Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces.
暂无分享,去创建一个
[1] A. Conter,et al. Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. , 1997, Journal of molecular biology.
[2] R E Harrington,et al. The effects of sequence context on DNA curvature. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[3] G. Koudelka,et al. Carboxyl-terminal domain dimer interface mutant 434 repressors have altered dimerization and DNA binding specificities. , 1998, Journal of molecular biology.
[4] T. Ellenberger,et al. Flexibility in DNA Recombination: Structure of the Lambda Integrase Catalytic Core , 1997, Science.
[5] K. Zakrzewska,et al. Sequence specificity of bacteriophage 434 repressor-operator complexation. , 1998, Journal of molecular biology.
[6] S Subbiah,et al. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. , 1989, Journal of molecular biology.
[7] A. Klug,et al. The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.
[8] M Suzuki,et al. Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. , 1997, Journal of molecular biology.
[9] Mikael Kubista,et al. Nucleosome Structural Features and Intrinsic Properties of the TATAAACGCC Repeat Sequence* , 1999, The Journal of Biological Chemistry.
[10] A. Segall,et al. Architectural elements in nucleoprotein complexes: interchangeability of specific and non‐specific DNA binding proteins. , 1994, The EMBO journal.
[11] H. Heumann,et al. Flexibility of the DNA enhances promoter affinity of Escherichia coli RNA polymerase. , 1991, The EMBO journal.
[12] Ronen Marmorstein,et al. Structure of the Elk-1–DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA , 2000, Nature Structural Biology.
[13] P. Dehaseth,et al. RNA polymerase bound to the PR promoter of bacteriophage λ inhibits open complex formation at the divergently transcribed PRM promoter : implications for an indirect mechanism of transcriptional activation by λ repressor , 1991 .
[14] A C Bell,et al. Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes. , 1993, Journal of molecular biology.
[15] M. Record,et al. Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water. , 1998, Trends in biochemical sciences.
[16] R. Dickerson,et al. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. , 1991, The Journal of biological chemistry.
[17] R. Sauer,et al. P22 c2 repressor. Domain structure and function. , 1983, Journal of Biological Chemistry.
[18] Christopher A. Hunter,et al. Sequence-dependent DNA structure: tetranucleotide conformational maps. , 2000 .
[19] C. Pargellis,et al. Autonomous DNA binding domains of λ integrase recognize two different sequence families , 1988, Cell.
[20] Ian R. Booth,et al. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli , 1988, Cell.
[21] D. Auble,et al. Promoter recognition by Escherichia coli RNA polymerase. Effects of substitutions in the spacer DNA separating the -10 and -35 regions. , 1986, The Journal of biological chemistry.
[22] F. Crick,et al. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.
[23] P. Dehaseth,et al. Interference by PR-bound RNA polymerase with PRM function in vitro. Modulation by the bacteriophage lambda cI protein. , 1993, The Journal of biological chemistry.
[24] G. Koudelka. Recognition of DNA structure by 434 repressor. , 1998, Nucleic acids research.
[25] G. Koudelka,et al. Mutually Exclusive Utilization of PRand PRM Promoters in Bacteriophage 434 OR , 2000, Journal of bacteriology.
[26] R. Dickerson,et al. Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G. , 1999, Journal of molecular biology.
[27] S. Harrison,et al. The phage 434 OR2/R1-69 complex at 2.5 A resolution. , 1993, Journal of molecular biology.
[28] R. Dickerson,et al. 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. , 2000, Journal of molecular biology.
[29] Mark Ptashne,et al. A new-specificity mutant of 434 repressor that defines an amino acid–base pair contact , 1987, Nature.
[30] R. Sauer,et al. [76] Bacteriophage λ repressor and cro protein: Interactions with operator DNA , 1980 .
[31] A. Sentenac,et al. Specific DNA binding by c-Myb: evidence for a double helix-turn-helix-related motif , 1991, Science.
[32] D W Hukins,et al. Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. , 1973, Journal of molecular biology.
[33] A. Jeltsch,et al. Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA. , 1994, Biochemistry.
[34] R. Doolittle,et al. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure , 1982, Nature.
[35] S. Harrison,et al. The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites. , 1993, Structure.
[36] M. A. El Hassan,et al. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. , 1996, Journal of molecular biology.
[37] M. Delepierre,et al. How NF-κB can be attracted by its cognate DNA , 1999 .
[38] C. Higgins,et al. The Downstream Regulatory Element of the proU Operon of Salmonella typhimurium Inhibits Open Complex Formation by RNA Polymerase at a Distance* , 2000, The Journal of Biological Chemistry.
[39] N. Hud,et al. DNA-cation interactions: The major and minor grooves are flexible ionophores. , 2001, Current opinion in structural biology.
[40] G. Koudelka,et al. DNA-induced conformational changes in bacteriophage 434 repressor. , 1999, Journal of molecular biology.
[41] R. K. Stephens,et al. Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]2 , 1999 .
[42] Catherine L. Lawson,et al. The three-dimensional structure of trp repressor , 1985, Nature.
[43] G. Koudelka. Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins. , 1991, Nucleic Acids Research.
[44] G B Koudelka,et al. Non-contacted bases affect the affinity of synthetic P22 operators for P22 repressor. , 1992, The Journal of biological chemistry.
[45] D M Crothers,et al. Identification and characterization of genomic nucleosome-positioning sequences. , 1997, Journal of molecular biology.
[46] W. Olson,et al. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. , 2003, Nucleic acids research.
[47] H. R. Wilson,et al. THE MOLECULAR CONFIGURATION OF DEOXYRIBONUCLEIC ACID. IV. X-RAY DIFFRACTION STUDY OF THE A FORM. , 1965, Journal of molecular biology.
[48] T. Richmond,et al. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.
[49] Bruno H. Zimm,et al. Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA , 1979 .
[50] D. VanDerveer,et al. Locating monovalent cations in the grooves of B-DNA. , 2001, Biochemistry.
[51] R. Rohs,et al. Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. , 2005, Structure.
[52] M. Brenowitz,et al. DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins. , 1998, Journal of molecular biology.
[53] J. Widom,et al. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. , 1999, Journal of molecular biology.
[54] T. Haran,et al. Signals for TBP/TATA box recognition. , 2000, Journal of molecular biology.
[55] G. Koudelka,et al. Dimerization specificity of P22 and 434 repressors is determined by multiple polypeptide segments , 1997, Journal of bacteriology.
[56] M Ptashne,et al. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution , 1988, Science.
[57] C. Higgins,et al. Osmotic regulation of porin expression: a role for DNA supercoiling , 1989, Molecular microbiology.
[58] S. Adhya,et al. RNA polymerase idling and clearance in gal promoters: use of supercoiled minicircle DNA template made in vivo. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[59] S. Mizutani,et al. A comparative study of the immunity region of lambdoid phages including Shiga-toxin-converting phages: molecular basis for cross immunity. , 2000, Genes & genetic systems.
[60] Structure and dynamics of MarA-DNA complexes: an NMR investigation. , 2001, Journal of molecular biology.
[61] G. Koudelka,et al. Repression of transcription initiation at 434 P(R) by 434 repressor: effects on transition of a closed to an open promoter complex. , 2001, Journal of molecular biology.
[62] K. Yamamoto,et al. Mutations in the glucocorticoid receptor DNA-binding domain mimic an allosteric effect of DNA. , 2000, Journal of molecular biology.
[63] C. Arrowsmith,et al. DNA Binding Specificity Studies of Four ETS Proteins Support an Indirect Read-out Mechanism of Protein-DNA Recognition* 210 , 2000, The Journal of Biological Chemistry.
[64] J. Feigon,et al. Localization of Divalent Metal Ions in the Minor Groove of DNA A-Tracts , 1997 .
[65] Monovalent cations regulate DNA sequence recognition by 434 repressor. , 2004 .
[66] M. Record,et al. Biophysical compensation mechanisms buffering E. coli protein-nucleic acid interactions against changing environments. , 1998, Trends in biochemical sciences.
[67] H. Sasmor,et al. Symmetric lac operator derivatives: effects of half-operator sequence and spacing on repressor affinity. , 1990, Gene.
[68] M. Sierk,et al. DNA deformability as a recognition feature in the reverb response element. , 2001, Biochemistry.
[69] I. Rouzina,et al. DNA bending by small, mobile multivalent cations. , 1998, Biophysical journal.
[70] S. Goodman,et al. Deformation of DNA during site-specific recombination of bacteriophage lambda: replacement of IHF protein by HU protein or sequence-directed bends. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[71] R. Sauer,et al. The lambda repressor contains two domains. , 1979, Proceedings of the National Academy of Sciences of the United States of America.
[72] C R Calladine,et al. The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. , 1995, Journal of molecular biology.
[73] T. Richmond,et al. DNA-dependent divalent cation binding in the nucleosome core particle , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[74] G B Koudelka,et al. DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[75] F. Bushman. The Bacteriophage 434 Right Operator Roles of OR1, OR2 and OR3 , 1993 .
[76] S. Phillips,et al. Crystal structure of the met represser–operator complex at 2.8 Å resolution reveals DNA recognition by β-strands , 1992, Nature.
[77] N. Craig,et al. E. coli integration host factor binds to specific sites in DNA , 1984, Cell.
[78] R. Marmorstein,et al. Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins. , 1998, Molecular cell.
[79] T. Curran,et al. Energy transfer analysis of Fos-Jun dimerization and DNA binding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[80] H R Drew,et al. Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[81] Paul Carlson,et al. DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 represser , 1992, Nature.
[82] A. Rich,et al. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[83] Richard A. Pfuetzner,et al. Crystal Structure of LexA A Conformational Switch for Regulation of Self-Cleavage , 2001, Cell.
[84] D. Auble,et al. Promoter recognition by Escherichia coli RNA polymerase. Influence of DNA structure in the spacer separating the -10 and -35 regions. , 1988, Journal of molecular biology.
[85] S. Harrison,et al. A structural taxonomy of DNA-binding domains , 1991, Nature.
[86] S. Harrison,et al. Structure of the represser–operator complex of bacteriophage 434 , 1987, Nature.
[87] G. Koudelka,et al. How 434 repressor discriminates between OR1 and OR3. The influence of contacted and noncontacted base pairs. , 1995, The Journal of biological chemistry.
[88] John W. R. Schwabe,et al. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements , 1993, Cell.
[89] A. Jeltsch,et al. Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. , 1996, The EMBO journal.
[90] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.
[91] R. Harrington,et al. Unconventional helical phasing of repetitive DNA motifs reveals their relative bending contributions. , 1998, Nucleic acids research.
[92] M. Sundaralingam,et al. Stereochemistry of nucleic acids and their constituents. X. solid‐slate base‐slacking patterns in nucleic acid constituents and polynucleotides , 1971, Biopolymers.
[93] M. A. El Hassan,et al. Structural mechanics of bent DNA. , 1996, Endeavour.
[94] M. Ptashne,et al. Repressor structure and the mechanism of positive control , 1983, Cell.
[95] G. Montelione,et al. Design of a "minimAl" homeodomain: the N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[96] Jeffrey A. Lefstin,et al. Allosteric effects of DNA on transcriptional regulators , 1998, Nature.
[97] K. Yamamoto,et al. Analysis of the DNA-binding affinity, sequence specificity and context dependence of the glucocorticoid receptor zinc finger region. , 1994, Journal of molecular biology.
[98] J. Feigon,et al. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. , 1999, Journal of molecular biology.
[99] J. Michael Schurr,et al. Dependence of the torsional rigidity of DNA on base composition , 1990, Nature.
[100] Wolfram Saenger,et al. Principles of Nucleic Acid Structure , 1983 .
[101] G G Hu,et al. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. , 1998, Biochemistry.
[102] 西村 善文. W. Saenger: Principles of Nucleic Acid Structure, Springer-Verlag, New York and Berlin, 1984, xx+556ページ, 24.5×16.5cm, 14,160円 (Springer Advanced Texts in Chemistry). , 1985 .
[103] L. Williams,et al. DNA structure: cations in charge? , 1999, Current opinion in structural biology.
[104] R E Harrington,et al. Bending and Torsional Flexibility of G/C-rich Sequences as Determined by Cyclization Assays (*) , 1995, The Journal of Biological Chemistry.
[105] G. Koudelka,et al. DNA sequence requirements for the activation of 434 P(RM) transcription by 434 repressor. , 2000, DNA and cell biology.
[106] S. Grossman,et al. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA target , 1992, Nature.
[107] S. Harrison,et al. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro , 1987, Nature.
[108] Richard E. Dickerson,et al. Crystal structure analysis of a complete turn of B-DNA , 1980, Nature.
[109] N. Seeman,et al. Double Helix at Atomic Resolution , 1973, Nature.
[110] Donald M. Crothers,et al. DNA sequence determinants of CAP-induced bending and protein binding affinity , 1988, Nature.
[111] R. Kodandapani,et al. A new pattern for helix–turn–helix recognition revealed by the PU.l ETS–domain–DNA complex , 1996, Nature.
[112] D. VanDerveer,et al. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. , 1998, Biochemistry.
[113] Cynthia Wolberger,et al. The Structure of GABPα/β: An ETS Domain- Ankyrin Repeat Heterodimer Bound to DNA , 1998 .
[114] Steven A Mauro,et al. The Role of the Minor Groove Substituents in Indirect Readout of DNA Sequence by 434 Repressor* , 2003, The Journal of Biological Chemistry.
[115] Jeffrey A. Lefstin,et al. Influence of a steroid receptor DNA-binding domain on transcriptional regulatory functions. , 1994, Genes & development.
[116] E. Androphy,et al. Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism. , 1998, Journal of molecular biology.
[117] C R Calladine,et al. Mechanics of sequence-dependent stacking of bases in B-DNA. , 1982, Journal of molecular biology.
[118] S. Belikov,et al. Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. , 1999, Nucleic acids research.
[119] R. Sauer,et al. The lambda and P22 phage repressors. , 1983, Journal of biomolecular structure & dynamics.
[120] Steven Hahn,et al. Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.
[121] I. Rouzina,et al. Force-induced melting of the DNA double helix. 2. Effect of solution conditions. , 2001, Biophysical journal.
[122] H. Nash,et al. The interaction of E. coli IHF protein with its specific binding sites , 1989, Cell.
[123] M. Ptashne. A Genetic Switch , 1986 .
[124] M. Egli,et al. Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. , 1999, Journal of molecular biology.
[125] D. Bazett-Jones,et al. DNA Structure Determines Protein Binding and Transcriptional Efficiency of the Proenkephalin cAMP-responsive Enhancer (*) , 1995, The Journal of Biological Chemistry.
[126] Mark Ptashne,et al. Interactions between DNA-bound repressors govern regulation by the λ phage repressor , 1979 .