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Volumn 337, Issue 1, 2004, Pages 65-76

Protein-DNA Hydrophobic Recognition in the Minor Groove is Facilitated by Sugar Switching

Author keywords

DNA accessible surface; DNA deformability; Hydrophobic interactions; Protein DNA recognition; Sugar pucker

Indexed keywords

AMINO ACID; DNA; NUCLEOTIDE; PROTEIN; PURINE; PYRIMIDINE; SOLVENT; SUGAR;

EID: 1442351139     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.01.011     Document Type: Article
Times cited : (73)

References (64)
  • 1
    • 0000127073 scopus 로고
    • Sequence-specific recognition of double helical nucleic acids by proteins
    • Seeman N.C., Rosenberg J.M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA. 73:1976;804-808.
    • (1976) Proc. Natl Acad. Sci. USA , vol.73 , pp. 804-808
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 2
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W.K., Gorin A.A., Lu X.J., Hock L.M., Zhurkin V.B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 95:1998;11163-11168.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 3
    • 0034655961 scopus 로고    scopus 로고
    • Nonsequence-specific DNA recognition: A structural perspective
    • Murphy F.V., Churchill M.E. Nonsequence-specific DNA recognition: a structural perspective. Struct. Fold. Des. 8:2000;R83-R89.
    • (2000) Struct. Fold. Des. , vol.8
    • Murphy, F.V.1    Churchill, M.E.2
  • 4
    • 0030812908 scopus 로고    scopus 로고
    • Transcription factor access to chromatin
    • Beato M., Eisfeld K. Transcription factor access to chromatin. Nucl. Acids Res. 25:1997;3559-3563.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 3559-3563
    • Beato, M.1    Eisfeld, K.2
  • 5
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of TATA element
    • Kim J.L., Nikolov D.B., Burley S.K. Co-crystal structure of TBP recognizing the minor groove of TATA element. Nature. 365:1993;520-527.
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 6
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 7
    • 0029131298 scopus 로고
    • Structural basis for DNA bending by the architectural transcription factor LEF-1
    • Love J.J., Li X., Case D.A., Giese K., Grosschedl R., Wright P.E. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature. 376:1995;791-795.
    • (1995) Nature , vol.376 , pp. 791-795
    • Love, J.J.1    Li, X.2    Case, D.A.3    Giese, K.4    Grosschedl, R.5    Wright, P.E.6
  • 8
    • 0033578010 scopus 로고    scopus 로고
    • Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins
    • Ohndorf U.-M., Rould M.A., He Q., Pabo C.O., Lippard S.J. Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature. 399:1999;708-712.
    • (1999) Nature , vol.399 , pp. 708-712
    • Ohndorf, U.-M.1    Rould, M.A.2    He, Q.3    Pabo, C.O.4    Lippard, S.J.5
  • 9
    • 0029075461 scopus 로고
    • Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex
    • Werner M.H., Huth J.R., Gronenborn A.M., Clore G.M. Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell. 81:1995;705-714.
    • (1995) Cell , vol.81 , pp. 705-714
    • Werner, M.H.1    Huth, J.R.2    Gronenborn, A.M.3    Clore, G.M.4
  • 10
    • 0035929239 scopus 로고    scopus 로고
    • Structural basis for SRY-dependent 46-X,Y sex reversal: Modulation of DNA bending by a naturally occurring point mutation
    • Murphy E.C., Zhurkin V.B., Louis J.M., Cornilescu G., Clore G.M. Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation. J. Mol. Biol. 312:2001;481-499.
    • (2001) J. Mol. Biol. , vol.312 , pp. 481-499
    • Murphy, E.C.1    Zhurkin, V.B.2    Louis, J.M.3    Cornilescu, G.4    Clore, G.M.5
  • 11
    • 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., Thornton J.M. Amino acid-base interactions: a three dimensional analysis of protein-DNA interactions at an atomic level. Nucl. Acids Res. 29:2001;2860-2874.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 12
    • 0022432240 scopus 로고
    • Structural junctions in DNA: The influence of flanking sequence on nuclease digestion specificities
    • Drew H.R., Travers A.A. Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities. Nucl. Acids Res. 13:1985;4445-4467.
    • (1985) Nucl. Acids Res. , vol.13 , pp. 4445-4467
    • Drew, H.R.1    Travers, A.A.2
  • 13
    • 0024294636 scopus 로고
    • Protein-DNA interaction. No code for recognition
    • Matthews B.W. Protein-DNA interaction. No code for recognition. Nature. 335:1988;294-295.
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.W.1
  • 14
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • Pabo C.O., Nekludova L. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol. 301:2000;597-624.
    • (2000) J. Mol. Biol. , vol.301 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 15
    • 0031722426 scopus 로고    scopus 로고
    • An analysis of the relationship between hydration and protein-DNA interactions
    • Woda J., Schneider B., Patel K., Mistry K., Berman H.M. An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75:1998;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
  • 16
    • 0029024850 scopus 로고
    • Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition
    • Eisenstein M., Shakked Z. Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248:1995;662-678.
    • (1995) J. Mol. Biol. , vol.248 , pp. 662-678
    • Eisenstein, M.1    Shakked, Z.2
  • 17
    • 0033573827 scopus 로고    scopus 로고
    • Structural features of protein-nucleic acid recognition sites
    • Nadassy K., Wodak S.J., Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry. 38:1999;1999-2017.
    • (1999) Biochemistry , vol.38 , pp. 1999-2017
    • Nadassy, K.1    Wodak, S.J.2    Janin, J.3
  • 19
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • Mandel-Gutfreund Y., Schueler O., Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J. Mol. Biol. 253:1995;370-382.
    • (1995) J. Mol. Biol. , vol.253 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 21
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu X.J., Shakked Z., Olson W.K. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300:2000;819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.J.1    Shakked, Z.2    Olson, W.K.3
  • 22
    • 0037388582 scopus 로고    scopus 로고
    • The double helix: A tale of two puckers
    • Rich A. The double helix: a tale of two puckers. Nature Struct. Biol. 10:2003;247-249.
    • (2003) Nature Struct. Biol. , vol.10 , pp. 247-249
    • Rich, A.1
  • 25
    • 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., Zhurkin V.B. Sequence-dependent B↔A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 81:2001;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
  • 26
    • 0028241531 scopus 로고
    • Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes
    • Nekludova L., Pabo C.O. Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. Proc. Natl Acad. Sci. USA. 91:1994;6948-6952.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 6948-6952
    • Nekludova, L.1    Pabo, C.O.2
  • 27
  • 28
    • 0030040722 scopus 로고    scopus 로고
    • A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein
    • Guzikevich-Guerstein G., Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol. 3:1996;32-37.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 32-37
    • Guzikevich-Guerstein, G.1    Shakked, Z.2
  • 29
    • 0029103236 scopus 로고
    • Reading the minor groove
    • Travers A.A. Reading the minor groove. Nature Struct. Biol. 2:1995;615-618.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 615-618
    • Travers, A.A.1
  • 30
    • 0028815978 scopus 로고
    • CRP-DNA complexes: Inducing the A-like form in the binding sites with an extended central spacer
    • Ivanov V.I., Minchenkova L.E., Chernov B.K., McPhie P., Ryu S., Garges S., et al. CRP-DNA complexes: inducing the A-like form in the binding sites with an extended central spacer. J. Mol. Biol. 245:1995;228-240.
    • (1995) J. Mol. Biol. , vol.245 , pp. 228-240
    • Ivanov, V.I.1    Minchenkova, L.E.2    Chernov, B.K.3    McPhie, P.4    Ryu, S.5    Garges, S.6
  • 32
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
    • El Hassan M.A., Calladine C.R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philos. Trans. Roy. Soc. London. 355:1997;43-100.
    • (1997) Philos. Trans. Roy. Soc. London , vol.355 , pp. 43-100
    • El Hassan, M.A.1    Calladine, C.R.2
  • 33
    • 0024282738 scopus 로고
    • 2: An analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance
    • 2: an analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance. Biochemistry. 27:1988;6013-6020.
    • (1988) Biochemistry , vol.27 , pp. 6013-6020
    • Zhou, N.1    Manogaran, S.2    Zon, G.3    James, T.L.4
  • 36
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I., Jernigan R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:1997;195-214.
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 37
    • 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
    • Glasfeld A., Koehler A.N., Schumacher M.A., Brennan R.G. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. J. Mol. Biol. 291:1999;347-361.
    • (1999) J. Mol. Biol. , vol.291 , pp. 347-361
    • Glasfeld, A.1    Koehler, A.N.2    Schumacher, M.A.3    Brennan, R.G.4
  • 38
    • 0020447308 scopus 로고
    • Flexibility of complementary dinucleoside phosphates-a Monte Carlo study
    • Ulyanov N.B., Zhurkin V.B. Flexibility of complementary dinucleoside phosphates-a Monte Carlo study. Mol. Biol. (Engl. transl.). 16:1982;857-867.
    • (1982) Mol. Biol. (Engl. Transl.) , vol.16 , pp. 857-867
    • Ulyanov, N.B.1    Zhurkin, V.B.2
  • 41
    • 0032972857 scopus 로고    scopus 로고
    • Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
    • Martin A.M., Sam M.D., Reich N.O., Perona J.J. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nature Struct. Biol. 6:1999;269-277.
    • (1999) Nature Struct. Biol. , vol.6 , pp. 269-277
    • Martin, A.M.1    Sam, M.D.2    Reich, N.O.3    Perona, J.J.4
  • 42
    • 0025914242 scopus 로고
    • Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
    • Schultz S.C., Shields G.C., Steitz T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 253:1991;1001-1007.
    • (1991) Science , vol.253 , pp. 1001-1007
    • Schultz, S.C.1    Shields, G.C.2    Steitz, T.A.3
  • 43
    • 0037473496 scopus 로고    scopus 로고
    • Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?
    • Bosch D., Campillo M., Pardo L. Binding of proteins to the minor groove of DNA: what are the structural and energetic determinants for kinking a basepair step? J. Comput. Chem. 24:2003;682-691.
    • (2003) J. Comput. Chem. , vol.24 , pp. 682-691
    • Bosch, D.1    Campillo, M.2    Pardo, L.3
  • 45
    • 0033032014 scopus 로고    scopus 로고
    • Intrinsic conformational properties of deoxyribonucleosides: Implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA
    • Foloppe N., MacKerell A.D. Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA. Biophys. J. 76:1999;3206-3218.
    • (1999) Biophys. J. , vol.76 , pp. 3206-3218
    • Foloppe, N.1    MacKerell, A.D.2
  • 46
    • 0029041940 scopus 로고
    • Stereochemical basis of DNA bending by transcription factors
    • Suzuki M., Yagi N. Stereochemical basis of DNA bending by transcription factors. Nucl. Acids Res. 23:1995;2083-2091.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 2083-2091
    • Suzuki, M.1    Yagi, N.2
  • 47
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • Dickerson R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucl. Acids Res. 26:1998;1906-1926.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 1906-1926
    • Dickerson, R.E.1
  • 48
    • 0024974069 scopus 로고
    • Sequence dependence of DNA conformational flexibility
    • Sarai A., Mazur J., Nussinov R., Jernigan R.L. Sequence dependence of DNA conformational flexibility. Biochemistry. 28:1989;7842-7849.
    • (1989) Biochemistry , vol.28 , pp. 7842-7849
    • Sarai, A.1    Mazur, J.2    Nussinov, R.3    Jernigan, R.L.4
  • 49
    • 0021711244 scopus 로고
    • Sequence-dependent anisotropic flexibility of B-DNA. a conformational study
    • Ulyanov N.B., Zhurkin V.B. Sequence-dependent anisotropic flexibility of B-DNA. A conformational study. J. Biomol. Struct. Dynam. 2:1984;361-385.
    • (1984) J. Biomol. Struct. Dynam. , vol.2 , pp. 361-385
    • Ulyanov, N.B.1    Zhurkin, V.B.2
  • 50
    • 0020385863 scopus 로고
    • Mechanics of sequence-dependent stacking of bases in B-DNA
    • Calladine C.R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161:1982;343-352.
    • (1982) J. Mol. Biol. , vol.161 , pp. 343-352
    • Calladine, C.R.1
  • 52
    • 0000857592 scopus 로고
    • The structure of sodium thymonucleate fibers. I. the influence of water content
    • Franklin R.E., Gosling R.G. The structure of sodium thymonucleate fibers. I. The influence of water content. Acta Crystallog. 6:1953;673-677.
    • (1953) Acta Crystallog. , vol.6 , pp. 673-677
    • Franklin, R.E.1    Gosling, R.G.2
  • 55
    • 0025150383 scopus 로고
    • Origins of structure in globular-proteins
    • Chan H.S., Dill K.A. Origins of structure in globular-proteins. Proc. Natl Acad. Sci. USA. 87:1990;6388-6392.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 6388-6392
    • Chan, H.S.1    Dill, K.A.2
  • 56
    • 0026742978 scopus 로고
    • The nucleic acid database. a comprehensive relational database of three-dimensional structures of nucleic acids
    • Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., et al. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
    • (1992) Biophys. J. , vol.63 , pp. 751-759
    • Berman, H.M.1    Olson, W.K.2    Beveridge, D.L.3    Westbrook, J.4    Gelbin, A.5    Demeny, T.6
  • 57
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base pair morphology
    • Gorin A.A., Zhurkin V.B., Olson W.K. B-DNA twisting correlates with base pair morphology. J. Mol. Biol. 247:1995;34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 58
    • 84988075035 scopus 로고
    • Algorithm for rapid calculation of excluded volume of large molecules
    • Higo J., Go N. Algorithm for rapid calculation of excluded volume of large molecules. J. Comput. Chem. 10:1989;376-379.
    • (1989) J. Comput. Chem. , vol.10 , pp. 376-379
    • Higo, J.1    Go, N.2
  • 59
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 60
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 221:1983;709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 61
    • 0027048948 scopus 로고
    • Crystal and molecular structure of d(GTGCGCAC): Investigation of the effects of base sequence on the conformation of octamer duplexes
    • Bingman C., Li X., Zon G., Sundaralingam M. Crystal and molecular structure of d(GTGCGCAC): investigation of the effects of base sequence on the conformation of octamer duplexes. Biochemistry. 31:1992;12803-12812.
    • (1992) Biochemistry , vol.31 , pp. 12803-12812
    • Bingman, C.1    Li, X.2    Zon, G.3    Sundaralingam, M.4
  • 62
    • 0031588009 scopus 로고    scopus 로고
    • Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction
    • Wood A.A., Nunn C.M., Trent J.O., Neidle S. Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction. J. Mol. Biol. 269:1997;827-841.
    • (1997) J. Mol. Biol. , vol.269 , pp. 827-841
    • Wood, A.A.1    Nunn, C.M.2    Trent, J.O.3    Neidle, S.4
  • 64
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2


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