate protein-DNA recognition? CK Reddy A Das B Jayaram, J Mol Biol 2001 314 619 632 10.1006/jmbi.2001.5154 11846571
    • (2001) J Mol Biol , vol.314 , pp. 619-632
    • Reddy, C.K.1    Das, A.2    Jayaram, B.3
  • 52
    • 0042868638 scopus 로고    scopus 로고
    • Role of water mediated interactions in protein-protein recognition landscapes
    • 10.1021/ja034729u. 15369374
    • Role of water mediated interactions in protein-protein recognition landscapes. GA Papoian J Ulander PG Wolynes, J Am Chem Soc 2003 125 9170 9178 10.1021/ja034729u 15369374
    • (2003) J Am Chem Soc , vol.125 , pp. 9170-9178
    • Papoian, G.A.1    Ulander, J.2    Wolynes, P.G.3
  • 53
    • 33646165863 scopus 로고    scopus 로고
    • Determination of the interfacial water content in protein-protein complexes from free energy simulations
    • 10.1529/biophysj.105.065524. 16284258
    • Determination of the interfacial water content in protein-protein complexes from free energy simulations. P Monecke T Borosch J Brickmann SM Kast, Biophys J 2006 90 841 850 10.1529/biophysj.105.065524 16284258
    • (2006) Biophys J , vol.90 , pp. 841-850
    • Monecke, P.1    Borosch, T.2    Brickmann, J.3    Kast, S.M.4
  • 54
    • 4143121554 scopus 로고    scopus 로고
    • Free energy of ligand binding to protein: Evaluation of the contribution of water molecules by computational methods
    • 15579003
    • Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods. P Cozzini M Fornabaio A Marabotti DJ Abraham GE Kellogg A Mozzarelli, Curr Med Chem 2004 11 3093 3118 15579003
    • (2004) Curr Med Chem , vol.11 , pp. 3093-3118
    • Cozzini, P.1    Fornabaio, M.2    Marabotti, A.3    Abraham, D.J.4    Kellogg, G.E.5    Mozzarelli, A.6
  • 55
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • 10.1021/jm00145a002. 3892003
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. PJ Goodford, J Med Chem 1985 28 849 857 10.1021/jm00145a002 3892003
    • (1985) J Med Chem , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 56
    • 0034738021 scopus 로고    scopus 로고
    • Heat capacity of hydrogen-bonded networks: An alternative view of protein folding thermodynamics
    • 10.1016/S0301-4622(00)00136. 10885396
    • Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics. A Cooper, Biophys Chem 2000 85 25 39 10.1016/S0301-4622(00)00136-8 10885396
    • (2000) Biophys Chem , vol.85 , pp. 25-39
    • Cooper, A.1
  • 57
    • 0031755274 scopus 로고    scopus 로고
    • Hydration of the phosphate group in double-helical DNA
    • 9788937
    • Hydration of the phosphate group in double-helical DNA. B Schneider K Patel HM Berman, Biophys J 1998 75 2422 2434 9788937
    • (1998) Biophys J , vol.75 , pp. 2422-2434
    • Schneider, B.1    Patel, K.2    Berman, H.M.3
  • 59
    • 84872271006 scopus 로고    scopus 로고
    • , [http://ndbserver.rutgers.edu]
    • The Nucleic Acid Database., [http://ndbserver.rutgers.edu]
    • The Nucleic Acid Database
  • 60
    • 22144451813 scopus 로고    scopus 로고
    • A computational tool to optimize ligand selectivity between two similar biomacromolecular targets
    • 10.1007/s10822-005-1485. 16075302
    • A computational tool to optimize ligand selectivity between two similar biomacromolecular targets. DL Chen GE Kellogg, J Comput Aided Mol Des 2005 19 69 82 10.1007/s10822-005-1485-7 16075302
    • (2005) J Comput Aided Mol des , vol.19 , pp. 69-82
    • Chen, D.L.1    Kellogg, G.E.2
  • 61
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • 11433033. 10.1093/nar/29.13.2860
    • Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. NM Luscombe RA Laskowski JM Thornton, Nucleic Acids Res 2001 29 2860 2874 11433033 10.1093/nar/29.13.2860
    • (2001) Nucleic Acids Res , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 62
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • 15178741. 10.1093/nar/gkh624
    • How do site-specific DNA-binding proteins find their targets? SE Halford JF Marko, Nucleic Acids Res 2004 32 3040 3052 15178741 10.1093/nar/gkh624
    • (2004) Nucleic Acids Res , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 63
    • 3142657230 scopus 로고    scopus 로고
    • Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
    • 10.1126/science.1097064. 15256668
    • Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. CG Kalodimos N Biris AM Bonvin MM Levandoski M Guennuegues R Boelens R Kaptein, Science 2004 305 386 389 10.1126/science. 1097064 15256668
    • (2004) Science , vol.305 , pp. 386-389
    • Kalodimos, C.G.1    Biris, N.2    Bonvin, A.M.3    Levandoski, M.M.4    Guennuegues, M.5    Boelens, R.6    Kaptein, R.7
  • 64
    • 26444598454 scopus 로고    scopus 로고
    • Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
    • 10.1002/prot.20607. 16121397
    • Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. D Lejeune N Delsaux B Charloteaux A Thomas R Brasseur, Proteins 2005 61 258 271 10.1002/prot.20607 16121397
    • (2005) Proteins , vol.61 , pp. 258-271
    • Lejeune, D.1    Delsaux, N.2    Charloteaux, B.3    Thomas, A.4    Brasseur, R.5
  • 65
    • 0030736323 scopus 로고    scopus 로고
    • Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
    • 10.1002/(SICI)1097-0282(1997)44:2<153::AID-BIP4>3.0.CO;2. 9354759
    • Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. L Jen-Jacobson, Biopolymers 1997 44 153 180 10.1002/(SICI)1097-0282(1997)44:2<153::AID-BIP4>3.0.CO;2-U 9354759
    • (1997) Biopolymers , vol.44 , pp. 153-180
    • Jen-Jacobson, L.1
  • 66
    • 0024378717 scopus 로고
    • Role of the hydrophobic effect in stability of site-specific protein-DNA complexes
    • 10.1016/0022-2836(89)90608. 2585510
    • Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. JH Ha RS Spolar MT Record Jr., J Mol Biol 1989 209 801 816 10.1016/0022-2836(89)90608-6 2585510
    • (1989) J Mol Biol , vol.209 , pp. 801-816
    • Ha, J.H.1    Spolar, R.S.2    Record Jr., M.T.3
  • 67
    • 0032489503 scopus 로고    scopus 로고
    • Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus
    • 10.1006/jmbi.1997.1558. 9500918
    • Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus. T Lundback H Hansson S Knapp R Ladenstein T Hard, J Mol Biol 1998 276 775 786 10.1006/jmbi.1997.1558 9500918
    • (1998) J Mol Biol , vol.276 , pp. 775-786
    • Lundback, T.1    Hansson, H.2    Knapp, S.3    Ladenstein, R.4    Hard, T.5
  • 68
    • 0037378942 scopus 로고    scopus 로고
    • Energetics of sequence-specific protein-DNA association: Binding of integrase Tn916 to its target DNA
    • 10.1021/bi0269355. 12653552
    • Energetics of sequence-specific protein-DNA association: binding of integrase Tn916 to its target DNA. S Milev AA Gorfe A Karshikoff RT Clubb HR Bosshard I Jelesarov, Biochemistry 2003 42 3481 3491 10.1021/bi0269355 12653552
    • (2003) Biochemistry , vol.42 , pp. 3481-3491
    • Milev, S.1    Gorfe, A.A.2    Karshikoff, A.3    Clubb, R.T.4    Bosshard, H.R.5    Jelesarov, I.6
  • 69
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • 10.1126/science.8303294. 8303294
    • Coupling of local folding to site-specific binding of proteins to DNA. RS Spolar MT Record Jr., Science 1994 263 777 784 10.1126/science.8303294 8303294
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record Jr., M.T.2
  • 70
    • 0000410374 scopus 로고    scopus 로고
    • Thermodynamics of the DNA binding reaction of transcription factor MASH-1
    • 10.1021/bi9725374. 9521744
    • Thermodynamics of the DNA binding reaction of transcription factor MASH-1. AGE Künne M Sieber D Meierhans RK Allemann, Biochemistry 1998 37 4217 4223 10.1021/bi9725374 9521744
    • (1998) Biochemistry , vol.37 , pp. 4217-4223
    • Künne, A.G.E.1    Sieber, M.2    Meierhans, D.3    Allemann, R.K.4
  • 71
    • 0033153360 scopus 로고    scopus 로고
    • Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates
    • 10.1021/bi990309z. 10353851
    • Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates. AG Kozlov TM Lohman, Biochemistry 1999 38 7388 7397 10.1021/bi990309z 10353851
    • (1999) Biochemistry , vol.38 , pp. 7388-7397
    • Kozlov, A.G.1    Lohman, T.M.2
  • 72
    • 33645971001 scopus 로고    scopus 로고
    • Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA
    • 10.1021/bi052543x. 16618108
    • Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA. AG Kozlov TM Lohman, Biochemistry 2006 45 5190 5205 10.1021/bi052543x 16618108
    • (2006) Biochemistry , vol.45 , pp. 5190-5205
    • Kozlov, A.G.1    Lohman, T.M.2
  • 73
    • 0031670461 scopus 로고    scopus 로고
    • Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride
    • 10.1002/(SICI)1097-0134(19981101)33:2<159::AID-PROT2>3.0.CO;2. 9779785
    • Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. H Fukada K Takahashi, Proteins 1998 33 159 166 10.1002/(SICI)1097-0134(19981101)33:2<159::AID-PROT2>3.0. CO;2-E 9779785
    • (1998) Proteins , vol.33 , pp. 159-166
    • Fukada, H.1    Takahashi, K.2
  • 74
    • 0032570633 scopus 로고    scopus 로고
    • Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain
    • 10.1006/jmbi.1997.1564. 9551098
    • Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. M Oda K Furukawa K Ogata A Sarai H Nakamura, J Mol Biol 1998 276 571 590 10.1006/jmbi.1997.1564 9551098
    • (1998) J Mol Biol , vol.276 , pp. 571-590
    • Oda, M.1    Furukawa, K.2    Ogata, K.3    Sarai, A.4    Nakamura, H.5
  • 75
    • 84872275281 scopus 로고    scopus 로고
    • , [http://www.tripos.com]
    • Tripos Inc., [http://www.tripos.com]
    • Tripos Inc.
  • 76
    • 84872275513 scopus 로고    scopus 로고
    • , [http://www.edusoft-lc.com]
    • eduSoft, LC., [http://www.edusoft-lc.com]
    • EduSoft, LC
  • 77
    • 0001126839 scopus 로고
    • New tools for modeling and understanding hydrophobicity and hydrophobic interactions
    • New tools for modeling and understanding hydrophobicity and hydrophobic interactions. GE Kellogg GS Joshi DJ Abraham, Med Chem Res 1992 1 444 453
    • (1992) Med Chem Res , vol.1 , pp. 444-453
    • Kellogg, G.E.1    Joshi, G.S.2    Abraham, D.J.3
  • 78
    • 31144439130 scopus 로고    scopus 로고
    • Paramyxovirus receptor-binding molecules: Engagement of one site on the hemagglutinin-neuraminidase protein modulates activity at the second site
    • 16414997. 10.1128/JVI.80.3.1204
    • Paramyxovirus receptor-binding molecules: engagement of one site on the hemagglutinin-neuraminidase protein modulates activity at the second site. M Porotto M Fornabaio O Greengard MT Murrell GE Kellogg A Moscona, J Virol 2006 80 1204 1213 16414997 10.1128/JVI.80.3.1204-1213.2006
    • (2006) J Virol , vol.80 , pp. 1204-1213
    • Porotto, M.1    Fornabaio, M.2    Greengard, O.3    Murrell, M.T.4    Kellogg, G.E.5    Moscona, A.6
  • 79
    • 0030723630 scopus 로고    scopus 로고
    • Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 a resolution
    • 9384586. 10.1093/emboj/16.23.7078
    • Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution. P Cramer CJ Larson GL Verdine CW Muller, Embo J 1997 16 7078 7090 9384586 10.1093/emboj/16.23.7078
    • (1997) Embo J , vol.16 , pp. 7078-7090
    • Cramer, P.1    Larson, C.J.2    Verdine, G.L.3    Muller, C.W.4
  • 80
    • 0030587774 scopus 로고    scopus 로고
    • Zif268 protein-DNA complex refined at 1.6 A: A model system for understanding zinc finger-DNA interactions
    • 10.1016/S0969-2126(96)00125. 8939742
    • Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. M Elrod-Erickson MA Rould L Nekludova CO Pabo, Structure 1996 4 1171 1180 10.1016/S0969-2126(96)00125-6 8939742
    • (1996) Structure , vol.4 , pp. 1171-1180
    • Elrod-Erickson, M.1    Rould, M.A.2    Nekludova, L.3    Pabo, C.O.4
  • 81
  • 82
    • 0032169864 scopus 로고    scopus 로고
    • A novel DNA-binding motif in MarA: The first structure for an AraC family transcriptional activator
    • 9724717. 10.1073/pnas.95.18.10413
    • A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. S Rhee RG Martin JL Rosner DR Davies, Proc Natl Acad Sci U S A 1998 95 10413 10418 9724717 10.1073/pnas.95.18.10413
    • (1998) Proc Natl Acad Sci U S a , vol.95 , pp. 10413-10418
    • Rhee, S.1    Martin, R.G.2    Rosner, J.L.3    Davies, D.R.4
  • 84
    • 0034602843 scopus 로고    scopus 로고
    • Structural basis of preinitiation complex assembly on human pol II promoters
    • 10619841. 10.1093/emboj/19.1.25
    • Structural basis of preinitiation complex assembly on human pol II promoters. FT Tsai PB Sigler, Embo J 2000 19 25 36 10619841 10.1093/emboj/19.1. 25
    • (2000) Embo J , vol.19 , pp. 25-36
    • Tsai, F.T.1    Sigler, P.B.2
  • 85
    • 0033529089 scopus 로고    scopus 로고
    • Structural basis for initiation of transcription from an RNA polymerase-promoter complex
    • 10.1038/19999. 10331394
    • Structural basis for initiation of transcription from an RNA polymerase-promoter complex. GM Cheetham D Jeruzalmi TA Steitz, Nature 1999 399 80 83 10.1038/19999 10331394
    • (1999) Nature , vol.399 , pp. 80-83
    • Cheetham, G.M.1    Jeruzalmi, D.2    Steitz, T.A.3
  • 86
    • 0032964122 scopus 로고    scopus 로고
    • DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B
    • 10.1038/8276. 10331876
    • DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B. G Meinke PB Sigler, Nat Struct Biol 1999 6 471 477 10.1038/8276 10331876
    • (1999) Nat Struct Biol , vol.6 , pp. 471-477
    • Meinke, G.1    Sigler, P.B.2
  • 87
    • 0034682619 scopus 로고    scopus 로고
    • Exploring the role of glutamine 50 in the homeodomain-DNA interface: Crystal structure of engrailed (Gln50 - > ala) complex at 2.0 a
    • 10.1021/bi000071a. 10889025
    • Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 - > ala) complex at 2.0 A. RA Grant MA Rould JD Klemm CO Pabo, Biochemistry 2000 39 8187 8192 10.1021/bi000071a 10889025
    • (2000) Biochemistry , vol.39 , pp. 8187-8192
    • Grant, R.A.1    Rould, M.A.2    Klemm, J.D.3    Pabo, C.O.4
  • 88
    • 0034031280 scopus 로고    scopus 로고
    • Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA
    • 10.1038/74055. 10742173
    • Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA. Y Mo B Vaessen K Johnston R Marmorstein, Nat Struct Biol 2000 7 292 297 10.1038/74055 10742173
    • (2000) Nat Struct Biol , vol.7 , pp. 292-297
    • Mo, Y.1    Vaessen, B.2    Johnston, K.3    Marmorstein, R.4
  • 90
    • 0035066732 scopus 로고    scopus 로고
    • The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites
    • 10.1038/86181. 11276249
    • The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. BS Chevalier RJ Monnat Jr. BL Stoddard, Nat Struct Biol 2001 8 312 316 10.1038/86181 11276249
    • (2001) Nat Struct Biol , vol.8 , pp. 312-316
    • Chevalier, B.S.1    Monnat, R.J.2    Stoddard, B.L.3
  • 92
    • 0028118764 scopus 로고
    • Hin recombinase bound to DNA: The origin of specificity in major and minor groove interactions
    • 10.1126/science.8278807. 8278807
    • Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. JA Feng RC Johnson RE Dickerson, Science 1994 263 348 355 10.1126/science.8278807 8278807
    • (1994) Science , vol.263 , pp. 348-355
    • Feng, J.A.1    Johnson, R.C.2    Dickerson, R.E.3
  • 93
    • 0035898540 scopus 로고    scopus 로고
    • Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate
    • 11447104. 10.1093/emboj/20.14.3631
    • Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. P Van Roey CA Waddling KM Fox M Belfort V Derbyshire, Embo J 2001 20 3631 3637 11447104 10.1093/emboj/20.14.3631
    • (2001) Embo J , vol.20 , pp. 3631-3637
    • Van Roey, P.1    Waddling, C.A.2    Fox, K.M.3    Belfort, M.4    Derbyshire, V.5
  • 94
    • 0035834053 scopus 로고    scopus 로고
    • Crystal structure of the Msx-1 homeodomain/DNA complex
    • 10.1021/bi0108148. 11580277
    • Crystal structure of the Msx-1 homeodomain/DNA complex. S Hovde C Abate-Shen JH Geiger, Biochemistry 2001 40 12013 12021 10.1021/bi0108148 11580277
    • (2001) Biochemistry , vol.40 , pp. 12013-12021
    • Hovde, S.1    Abate-Shen, C.2    Geiger, J.H.3
  • 95
    • 0035914475 scopus 로고    scopus 로고
    • Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition
    • 10.1006/jmbi.2001.4975. 11800559
    • Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. JC Miller CO Pabo, J Mol Biol 2001 313 309 315 10.1006/jmbi.2001.4975 11800559
    • (2001) J Mol Biol , vol.313 , pp. 309-315
    • Miller, J.C.1    Pabo, C.O.2
  • 96
    • 0037083987 scopus 로고    scopus 로고
    • Testing water-mediated DNA recognition by the Hin recombinase
    • 11847127. 10.1093/emboj/21.4.801
    • Testing water-mediated DNA recognition by the Hin recombinase. TK Chiu C Sohn RE Dickerson RC Johnson, Embo J 2002 21 801 814 11847127 10.1093/emboj/21.4.801
    • (2002) Embo J , vol.21 , pp. 801-814
    • Chiu, T.K.1    Sohn, C.2    Dickerson, R.E.3    Johnson, R.C.4
  • 97
    • 0036651455 scopus 로고    scopus 로고
    • Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2
    • 10.1016/S0969-2126(02)00790. 12121651
    • Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2. A Ke JR Mathias AK Vershon C Wolberger, Structure 2002 10 961 971 10.1016/S0969-2126(02)00790-6 12121651
    • (2002) Structure , vol.10 , pp. 961-971
    • Ke, A.1    Mathias, J.R.2    Vershon, A.K.3    Wolberger, C.4
  • 98
    • 0026657433 scopus 로고
    • Refined 1.8 a crystal structure of the lambda repressor-operator complex
    • 10.1016/0022-2836(92)90690. 1387915
    • Refined 1.8 A crystal structure of the lambda repressor-operator complex. LJ Beamer CO Pabo, J Mol Biol 1992 227 177 196 10.1016/0022-2836(92)90690-L 1387915
    • (1992) J Mol Biol , vol.227 , pp. 177-196
    • Beamer, L.J.1    Pabo, C.O.2
  • 99
    • 0032483544 scopus 로고    scopus 로고
    • Crystal structure of a Smad MH1 domain bound to DNA: Insights on DNA binding in TGF-beta signaling
    • 10.1016/S0092-8674(00)81600. 9741623
    • Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling. Y Shi YF Wang L Jayaraman H Yang J Massague NP Pavletich, Cell 1998 94 585 594 10.1016/S0092-8674(00)81600-1 9741623
    • (1998) Cell , vol.94 , pp. 585-594
    • Shi, Y.1    Wang, Y.F.2    Jayaraman, L.3    Yang, H.4    Massague, J.5    Pavletich, N.P.6
  • 100
    • 0028173030 scopus 로고
    • Crystal structure of LacI member, PurR, bound to DNA: Minor groove binding by alpha helices
    • 10.1126/science.7973627. 7973627
    • Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. MA Schumacher KY Choi H Zalkin RG Brennan, Science 1994 266 763 770 10.1126/science.7973627 7973627
    • (1994) Science , vol.266 , pp. 763-770
    • Schumacher, M.A.1    Choi, K.Y.2    Zalkin, H.3    Brennan, R.G.4
  • 101
    • 0029670530 scopus 로고    scopus 로고
    • A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex
    • 10.1038/380456a0. 8602247
    • A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. R Kodandapani F Pio CZ Ni G Piccialli M Klemsz S McKercher RA Maki KR Ely, Nature 1996 380 456 460 10.1038/380456a0 8602247
    • (1996) Nature , vol.380 , pp. 456-460
    • Kodandapani, R.1    Pio, F.2    Ni, C.Z.3    Piccialli, G.4    Klemsz, M.5    McKercher, S.6    Maki, R.A.7    Ely, K.R.8
  • 102
    • 0032804235 scopus 로고    scopus 로고
    • The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions
    • 10.1006/jmbi.1999.2946. 10438625
    • The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. A Glasfeld AN Koehler MA Schumacher RG Brennan, J Mol Biol 1999 291 347 361 10.1006/jmbi.1999.2946 10438625
    • (1999) J Mol Biol , vol.291 , pp. 347-361
    • Glasfeld, A.1    Koehler, A.N.2    Schumacher, M.A.3    Brennan, R.G.4
  • 103
    • 0031749528 scopus 로고    scopus 로고
    • A new DNA-binding motif in the Skn-1 binding domain-DNA complex
    • 10.1038/nsb0698. 9628487
    • A new DNA-binding motif in the Skn-1 binding domain-DNA complex. PB Rupert GW Daughdrill B Bowerman BW Matthews, Nat Struct Biol 1998 5 484 491 10.1038/nsb0698-484 9628487
    • (1998) Nat Struct Biol , vol.5 , pp. 484-491
    • Rupert, P.B.1    Daughdrill, G.W.2    Bowerman, B.3    Matthews, B.W.4
  • 106
    • 0030779907 scopus 로고    scopus 로고
    • Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA
    • 9312061. 10.1093/emboj/16.19.6044
    • Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA. G van Pouderoyen RF Ketting A Perrakis RH Plasterk TK Sixma, Embo J 1997 16 6044 6054 9312061 10.1093/emboj/16.19.6044
    • (1997) Embo J , vol.16 , pp. 6044-6054
    • Van Pouderoyen, G.1    Ketting, R.F.2    Perrakis, A.3    Plasterk, R.H.4    Sixma, T.K.5
  • 108
    • 4143097044 scopus 로고    scopus 로고
    • Isolation and characterization of new homing endonuclease specificities at individual target site positions
    • 10.1016/j.jmb.2004.07.031. 15313605
    • Isolation and characterization of new homing endonuclease specificities at individual target site positions. D Sussman M Chadsey S Fauce A Engel A Bruett R Monnat Jr. BL Stoddard LM Seligman, J Mol Biol 2004 342 31 41 10.1016/j.jmb.2004.07.031 15313605
    • (2004) J Mol Biol , vol.342 , pp. 31-41
    • Sussman, D.1    Chadsey, M.2    Fauce, S.3    Engel, A.4    Bruett, A.5    Monnat Jr., R.6    Stoddard, B.L.7    Seligman, L.M.8
  • 109
    • 0028828745 scopus 로고
    • Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA
    • 10.1126/science.270.5234.262. 7569974
    • Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. T Li MR Stark AD Johnson C Wolberger, Science 1995 270 262 269 10.1126/science.270.5234.262 7569974
    • (1995) Science , vol.270 , pp. 262-269
    • Li, T.1    Stark, M.R.2    Johnson, A.D.3    Wolberger, C.4
  • 110
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • 10.1038/365512a0. 8413604
    • Crystal structure of a yeast TBP/TATA-box complex. Y Kim JH Geiger S Hahn PB Sigler, Nature 1993 365 512 520 10.1038/365512a0 8413604
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 111
    • 0026656038 scopus 로고
    • Crystal structure at 1.7 a of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target
    • 10.1038/359505a0. 1328886
    • Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. RS Hegde SR Grossman LA Laimins PB Sigler, Nature 1992 359 505 512 10.1038/359505a0 1328886
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.S.1    Grossman, S.R.2    Laimins, L.A.3    Sigler, P.B.4
  • 112
    • 0030609996 scopus 로고    scopus 로고
    • Engrailed (Gln50 - >lys) homeodomain-DNA complex at 1.9 a resolution: Structural basis for enhanced affinity and altered specificity
    • 10.1016/S0969-2126(97)00256. 9309220
    • Engrailed (Gln50 - >Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. L Tucker-Kellogg MA Rould KA Chambers SE Ades RT Sauer CO Pabo, Structure 1997 5 1047 1054 10.1016/S0969-2126(97)00256-6 9309220
    • (1997) Structure , vol.5 , pp. 1047-1054
    • Tucker-Kellogg, L.1    Rould, M.A.2    Chambers, K.A.3    Ades, S.E.4    Sauer, R.T.5    Pabo, C.O.6
  • 113
    • 0031851485 scopus 로고    scopus 로고
    • Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex
    • 9699632
    • Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. E Fraenkel CO Pabo, Nat Struct Biol 1998 5 692 697 9699632
    • (1998) Nat Struct Biol , vol.5 , pp. 692-697
    • Fraenkel, E.1    Pabo, C.O.2
  • 114
    • 0028900074 scopus 로고
    • DNA-binding specificity of NGFI-A and related zinc finger transcription factors
    • 7891721
    • DNA-binding specificity of NGFI-A and related zinc finger transcription factors. AH Swirnoff J Milbrandt, Mol Cell Biol 1995 15 2275 2287 7891721
    • (1995) Mol Cell Biol , vol.15 , pp. 2275-2287
    • Swirnoff, A.H.1    Milbrandt, J.2
  • 115
    • 0029883976 scopus 로고    scopus 로고
    • Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: Fluorescence and circular dichroism studies
    • 10.1021/bi952555q. 8672437
    • Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies. JG McAfee SP Edmondson I Zegar JW Shriver, Biochemistry 1996 35 4034 4045 10.1021/bi952555q 8672437
    • (1996) Biochemistry , vol.35 , pp. 4034-4045
    • McAfee, J.G.1    Edmondson, S.P.2    Zegar, I.3    Shriver, J.W.4
  • 116
    • 0030004590 scopus 로고    scopus 로고
    • Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli
    • 8636021
    • Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli. RG Martin KW Jair RE Wolf Jr. JL Rosner, J Bacteriol 1996 178 2216 2223 8636021
    • (1996) J Bacteriol , vol.178 , pp. 2216-2223
    • Martin, R.G.1    Jair, K.W.2    Wolf Jr., R.E.3    Rosner, J.L.4
  • 117
    • 0031882652 scopus 로고    scopus 로고
    • New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB
    • 9420329
    • New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. T Lagrange AN Kapanidis H Tang D Reinberg RH Ebright, Genes Dev 1998 12 34 44 9420329
    • (1998) Genes Dev , vol.12 , pp. 34-44
    • Lagrange, T.1    Kapanidis, A.N.2    Tang, H.3    Reinberg, D.4    Ebright, R.H.5
  • 118
    • 0037133504 scopus 로고    scopus 로고
    • Kinetic and thermodynamic basis of promoter strength: Multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence
    • 10.1021/bi0158472. 11888274
    • Kinetic and thermodynamic basis of promoter strength: multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence. RP Bandwar Y Jia NM Stano SS Patel, Biochemistry 2002 41 3586 3595 10.1021/bi0158472 11888274
    • (2002) Biochemistry , vol.41 , pp. 3586-3595
    • Bandwar, R.P.1    Jia, Y.2    Stano, N.M.3    Patel, S.S.4
  • 119
    • 0026560372 scopus 로고
    • Participation of non-zinc finger residues in DNA binding by two nuclear orphan receptors
    • 10.1126/science.1314418. 1314418
    • Participation of non-zinc finger residues in DNA binding by two nuclear orphan receptors. TE Wilson RE Paulsen KA Padgett J Milbrandt, Science 1992 256 107 110 10.1126/science.1314418 1314418
    • (1992) Science , vol.256 , pp. 107-110
    • Wilson, T.E.1    Paulsen, R.E.2    Padgett, K.A.3    Milbrandt, J.4
  • 120
    • 0028108227 scopus 로고
    • Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50
    • 10.1021/bi00197a022. 8049221
    • Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50. SE Ades RT Sauer, Biochemistry 1994 33 9187 9194 10.1021/bi00197a022 8049221
    • (1994) Biochemistry , vol.33 , pp. 9187-9194
    • Ades, S.E.1    Sauer, R.T.2
  • 121
    • 0028938415 scopus 로고
    • Characterization of the Elk-1 ETS DNA-binding domain
    • 10.1074/jbc.270.11.5805. 7890710
    • Characterization of the Elk-1 ETS DNA-binding domain. P Shore L Bisset J Lakey JP Waltho R Virden AD Sharrocks, J Biol Chem 1995 270 5805 5811 10.1074/jbc.270.11.5805 7890710
    • (1995) J Biol Chem , vol.270 , pp. 5805-5811
    • Shore, P.1    Bisset, L.2    Lakey, J.3    Waltho, J.P.4    Virden, R.5    Sharrocks, A.D.6
  • 122
    • 0030610426 scopus 로고    scopus 로고
    • The structure of I-Crel, a group I intron-encoded homing endonuclease
    • 10.1038/nsb0697. 9187655
    • The structure of I-Crel, a group I intron-encoded homing endonuclease. PJ Heath KM Stephens RJ Monnat Jr. BL Stoddard, Nat Struct Biol 1997 4 468 476 10.1038/nsb0697-468 9187655
    • (1997) Nat Struct Biol , vol.4 , pp. 468-476
    • Heath, P.J.1    Stephens, K.M.2    Monnat Jr., R.J.3    Stoddard, B.L.4
  • 123
    • 0031556945 scopus 로고    scopus 로고
    • Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site
    • 10.1006/jmbi.1996.0754. 9048944
    • Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site. V Derbyshire JC Kowalski JT Dansereau CR Hauer M Belfort, J Mol Biol 1997 265 494 506 10.1006/jmbi.1996.0754 9048944
    • (1997) J Mol Biol , vol.265 , pp. 494-506
    • Derbyshire, V.1    Kowalski, J.C.2    Dansereau, J.T.3    Hauer, C.R.4    Belfort, M.5
  • 124
    • 0027412087 scopus 로고
    • Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins
    • 8096059
    • Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins. KM Catron N Iler C Abate, Mol Cell Biol 1993 13 2354 2365 8096059
    • (1993) Mol Cell Biol , vol.13 , pp. 2354-2365
    • Catron, K.M.1    Iler, N.2    Abate, C.3
  • 125
    • 0025182048 scopus 로고
    • Purification of the Escherichia coli purine regulon repressor and identification of corepressors
    • 2211500
    • Purification of the Escherichia coli purine regulon repressor and identification of corepressors. RJ Rolfes H Zalkin, J Bacteriol 1990 172 5637 5642 2211500
    • (1990) J Bacteriol , vol.172 , pp. 5637-5642
    • Rolfes, R.J.1    Zalkin, H.2
  • 126
    • 0032884399 scopus 로고    scopus 로고
    • Mutants of ETS domain PU.1 and GGAA/T recognition: Free energies and kinetics
    • 10548056
    • Mutants of ETS domain PU.1 and GGAA/T recognition: free energies and kinetics. F Pio N Assa-Munt J Yguerabide RA Maki, Protein Sci 1999 8 2098 2109 10548056
    • (1999) Protein Sci , vol.8 , pp. 2098-2109
    • Pio, F.1    Assa-Munt, N.2    Yguerabide, J.3    Maki, R.A.4
  • 127
    • 0036192889 scopus 로고    scopus 로고
    • DNA-binding interactions and conformational fluctuations of Tc3 transposase DNA binding domain examined with single molecule fluorescence spectroscopy
    • 11867477
    • DNA-binding interactions and conformational fluctuations of Tc3 transposase DNA binding domain examined with single molecule fluorescence spectroscopy. DC Daniel M Thompson NW Woodbury, Biophys J 2002 82 1654 1666 11867477
    • (2002) Biophys J , vol.82 , pp. 1654-1666
    • Daniel, D.C.1    Thompson, M.2    Woodbury, N.W.3
  • 128
    • 0023955176 scopus 로고
    • Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study
    • 3277190. 10.1073/pnas.85.4.975
    • Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. J Carey, Proc Natl Acad Sci U S A 1988 85 975 979 3277190 10.1073/pnas.85.4.975
    • (1988) Proc Natl Acad Sci U S a , vol.85 , pp. 975-979
    • Carey, J.1
  • 129
    • 0028142407 scopus 로고
    • Heterodimerization of the yeast homeodomain transcriptional regulators alpha 2 and a1 induces an interfacial helix in alpha 2
    • 10.1021/bi00197a033. 8049230
    • Heterodimerization of the yeast homeodomain transcriptional regulators alpha 2 and a1 induces an interfacial helix in alpha 2. CL Phillips MR Stark AD Johnson FW Dahlquist, Biochemistry 1994 33 9294 9302 10.1021/bi00197a033 8049230
    • (1994) Biochemistry , vol.33 , pp. 9294-9302
    • Phillips, C.L.1    Stark, M.R.2    Johnson, A.D.3    Dahlquist, F.W.4
  • 130
    • 0018143102 scopus 로고
    • An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking
    • 10.1002/bip.1978.360171005
    • An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. RL Ornstein R Rein DL Breen RD MacElroy, Biopolymers 1978 17 2341 2360 10.1002/bip.1978.360171005
    • (1978) Biopolymers , vol.17 , pp. 2341-2360
    • Ornstein, R.L.1    Rein, R.2    Breen, D.L.3    MacElroy, R.D.4
  • 131
    • 0026078079 scopus 로고
    • Cooperative binding of the E2 protein of bovine papillomavirus to adjacent E2-responsive sequences
    • 1848322
    • Cooperative binding of the E2 protein of bovine papillomavirus to adjacent E2-responsive sequences. P Monini SR Grossman B Pepinsky EJ Androphy LA Laimins, J Virol 1991 65 2124 2130 1848322
    • (1991) J Virol , vol.65 , pp. 2124-2130
    • Monini, P.1    Grossman, S.R.2    Pepinsky, B.3    Androphy, E.J.4    Laimins, L.A.5


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