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Volumn 42, Issue 5, 2014, Pages 3381-3394

Bioinformatic analysis of the protein/DNA interface

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ISOLEUCINE; LEUCINE; METHIONINE; NUCLEASE; PHENYLALANINE; TRANSCRIPTION FACTOR; VALINE;

EID: 84899026778     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1273     Document Type: Article
Times cited : (35)

References (103)
  • 1
    • 0024294636 scopus 로고
    • No code for recognition
    • Matthews, B.W. (1988) No code for recognition. Nature, 335, 294-295.
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.W.1
  • 2
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • Pabo, C.O. and Nekludova, L. (2000) Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognitioñJ. Mol. Biol., 301, 597-624.
    • (2000) J Mol. Biol. , vol.301 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 4
    • 84873894991 scopus 로고    scopus 로고
    • Local conformational changes in the DNA interfaces of proteins
    • Sunami, T. and Kono, H. (2013) Local conformational changes in the DNA interfaces of proteins. PLoS One, 8, e56080.
    • (2013) PLoS One , vol.8
    • Sunami, T.1    Kono, H.2
  • 5
    • 0000127073 scopus 로고
    • Sequence specific recognition of double helical nucleic acids by proteins
    • Seeman, N.C., Rosenberg, J.M. and Rich, A. (1976) Sequence specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808.
    • (1976) Proc. Natl Acad. Sci. USA , vol.73 , pp. 804-808
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 7
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions
    • Stormo, G.D. and Zhao, Y. (2010) Determining the specificity of protein-DNA interactions. Nat. Rev. Genet., 11, 751-760.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 8
    • 0000058799 scopus 로고
    • Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically
    • Sarai, A. and Takeda, Y. (1989) Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl Acad. Sci. USA, 86, 6513-6517.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 6513-6517
    • Sarai, A.1    Takeda, Y.2
  • 9
    • 20544460658 scopus 로고    scopus 로고
    • Protein-DNA recognition patterns and predictions
    • Sarai, A. and Kono, H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
    • (2005) Annu. Rev. Biophys. Biomol. Struct. , vol.34 , pp. 379-398
    • Sarai, A.1    Kono, H.2
  • 10
    • 54549096025 scopus 로고    scopus 로고
    • Protein-DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
    • Ahmad, S., Keskin, O., Sarai, A. and Nussinov, R. (2008) Protein-DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res., 36, 5922-5932.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5922-5932
    • Ahmad, S.1    Keskin, O.2    Sarai, A.3    Nussinov, R.4
  • 11
    • 0026682657 scopus 로고
    • Transcription factors: Structural families and principles of DNA recognition
    • Pabo, C.O. and Sauer, R.T. (1992) Transcription factors: Structural families and principles of DNA recognition. Annu. Rev. Biochem., 61, 1053-1095.
    • (1992) Annu. Rev. Biochem. , vol.61 , pp. 1053-1095
    • Pabo, C.O.1    Sauer, R.T.2
  • 13
    • 0027937601 scopus 로고
    • Stereochemical basis of DNA recognition by Zn fingers
    • Suzuki, M., Gerstein, M. and Yagi, N. (1994) Stereochemical basis of DNA recognition by Zn fingers. Nucleic Acids Res., 22, 3397-3405. (Pubitemid 24280633
    • (1994) Nucleic Acids Research , vol.22 , Issue.16 , pp. 3397-3405
    • Suzuki, M.1    Gerstein, M.2    Yagi, N.3
  • 14
    • 0031042082 scopus 로고    scopus 로고
    • Physical basis of a protein-DNA recognition code
    • Choo, Y. and Klug, A. (1997) Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol., 7, 117-125.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 117-125
    • Choo, Y.1    Klug, A.2
  • 15
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • DOI 10.1093/nar/26.10.2306
    • Mandel-Gutfreund, Y. and Margalit, H. (1998) Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites. Nucleic Acids Res., 26, 2306-2312. (Pubitemid 28297328
    • (1998) Nucleic Acids Research , vol.26 , Issue.10 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 16
    • 0029417120 scopus 로고
    • Binding geometry of alpha-helices that recognize DNA
    • Suzuki, M. and Gerstein, M. (1995) Binding geometry of alpha-helices that recognize DNA. Proteins, 23, 525-535.
    • (1995) Proteins , vol.23 , pp. 525-535
    • Suzuki, M.1    Gerstein, M.2
  • 17
    • 0038681269 scopus 로고    scopus 로고
    • Statistical models for discerning protein structures containing the DNA-binding helix-Turn-helix motif
    • McLaughlin, W.A. and Berman, H.M. (2003) Statistical models for discerning protein structures containing the DNA-binding helix-Turn-helix motif. J. Mol. Biol., 330, 43-55.
    • (2003) J. Mol. Biol. , vol.330 , pp. 43-55
    • McLaughlin, W.A.1    Berman, H.M.2
  • 19
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • Luscombe, N.M. and Thornton, J.M. (2002) Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009.
    • (2002) J. Mol. Biol. , vol.320 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 20
    • 26444598454 scopus 로고    scopus 로고
    • Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
    • DOI 10.1002/prot.20607
    • Lejeune, D., Delsaux, N., Charloteaux, B., Thomas, A. and Brasseur, R. (2005) Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure. Proteins, 61, 258-271. (Pubitemid 41429134
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.2 , pp. 258-271
    • Lejeune, D.1    Delsaux, N.2    Charloteaux, B.3    Thomas, A.4    Brasseur, R.5
  • 21
    • 0033573827 scopus 로고    scopus 로고
    • Structural features of protein-nucleic acid recognition sites
    • Nadassy, K., Wodak, S.J. and Janin, J. (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry, 38, 1999-2017.
    • (1999) Biochemistry , vol.38 , pp. 1999-2017
    • Nadassy, K.1    Wodak, S.J.2    Janin, J.3
  • 22
    • 0346258292 scopus 로고    scopus 로고
    • Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
    • DOI 10.1093/nar/gkg922
    • Jones, S., Shanahan, H.P., Berman, H.M. and Thornton, J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198. (Pubitemid 38008449
    • (2003) Nucleic Acids Research , vol.31 , Issue.24 , pp. 7189-7198
    • Jones, S.1    Shanahan, H.P.2    Berman, H.M.3    Thornton, J.M.4
  • 23
    • 2542557409 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    • DOI 10.1002/prot.20111
    • Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2004) Structurebased prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55, 885-894. (Pubitemid 38702948
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.4 , pp. 885-894
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 24
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 25
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • Mandel-Gutfreund, Y., Schueler, O. and Margalit, H. (1995) Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. J. Mol. Biol., 253, 370-382.
    • (1995) J. Mol. Biol. , vol.253 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 26
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (2001) Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874. (Pubitemid 32685051
    • (2001) Nucleic Acids Research , vol.29 , Issue.13 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 28
    • 2442687873 scopus 로고    scopus 로고
    • Stair motifs at protein-DNA interfaces: Nonadditivity of H-bond stacking, and cation-pi interactions
    • Biot, C., Wintjens, R. and Rooman, M. (2004) Stair motifs at protein-DNA interfaces: Nonadditivity of H-bond, stacking, and cation-pi interactions. J. Am. Chem. Soc., 126, 6220-6221.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 6220-6221
    • Biot, C.1    Wintjens, R.2    Rooman, M.3
  • 29
    • 0023708040 scopus 로고
    • Water: An integral part of nucleic acid structure
    • Westhof, E. (1988) Water: An integral part of nucleic acid structure. Annu. Rev. Biophys. Chem., 17, 125-144.
    • (1988) Annu. Rev. Biophys. Chem. , vol.17 , pp. 125-144
    • Westhof, E.1
  • 30
    • 0031047683 scopus 로고    scopus 로고
    • The role of water in protein-DNA interactions
    • Schwabe, J.W. (1997) The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol., 7, 126-134.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 126-134
    • Schwabe, J.W.1
  • 33
    • 12444259635 scopus 로고    scopus 로고
    • Building an automated classification of DNA-binding protein domains
    • Ponomarenko, J.V., Bourne, P.E. and Shindyalov, I.N. (2002) Building an automated classification of DNA-binding protein domains. Bioinformatics, 18(Suppl. 2), S192-S201. (Pubitemid 41073236
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Ponomarenko, J.V.1    Bourne, P.E.2    Shindyalov, I.N.3
  • 34
    • 52949123643 scopus 로고    scopus 로고
    • Insights into protein-DNA interactions through structure network analysis
    • Sathyapriya, R., Vijayabaskar, M.S. and Vishveshwara, S. (2008) Insights into protein-DNA interactions through structure network analysis. PLoS Comput. Biol., 4, e1000170.
    • (2008) PLoS Comput. Biol. , vol.4
    • Sathyapriya, R.1    Vijayabaskar, M.S.2    Vishveshwara, S.3
  • 35
    • 59849107303 scopus 로고    scopus 로고
    • Dissection, residue conservation, and structural classification of protein-DNA interfaces
    • Biswas, S., Guharoy, M. and Chakrabarti, P. (2009) Dissection, residue conservation, and structural classification of protein-DNA interfaces. Proteins, 74, 643-654.
    • (2009) Proteins , vol.74 , pp. 643-654
    • Biswas, S.1    Guharoy, M.2    Chakrabarti, P.3
  • 36
    • 11844279783 scopus 로고    scopus 로고
    • Structural alignment of protein-DNA interfaces: Insights into the determinants of binding specificity
    • Siggers, T.W., Silkov, A. and Honig, B. (2005) Structural alignment of protein-DNA interfaces: Insights into the determinants of binding specificity. J. Mol. Biol., 345, 1027-1045.
    • (2005) J. Mol. Biol. , vol.345 , pp. 1027-1045
    • Siggers, T.W.1    Silkov, A.2    Honig, B.3
  • 37
    • 33748290192 scopus 로고    scopus 로고
    • Classification of protein-dna complexes based on structural descriptors
    • DOI 10.1016/j.str.2006.06.018, PII S0969212606003029
    • Prabakaran, P., Siebers, J.G., Ahmad, S., Gromiha, M.M., Singarayan, M.G. and Sarai, A. (2006) Classification of protein-DNA complexes based on structural descriptors. Structure, 14, 1355-1367. (Pubitemid 44331615
    • (2006) Structure , vol.14 , Issue.9 , pp. 1355-1367
    • Prabakaran, P.1    Siebers, J.G.2    Ahmad, S.3    Gromiha, M.M.4    Singarayan, M.G.5    Sarai, A.6
  • 38
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • Unger, R., Harel, D., Wherland, S. and Sussman, J.L. (1989) A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins, 5, 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 39
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff, C. and Baker, D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
    • (1998) J. Mol. Biol. , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 40
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodny, R., Koehl, P., Guibas, L. and Levitt, M. (2002) Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol., 323, 297-307.
    • (2002) J. Mol. Biol. , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 41
    • 3242891058 scopus 로고    scopus 로고
    • SA-Search: A web tool for protein structure mining based on a Structural Alphabet
    • Guyon, F., Camproux, A.C., Hochez, J. and Tuffery, P. (2004) SA-Search: A web tool for protein structure mining based on a Structural Alphabet. Nucleic Acids Res., 32, W545-W548.
    • (2004) Nucleic Acids Res. , vol.32
    • Guyon, F.1    Camproux, A.C.2    Hochez, J.3    Tuffery, P.4
  • 42
    • 2942541294 scopus 로고    scopus 로고
    • Use of a structural alphabet for analysis of short loops connecting repetitive structures
    • Fourrier, L., Benros, C. and de Brevern, A.G. (2004) Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinform., 5, 58.
    • (2004) BMC Bioinform. , vol.5 , pp. 58
    • Fourrier, L.1    Benros, C.2    De Brevern, A.G.3
  • 43
    • 33644840330 scopus 로고    scopus 로고
    • Assessing a novel approach for predicting local 3D protein structures from sequence
    • Benros, C., de Brevern, A.G., Etchebest, C. and Hazout, S. (2006) Assessing a novel approach for predicting local 3D protein structures from sequence. Prot. Struct. Funct. Bioinform., 62, 865-880.
    • (2006) Prot. Struct. Funct. Bioinform. , vol.62 , pp. 865-880
    • Benros, C.1    De Brevern, A.G.2    Etchebest, C.3    Hazout, S.4
  • 44
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    • de Brevern, A.G., Etchebest, C. and Hazout, S. (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41, 271-287.
    • (2000) Prots. Struct. Funct. Genet. , vol.41 , pp. 271-287
    • De Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 46
    • 46349098220 scopus 로고    scopus 로고
    • DNA conformations and their sequence preferences
    • DOI 10.1093/nar/gkn260
    • Svozil, D., Kalina, J., Omelka, M. and Schneider, B. (2008) DNA conformations and their sequence preferences. Nucleic Acids Res., 36, 3690-3706. (Pubitemid 351917531
    • (2008) Nucleic Acids Research , vol.36 , Issue.11 , pp. 3690-3706
    • Svozil, D.1    Kalina, J.2    Omelka, M.3    Schneider, B.4
  • 49
    • 3242886389 scopus 로고    scopus 로고
    • MolProbity: Structure validation and all-Atom contact analysis for nucleic acids and their complexes
    • WEB SERVER ISS. W615-W619 DOI 10.1093/nar/gkh398
    • Davis, I.W., Murray, L.W., Richardson, J.S. and Richardson, D.C. (2004) MOLPROBITY: Structure validation and all-Atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res., 32, W615-W619. (Pubitemid 38997409
    • (2004) Nucleic Acids Research , vol.32
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 52
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: Visual molecular dynamics. J. Mol. Graph., 14, 33-38, 27-38.
    • (1996) J. Mol. Graph. , vol.14 , Issue.33-38 , pp. 27-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 54
    • 33747831751 scopus 로고    scopus 로고
    • Protein block expert (pbe): A web-based protein structure analysis server using a structural alphabet
    • WEB. SERV. ISS. DOI 10.1093/nar/gkl199
    • Tyagi, M., Sharma, P., Swamy, C.S., Cadet, F., Srinivasan, N., de Brevern, A.G. and Offmann, B. (2006) Protein Block Expert (PBE): A web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res., 34, W119-W123. (Pubitemid 44529747
    • (2006) Nucleic Acids Research , vol.34
    • Tyagi, M.1    Sharma, P.2    Swamy, C.S.3    Cadet, F.4    Srinivasan, N.5    De Brevern, A.G.6    Offmann, B.7
  • 55
    • 84879550825 scopus 로고    scopus 로고
    • Automatic workflow for the classification of local DNA conformations
    • Cech, P., Kukal, J., Cerny, J., Schneider, B. and Svozil, D. (2013) Automatic workflow for the classification of local DNA conformations. BMC Bioinform., 14, 205.
    • (2013) BMC Bioinform. , vol.14 , pp. 205
    • Cech, P.1    Kukal, J.2    Cerny, J.3    Schneider, B.4    Svozil, D.5
  • 56
    • 23144437382 scopus 로고    scopus 로고
    • New assessment of a structural alphabet
    • de Brevern, A.G. (2005) New assessment of a structural alphabet. In Silico Biol., 5, 283-289.
    • (2005) Silico Biol. , vol.5 , pp. 283-289
    • De Brevern, A.G.1
  • 57
    • 0036893073 scopus 로고    scopus 로고
    • Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
    • DOI 10.1110/ps.0220502
    • de Brevern, A.G., Valadie, H., Hazout, S. and Etchebest, C. (2002) Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship. Protein Sci., 11, 2871-2886. (Pubitemid 35365253
    • (2002) Protein Science , vol.11 , Issue.12 , pp. 2871-2886
    • De Brevern, A.G.1    Valadie, H.2    Hazout, S.3    Etchebest, C.4
  • 58
    • 0021103971 scopus 로고
    • Sequence-dependent conformation of an A-DNA double helix The crystal structure of the octamer d(G-G-T-A-T-A-C-C)
    • Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W.B.T., Salisbury, S.A. and Viswamitra, M.A. (1983) Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C) J. Mol. Biol., 166, 183-201.
    • (1983) J Mol. Biol. , vol.166 , pp. 183-201
    • Shakked, Z.1    Rabinovich, D.2    Kennard, O.3    Cruse, W.B.T.4    Salisbury, S.A.5    Viswamitra, M.A.6
  • 59
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu, X.-J., Shakked, Z. and Olson, W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol., 300, 819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.-J.1    Shakked, Z.2    Olson, W.K.3
  • 60
    • 0642374383 scopus 로고    scopus 로고
    • The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites
    • Steffen, N.R., Murphy, S.D., Lathrop, R.H., Opel, M.L., Tolleri, L. and Hatfield, G.W. (2002) The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites. Genome Inform., 13, 153-162.
    • (2002) Genome Inform. , vol.13 , pp. 153-162
    • Steffen, N.R.1    Murphy, S.D.2    Lathrop, R.H.3    Opel, M.L.4    Tolleri, L.5    Hatfield, G.W.6
  • 61
    • 0009034911 scopus 로고
    • Molecular structures of nucleosides and nucleotides 2 orthogonal coordinates for standard nucleic acid base residues
    • Taylor, R. and Kennard, O. (1982) Molecular Structures of Nucleosides and Nucleotides. 2. orthogonal coordinates for standard nucleic acid base residues. J. Am. Chem. Soc., 104, 3209-3212.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 3209-3212
    • Taylor, R.1    Kennard, O.2
  • 65
    • 59649112203 scopus 로고    scopus 로고
    • Crystal structure of a p53 core tetramer bound to DNA
    • Malecka, K.A., Ho, W.C. and Marmorstein, R. (2009) Crystal structure of a p53 core tetramer bound to DNA. Oncogene, 28, 325-333.
    • (2009) Oncogene , vol.28 , pp. 325-333
    • Malecka, K.A.1    Ho, W.C.2    Marmorstein, R.3
  • 66
    • 0028979479 scopus 로고
    • Structure of NF-kappa B p50 homodimer bound to a kappa B site
    • Ghosh, G., van Duyne, G., Ghosh, S. and Sigler, P.B. (1995) Structure of NF-kappa B p50 homodimer bound to a kappa B site. Nature, 373, 303-310.
    • (1995) Nature , vol.373 , pp. 303-310
    • Ghosh, G.1    Van Duyne, G.2    Ghosh, S.3    Sigler, P.B.4
  • 67
    • 0032135105 scopus 로고    scopus 로고
    • Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by Ets proteins
    • Mo, Y., Vaessen, B., Johnston, K. and Marmorstein, R. (1998) Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by Ets proteins. Mol. Cell, 2, 201-212.
    • (1998) Mol. Cell , vol.2 , pp. 201-212
    • Mo, Y.1    Vaessen, B.2    Johnston, K.3    Marmorstein, R.4
  • 69
    • 0034890853 scopus 로고    scopus 로고
    • Beyond the ''recognition code'': Structures of two Cys2His2 zinc finger/TATA box complexes
    • Wolfe, S.A., Grant, R.A., Elrod-Erickson, M. and Pabo, C.O. (2001) Beyond the ''recognition code'': Structures of two Cys2His2 zinc finger/TATA box complexes. Structure, 9, 717-723.
    • (2001) Structure , vol.9 , pp. 717-723
    • Wolfe, S.A.1    Grant, R.A.2    Elrod-Erickson, M.3    Pabo, C.O.4
  • 70
    • 33749155924 scopus 로고    scopus 로고
    • Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA
    • Segal, D.J., Crotty, J.W., Bhakta, M.S., Barbas, C.F. III and Horton, N.C. (2006) Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA.J. Mol. Biol., 363, 405-421.
    • (2006) J Mol. Biol. , vol.363 , pp. 405-421
    • Segal, D.J.1    Crotty, J.W.2    Bhakta, M.S.3    Barbas III, C.F.4    Horton, N.C.5
  • 71
    • 0031057121 scopus 로고    scopus 로고
    • Structure of Pit-1 POU domain bound to DNA as a dimer: Unexpected arrangement and flexibility
    • Jacobson, E.M., Li, P., Leon-del-Rio, A., Rosenfeld, M.G. and Aggarwal, A.K. (1997) Structure of Pit-1 POU domain bound to DNA as a dimer: Unexpected arrangement and flexibility. Genes Dev., 11, 198-212. (Pubitemid 27081896
    • (1997) Genes and Development , vol.11 , Issue.2 , pp. 198-212
    • Jacobson, E.M.1    Li, P.2    Leon-Del-Rio, A.3    Rosenfeld, M.G.4    Aggarwal, A.K.5
  • 72
    • 0034665030 scopus 로고    scopus 로고
    • Direct and indirect readout in mutant Met repressor-operator complexes
    • Garvie, C.W. and Phillips, S.E. (2000) Direct and indirect readout in mutant Met repressor-operator complexes. Structure, 8, 905-914.
    • (2000) Structure , vol.8 , pp. 905-914
    • Garvie, C.W.1    Phillips, S.E.2
  • 73
    • 4444373591 scopus 로고    scopus 로고
    • An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site
    • DOI 10.1016/j.str.2004.07.014, PII S0969212604002837
    • Xu, Q.S., Kucera, R.B., Roberts, R.J. and Guo, H.C. (2004) An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure, 12, 1741-1747. (Pubitemid 39200525
    • (2004) Structure , vol.12 , Issue.9 , pp. 1741-1747
    • Xu, Q.S.1    Kucera, R.B.2    Roberts, R.J.3    Guo, H.-C.4
  • 74
    • 63349094041 scopus 로고    scopus 로고
    • Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation
    • Takeuchi, R., Certo, M., Caprara, M.G., Scharenberg, A.M. and Stoddard, B.L. (2009) Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Res., 37, 877-890.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 877-890
    • Takeuchi, R.1    Certo, M.2    Caprara, M.G.3    Scharenberg, A.M.4    Stoddard, B.L.5
  • 75
    • 33644851082 scopus 로고    scopus 로고
    • DNA nicking by HinP1I endonuclease: Bending, base flipping and minor groove expansion
    • DOI 10.1093/nar/gkj484
    • Horton, J.R., Zhang, X., Maunus, R., Yang, Z., Wilson, G.G., Roberts, R.J. and Cheng, X. (2006) DNA nicking by HinP1I endonuclease: Bending, base flipping and minor groove expansion. Nucleic Acids Res., 34, 939-948. (Pubitemid 43380677
    • (2006) Nucleic Acids Research , vol.34 , Issue.3 , pp. 939-948
    • Horton, J.R.1    Zhang, X.2    Maunus, R.3    Yang, Z.4    Wilson, G.G.5    Roberts, R.J.6    Cheng, X.7
  • 76
    • 71949104396 scopus 로고    scopus 로고
    • Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations
    • Watanabe, N., Takasaki, Y., Sato, C., Ando, S. and Tanaka, I. (2009) Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations. Acta Crystallogr. D Biol. Crystallogr., 65, 1326-1333.
    • (2009) Acta Crystallogr. D Biol. Crystallogr. , vol.65 , pp. 1326-1333
    • Watanabe, N.1    Takasaki, Y.2    Sato, C.3    Ando, S.4    Tanaka, I.5
  • 77
    • 69049101233 scopus 로고    scopus 로고
    • Cavities in protein-DNA and protein-RNA interfaces
    • Sonavane, S. and Chakrabarti, P. (2009) Cavities in protein-DNA and protein-RNA interfaces. Nucleic Acids Res., 37, 4613-4620.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 4613-4620
    • Sonavane, S.1    Chakrabarti, P.2
  • 78
    • 0000860802 scopus 로고
    • Polyelectrolyte theories and their applications to DNA
    • Anderson, C.F. and Record, M.T. Jr (1982) Polyelectrolyte theories and their applications to DNA. Annu. Rev. Phys. Chem., 33, 191-222.
    • (1982) Annu. Rev. Phys. Chem. , vol.33 , pp. 191-222
    • Anderson, C.F.1    Record Jr., M.T.2
  • 79
    • 0026558204 scopus 로고
    • Direct measurement of the intermolecular forces between counterion-condensed DNA double helices
    • Rau, D.C. and Parsegian, V.A. (1992) Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Biophys. J., 61, 246-259.
    • (1992) Biophys. J. , vol.61 , pp. 246-259
    • Rau, D.C.1    Parsegian, V.A.2
  • 80
    • 0028222102 scopus 로고
    • Influence of base composition, base sequence, and duplex structure on DNA hydration: Apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 C
    • Chalikian, T.V., Sarvazyan, A.P., Plum, G.E. and Breslauer, K.J. (1994) The influence of base composition, base sequence, and duplex structure on DNA hydration: Apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 oC. Biochemistry, 33, 2394-2401. (Pubitemid 24099644
    • (1994) Biochemistry , vol.33 , Issue.9 , pp. 2394-2401
    • Chalikian, T.V.1    Sarvazyan, A.P.2    Plum, G.E.3    Bresiauer, K.J.4
  • 81
    • 0028823008 scopus 로고
    • Hydration of the DNA bases is local
    • Schneider, B. and Berman, H.M. (1995) Hydration of the DNA bases is local. Biophys. J., 69, 2661-2669.
    • (1995) Biophys. J. , vol.69 , pp. 2661-2669
    • Schneider, B.1    Berman, H.M.2
  • 82
    • 0031755274 scopus 로고    scopus 로고
    • Hydration of the phosphate group in double helical DNA
    • Schneider, B., Patel, K. and Berman, H.M. (1998) Hydration of the phosphate group in double helical DNA. Biophys. J., 75, 2422-2434.
    • (1998) Biophys. J. , vol.75 , pp. 2422-2434
    • Schneider, B.1    Patel, K.2    Berman, H.M.3
  • 83
    • 0032515407 scopus 로고    scopus 로고
    • Stereochemistry of binding of metal cations and water to a phosphate group
    • Schneider, B. and Kabelac, M. (1998) Stereochemistry of binding of metal cations and water to a phosphate group. J. Am. Chem. Soc., 120, 161-165.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 161-165
    • Schneider, B.1    Kabelac, M.2
  • 84
    • 0031722426 scopus 로고    scopus 로고
    • An analysis of the relationship between hydration and protein-DNA interactions
    • Woda, J., Schneider, B., Patel, K., Mistry, K. and Berman, H.M. (1998) An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J., 75, 2170-2177.
    • (1998) Biophys. J. , vol.75 , pp. 2170-2177
    • Woda, J.1    Schneider, B.2    Patel, K.3    Mistry, K.4    Berman, H.M.5
  • 85
    • 0025308916 scopus 로고
    • Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
    • Anderson, C.F. and Record, M.T. Jr (1990) Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications. Annu. Rev. Biophys. Chem., 19, 423-465.
    • (1990) Annu. Rev. Biophys. Chem. , vol.19 , pp. 423-465
    • Anderson, C.F.1    Record Jr., M.T.2
  • 87
    • 0031790423 scopus 로고    scopus 로고
    • Thermodynamic analysis of biomolecules: A volumetric approach
    • Chalikian, T.V. and Breslauer, K.J. (1998) Thermodynamic analysis of biomolecules: A volumetric approach. Curr. Opin. Struct. Biol., 8, 657-664.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 657-664
    • Chalikian, T.V.1    Breslauer, K.J.2
  • 88
    • 0035880916 scopus 로고    scopus 로고
    • Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces
    • Nadassy, K., Tomas-Oliveira, I., Alberts, I., Janin, J. and Wodak, S.J. (2001) Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucleic Acids Res., 29, 3362-3376. (Pubitemid 32799109
    • (2001) Nucleic Acids Research , vol.29 , Issue.16 , pp. 3362-3376
    • Nadassy, K.1    Tomas-Oliveira, I.2    Alberts, I.3    Janin, J.4    Wodak, S.J.5
  • 89
    • 0035976713 scopus 로고    scopus 로고
    • Do water molecules mediate protein-DNA recognitioñJ
    • Reddy, C.K., Das, A. and Jayaram, B. (2001) Do water molecules mediate protein-DNA recognitioñJ. Mol. Biol., 314, 619-632.
    • (2001) Mol. Biol. , vol.314 , pp. 619-632
    • Reddy, C.K.1    Das, A.2    Jayaram, B.3
  • 91
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
    • Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. and Richmond, T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol., 319, 1097-1113.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 93
    • 0032502924 scopus 로고    scopus 로고
    • Role of protein-induced bending in the specificity of DNA recognition: Crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT
    • DOI 10.1006/jmbi.1998.1655
    • Horton, N.C. and Perona, J.J. (1998) Role of protein-induced bending in the specificity of DNA-recognition: Crystal structure of EcoRV endonuclease complexed with d(AAAGAT)+d(ATCT T) J. Mol. Biol., 277, 779-787. (Pubitemid 28195981
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 779-787
    • Horton, N.C.1    Perona, J.J.2
  • 94
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar, R.S. and Record, M.T. Jr (1994) Coupling of local folding to site-specific binding of proteins to DNA. Science, 263, 777-784. (Pubitemid 24093205
    • (1994) Science , vol.263 , Issue.5148 , pp. 777-784
    • Spolar, R.S.1    Record Jr., M.T.2
  • 95
    • 2542609960 scopus 로고    scopus 로고
    • Helix bending as a factor in protein/DNA recognition
    • Dickerson, R.E. and Chiu, T.K. (1997) Helix bending as a factor in protein/DNA recognition. Biopolymers, 44, 361-403.
    • (1997) Biopolymers , vol.44 , pp. 361-403
    • Dickerson, R.E.1    Chiu, T.K.2
  • 96
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • DOI 10.1002/(SICI)1097-0134(19990401)35:1<114::AID-PROT11>3.0.CO;2- T
    • Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 35, 114-131. (Pubitemid 29128158
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.1 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 97
    • 1442351139 scopus 로고    scopus 로고
    • Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching
    • Tolstorukov, M.Y., Jernigan, R.L. and Zhurkin, V.B. (2004) Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J. Mol. Biol., 337, 65-76.
    • (2004) J. Mol. Biol. , vol.337 , pp. 65-76
    • Tolstorukov, M.Y.1    Jernigan, R.L.2    Zhurkin, V.B.3
  • 98
    • 60149104606 scopus 로고    scopus 로고
    • Signatures of protein-DNA recognition in free DNA binding sites
    • Locasale, J.W., Napoli, A.A., Chen, S., Berman, H.M. and Lawson, C.L. (2009) Signatures of protein-DNA recognition in free DNA binding sites. J. Mol. Biol., 386, 1054-1065.
    • (2009) J. Mol. Biol. , vol.386 , pp. 1054-1065
    • Locasale, J.W.1    Napoli, A.A.2    Chen, S.3    Berman, H.M.4    Lawson, C.L.5
  • 99
    • 0023029727 scopus 로고
    • DNA conformation is determined by economics in the hydration of phosphate groups
    • DOI 10.1038/324385a0
    • Saenger, W., Hunter, W.N. and Kennard, O. (1986) DNA conformation is determined by economics in the hydration of phosphate groups. Nature, 324, 385-388. (Pubitemid 17180118
    • (1986) Nature , vol.324 , Issue.6095 , pp. 385-388
    • Saenger, W.1    Hunter, W.N.2    Kennard, O.3
  • 100
    • 0035193091 scopus 로고    scopus 로고
    • Sequence-dependent B<->A transition in DNA evaluated with dimeric and trimeric scales
    • Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L. and Zhurkin, V.B. (2001) Sequence-dependent B<->A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J., 81, 3409-3421.
    • (2001) Biophys. J. , vol.81 , pp. 3409-3421
    • Tolstorukov, M.Y.1    Ivanov, V.I.2    Malenkov, G.G.3    Jernigan, R.L.4    Zhurkin, V.B.5
  • 101
    • 0024462296 scopus 로고
    • The conformation of the DNA double helix in the crystal is dependent on its environment
    • DOI 10.1038/342456a0
    • Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F. and Rabinovich, D. (1989) The conformation of the DNA double helix in the crystal Is dependent on its environment. Nature, 342, 456-460. (Pubitemid 19277526
    • (1989) Nature , vol.342 , Issue.6248 , pp. 456-460
    • Shakked, Z.1    Guerstein-Guzikevich, G.2    Eisenstein, M.3    Frolow, F.4    Rabinovich, D.5
  • 102
    • 0010812619 scopus 로고
    • The influence of the environment on DNA structures determined by X-ray crystallography
    • Shakked, Z. (1991) The influence of the environment on DNA structures determined by X-ray crystallography. Curr. Opin. Struct. Biol., 1, 446-451.
    • (1991) Curr. Opin. Struct. Biol. , vol.1 , pp. 446-451
    • Shakked, Z.1
  • 103
    • 73749085274 scopus 로고    scopus 로고
    • Non-B DNA structure-induced genetic instability and evolution
    • Zhao, J., Bacolla, A., Wang, G. and Vasquez, K.M. (2010) Non-B DNA structure-induced genetic instability and evolution. Cell. Mol. Life Sci., 67, 43-62.
    • (2010) Cell. Mol. Life Sci. , vol.67 , pp. 43-62
    • Zhao, J.1    Bacolla, A.2    Wang, G.3    Vasquez, K.M.4


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