Nonsequence-specific DNA recognition: A structural perspective

Structure

Volumn 8, Issue 4, 2000, Pages

  Murphy IV, Frank V ^a,b   Churchill, Mair Ea ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; CURVED DNA; DNA FRAGMENT; HIGH MOBILITY GROUP PROTEIN; HISTONE;

DNA BINDING; DNA PROTEIN COMPLEX; DNA STRUCTURE; DROSOPHILA MELANOGASTER; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN STRUCTURE; SHORT SURVEY; THERMODYNAMICS;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0034655961     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00126-X     Document Type: Review

References (39)

1. 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;804-805.
2. Pabo C., Sauer R. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61:1992;1053-1095.
3. Bewley C., Gronenborn A.M., Clore M.G. Minor groove-binding architectural proteins: structure, function, and DNA recognition. Annu. Rev. Biophys. Biomol. Struct. 27:1998;105-131.
4. von Hippel P.H. Protein-DNA recognition: new perspectives and underlying themes. Science. 263:1994;769-770.
5. Kornberg R.D. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell. 98:1999;285-295.
6. Bustin M., Reeves R. High-mobility-group chromosomal proteins: architectural components that facilitate chromatin function. Prog. Nuc. Acid Res. Mol. Biol. 54:1996;35-100.
7. Murphy F.V. IV, Sweet R.M., Churchill M.E.A. The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J. 18:1999;6610-6618.
8. Robinson H., Gao Y-G., McCrary B.S., Edmondson S.P., Shriver J.W., Wang A.H-J. The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature. 392:1998;202-205.
9. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
10. Baxevanis A.D., Landsman D. The HMG-1 box protein family: classification and functional relationships. Nucleic Acids Res. 23:1995;1604-1613.
11. Giese K., Amsterdam A., Grosschedl R. DNA-binding properties of the HMG-domain of the lymphoid-specific transcriptional regulator LEF-1. Genes Dev. 5:1991;2567-2578.
12. Nightingale K., Dimitrov S., Reeves R., Wolffe A. Evidence for a shared structural role for HMG1 and linker histones B4 and H1 in organizing chromatin. EMBO J. 15:1996;548-561.
13. Bustin M. Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol. Cell Biol. 19:1999;5237-5246.
14. Read C.M., Cary P.D., Crane-Robinson C., Driscoll P.C., Norman D.G. Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Res. 21:1993;3427-3436.
15. Weir H.M., Kraulis P.J., Hill C.S., Raine A., Laue E.D., Thomas J.O. Structure of the HMG box motif in the B-domain of HMG1. EMBO J. 12:1993;1311-1319.
16. Jones D.N.M., Neuhaus D.et al. The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila Melanogaster. Structure. 2:1994;609-627.
17. 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.
18. 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.
19. 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.
20. Grosschedl R., Giese K., Pagel J. HMG domain proteins - architectural elements in the assembly of nucleoprotein structures. Trends Genet. 10:1994;94-100.
21. Takahara P.M., Frederick C.A., Lippard S.J. Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J. Am. Chem. Soc. 118:1996;12309-12321.
22. Allain F.H-T., Feigon J.et al. Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding. EMBO J. 18:1999;2563-2579.
23. Balaeff A., Churchill M.E.A., Schulten K. Structure prediction of a complex between the chromosomal protein HMG-D and DNA. Proteins. 30:1998;113-135.
24. Payet D., Hillisch A., Lowe N., Diekmann S., Travers A. The recognition of distorted DNA structures by HMG-D: a footprinting and molecular modeling study. J. Mol. Biol. 294:1999;79-91.
25. Pil P., Lippard S.J. Specific binding of chromosomal protein HMG-1 to DNA damaged by the anticancer drug cisplatin. Science. 256:1992;234-237.
26. Dunham S.U., Lippard S.J. DNA sequence context and protein composition modulate HMG-domain protein recognition of cisplatin-modified DNA. Biochemistry. 36:1997;11428-11436.
27. McAfee J.G., Edmondson S.P., Zegar I., Shriver J.W. Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies. Biochemistry. 35:1996;4034-4045.
28. Bauman H., Knapp S., Lundbäck T., Ladenstein R., Härd T. Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus. Nat. Struct. Biol. 1:1994;808-819.
29. Gao Y-G., Wang A.H-J.et al. The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat. Struct. Biol. 5:1998;782-786.
30. Luger K., Richmond T.J. DNA binding within the nucleosome core. Curr. Opin. Struct. Biol. 8:1998;33-40.
31. Revzin A. Non-Specific DNA-Protein Interactions. 1990;CRC Press, Boca Raton, Florida.
32. Schwabe J.W. The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol. 7:1997;126-134.
33. Ladbury J.E., Wright J.G., Sturtevant J.M., Sigler P.B. A thermodynamic study of the Trp repressor-operator interaction. J. Mol. Biol. 238:1994;669-681.
34. Sidorova N.Y., Rau D.C. Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc. Natl Acad. Sci. USA. 93:1996;12272-12277.
35. Tanha J., Lee J.S. Thermodynamic analysis of monoclonal antibody binding to duplex DNA. Nucleic Acids Res. 7:1997;1442-1449.
36. Oda M., Furukawa K., Ogata K., Sarai A., Nakamura H. Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain. J. Mol. Biol. 276:1998;571-590.
37. Lündback T., Hansson H., Knapp S., Ladenstein R., Härd T. Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus. J. Mol. Biol. 276:1998;775-786.
38. Jones S., Heyningen P.v., Berman H.M., Thornton J.M. Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287:1999;877-896.
39. Lavery R., Sklenar H. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6:1989;655-667.