Influence of ions, hydration, and the transcriptional inhibitor P4N on the conformations of the Sp1 binding site

Journal of Molecular Biology

Volumn 349, Issue 4, 2005, Pages 731-744

  Dohm, Julie A ^a   Hsu, Ming Hua ^b   Hwu, Jih Ru ^b   Huang, Ru Chih C ^a   Moudrianakis, Evangelos N ^a   Lattman, Eaton E ^c   Gittis, Apostolos G ^c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

A DNA crystal structure; Drug DNA interactions; Flipped out bases; NDGA derivatives; Sp1 consensus sequence

Indexed keywords

2,3 DIMETHYL 1,4 BIS[3,4 [3 (PIPERIDINO)ETHOXYPHENYL]]BUTANE; ANTINEOPLASTIC AGENT; ANTIVIRUS AGENT; COBALT; DOUBLE STRANDED DNA; ION; MACROGOL 400; METHENAMINE; POLYAMINE; SPERMIDINE; TRANSCRIPTION FACTOR SP1; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; DENSITY; DRUG TARGETING; ELECTRON; HYDRATION; MOLECULE; NUCLEOTIDE BINDING SITE; PRECIPITATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN TARGETING;

EID: 19444363382     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.04.001     Document Type: Article

References (51)

1. X.J. Lu, Z. Shakked, and W.K. Olson A-form conformational motifs in ligand-bound DNA structures J. Mol. Biol. 300 2000 819 840
2. M.C. Wahl, and M. Sundaralingam Crystal structures of A-DNA duplexes Biopolymers 44 1997 45 63
3. J.A. Subirana, and M. Soler-Lopez Cations as hydrogen bond donors: a view of electrostatic interactions in DNA Annu. Rev. Biophys. Biomol. Struct. 32 2003 27 45
4. D.B. Tippin, and M. Sundaralingam Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA J. Mol. Biol. 267 1997 1171 1185
5. J.M. Vargason, K. Henderson, and P.S. Ho A crystallographic map of the transition from B-DNA to A-DNA Proc. Natl Acad. Sci. USA 98 2001 7265 7270
6. X.L. Yang, and A.H. Wang Structural studies of atom-specific anticancer drugs acting on DNA Pharmacol. Ther. 83 1999 181 215
7. A. Gelasco, and S.J. Lippard NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin Biochemistry 37 1998 9230 9239
8. M. Sastry, and D.J. Patel Solution structure of the mithramycin dimer-DNA complex Biochemistry 32 1993 6588 6604
9. S. Kamitori, and F. Takusagawa Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D J. Mol. Biol. 225 1992 445 456
10. M.H. Hou, H. Robinson, Y.G. Gao, and A.H. Wang Crystal structure of actinomycin D bound to the CTG triplet repeat sequences linked to neurological diseases Nucl. Acids Res. 30 2002 4910 4917
11. H. Robinson, Y.G. Gao, X. Yang, R. Sanishvili, A. Joachimiak, and A.H. Wang Crystallographic analysis of a novel complex of actinomycin D bound to the DNA decamer CGATCGATCG Biochemistry 40 2001 5587 5592
12. J.N. Gnabre, J.N. Brady, D.J. Clanton, Y. Ito, J. Dittmer, R.B. Bates, and R.C. Huang Inhibition of human immunodeficiency virus type 1 transcription and replication by DNA sequence-selective plant lignans Proc. Natl Acad. Sci. USA 92 1995 11239 11243
13. L.H. Hurley, and D. Sun (+)-CC-1065 as a probe for intrinsic and protein-induced bending of DNA J. Mol. Recognit. 7 1994 123 132
14. T. Cook, B. Gebelein, and R. Urrutia Sp1 and its likes: biochemical and functional predictions for a growing family of zinc finger transcription factors Ann. N Y Acad. Sci. 880 1999 94 102
15. J.R. Hwu, W.N. Tseng, J. Gnabre, P. Giza, and R.C. Huang Antiviral activities of methylated nordihydroguaiaretic acids. 1. Synthesis, structure identification, and inhibition of tat-regulated HIV transactivation J. Med. Chem. 41 1998 2994 3000
16. J.M. Berg Sp1 and the subfamily of zinc finger proteins with guanine-rich binding sites Proc. Natl Acad. Sci. USA 89 1992 11109 11110
17. Y. Shi, and J.M. Berg DNA unwinding induced by zinc finger protein binding Biochemistry 35 1996 3845 3848
18. J.L. Kim, D.B. Nikolov, and S.K. Burley Co-crystal structure of TBP recognizing the minor groove of a TATA element Nature 365 1993 520 527
19. A.E. Maris, M.R. Sawaya, M. Kaczor-Grzeskowiak, M.R. Jarvis, S.M. Bearson, and M.L. Kopka Dimerization allows DNA target site recognition by the NarL response regulator Nature Struct. Biol. 9 2002 771 778
20. R. Lavery, and H. Sklenar Defining the structure of irregular nucleic acids: conventions and principles J. Biomol. Struct. Dynam. 6 1989 655 667
21. G. Savitha, and M.A. Viswamitra An A-DNA structure with two independent duplexes in the asymmetric unit Acta Crystallog. sect. D 55 1999 1136 1143
22. N.G. Abrescia, A. Thompson, T. Huynh-Dinh, and J.A. Subirana Crystal structure of an antiparallel DNA fragment with Hoogsteen base-pairing Proc. Natl Acad. Sci. USA 99 2002 2806 2811
23. D.B. Tippin Structure of d(CCCTAGGG): comparison with nine isomorphous octamer sequences reveals four distinct patterns of sequence-dependent intermolecular interactions Acta Crystallog. sect. D 52 1996 997 1003
24. B. Ramakrishnan, and M. Sundaralingam High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets J. Mol. Biol. 231 1993 431 444
25. C.M. Nunn, and S. Neidle The high resolution crystal structure of the DNA decamer d(AGGCATGCCT) J. Mol. Biol. 256 1996 340 351
26. C.M. Nunn, and S. Neidle Structure of the DNA decamer d(GGCAATTGCG) contains both major- and minor-groove binding G.(G.C) base triplets Acta Crystallog. sect. D 54 1998 577 583
27. C.C. Chang, J.D. Heller, J. Kuo, and R.C. Huang Tetra-O-methyl nordihydroguaiaretic acid induces growth arrest and cellular apoptosis by inhibiting Cdc2 and survivin expression Proc. Natl Acad. Sci. USA 101 2004 13239 13244
28. J.D. Heller, J. Kuo, T.C. Wu, W.M. Kast, and R.C. Huang Tetra-O-methyl nordihydroguaiaretic acid induces G2 arrest in mammalian cells and exhibits tumoricidal activity in vivo Cancer Res. 61 2001 5499 5504
29. I. Haq Thermodynamics of drug-DNA interactions Arch Biochem. Biophys. 403 2002 1 15
30. W.H. Braunlin, and Q. Xu Hexaamminecobalt(III) binding environments on double-helical DNA Biopolymers 32 1992 1703 1711
31. H.M. Berman, W.K. Olson, D.L. Beveridge, J. Westbrook, A. Gelbin, and T. Demeny The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids Biophys. J. 63 1992 751 759
32. V.A. Bloomfield DNA condensation by multivalent cations Biopolymers 44 1997 269 282
33. D. Miyoshi, A. Nakao, and N. Sugimoto Molecular crowding regulates the structural switch of the DNA G-quadruplex Biochemistry 41 2002 15017 15024
34. M. Egli, V. Tereshko, M. Teplova, G. Minasov, A. Joachimiak, and R. Sanishvili X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution Biopolymers 48 1998 234 252
35. M. Eisenstein, and Z. Shakked Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition J. Mol. Biol. 248 1995 662 678
36. M. McCall, T. Brown, W.N. Hunter, and O. Kennard The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA Nature 322 1986 661 664
37. J. Barciszewski, J. Jurczak, S. Porowski, T. Specht, and V.A. Erdmann The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions Eur. J. Biochem. 260 1999 293 307
38. K. Igarashi, and K. Kashiwagi Polyamines: mysterious modulators of cellular functions Biochem. Biophys. Res. Commun. 271 2000 559 564
39. N. Korolev, A.P. Lyubartsev, L. Nordenskiold, and A. Laaksonen Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study J. Mol. Biol. 308 2001 907 917
40. L. Urpi, J. Navaza, and J.A. Subirana Alternation of DNA and solvent layers in the A form of d(GGCGCC) obtained by ethanol crystallization J. Biomol. Struct. Dynam. 18 2000 363 369
41. L. Nekludova, C.O. Pabo, and D.N.A. Distinctive 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
42. J.M. Gottesfeld, L. Neely, J.W. Trauger, E.E. Baird, and P.B. Dervan Regulation of gene expression by small molecules Nature 387 1997 202 205
43. L. Neely, J.W. Trauger, E.E. Baird, P.B. Dervan, and J.M. Gottesfeld Importance of minor groove binding zinc fingers within the transcription factor IIIA-DNA complex J. Mol. Biol. 274 1997 439 445
44. Z. Otwinowski, and W. Minor Processing of X-ray data collected in oscillation mode Methods Enzymol. 276 1997 307 326
45. Collaborative Computational Project, N The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
46. J. Navaza AMoRe: an automated package for molecular replacement Acta Crystallog. sect. A 50 1994 157 163
47. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallog. 30 1997 1022 1025
48. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography, NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
49. T.A. Jones, J.Y. Zou, S.W. Cowan, and Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
50. R.E. Dickerson DNA bending: the prevalence of kinkiness and the virtues of normality Nucl. Acids Res. 26 1998 1906 1926
51. X.J. Lu, and W.K. Olson 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucl. Acids Res. 31 2003 5108 5121