The recognition of distorted DNA structures by HMG-D: A footprinting and molecular modelling study

Journal of Molecular Biology

Volumn 294, Issue 1, 1999, Pages 79-91

  Payet, Dominique ^a   Hillisch, Alexander ^b   Lowe, Nicholas ^a   Diekmann, Stephan ^b   Travers, Andrew ^a  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Bulged DNA; DNA bending; DNA footprinting; HMG D; Molecular modelling

Indexed keywords

ADENINE; CHROMOSOME PROTEIN; CURVED DNA; HIGH MOBILITY GROUP PROTEIN; OLIGOMER; THREONINE; TRANSCRIPTION FACTOR; VALINE;

ARTICLE; CONTROLLED STUDY; DNA BINDING; DNA FOOTPRINTING; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; DROSOPHILA; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; SEQUENCE HOMOLOGY; VERTEBRATE;

EUKARYOTA; VERTEBRATA;

EID: 0033584886     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3246     Document Type: Article

References (42)

1. Allain F. H., Yen Y. M., Masse J. E., Schultze P., Dieckmann T., Johnson R. C., Feigon J. Solution structure of the HMG protein NHP6A and its interaction with DNA revealsls the structural determinants for non-sequence-specific binding. EMBO J. 18:1999;2563-2579.
2. Balaeff A., Churchill M. E., Schulten K. Structure prediction of a complex between the chromosomal protein HMG-D and DNA. Proteins: Struct. Funct. Genet. 30:1998;113-135.
3. Bianchi M. E., Beltrame M., Paonessa G. Specific recognition of cruciform DNA by nuclear protein HMG1. Science. 243:1989;1056-1059.
4. Chow C. S., Whitehead J. P., Lippard S. J. HMG domain proteins induce sharp bends in cisplatin-modified DNA. Biochemistry. 33:1994;15124-15130.
5. Churchill M. E. A., Jones D. N. M., Glaser T., Hefner H., Searles M. A., Travers A. A. HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG. EMBO J. 14:1995;1264-1275.
6. Cornell W. D., Cieplak P., Bayly C. I., Gould I. R., Merz K. M. Jr, Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
7. Dornberger U., Hillisch A., Gollmick F. A., Fritzsche H., Diekmann S. Solution structure of a five-adenine bulge loop within a DNA duplex. Biochemistry. 38:1999;12860-12868.
8. Falciola L., Murchie A. I., Lilley D. M. J., Bianchi M. Mutational analysis of the DNA binding domain A of chromosomal protein HMG1. Nucl. Acids Res. 22:1994;285-292.
9. Farid R. S., Bianchi M. E., Falciola L., Engelsberg B. N., Billings P. C. Differential binding of HMG1, HMG2 and a single HMG box to cisplatin-damaged DNA. Toxicol. Appl. Pharmacol. 141:1996;532-539.
10. Ferrari S., Harvey V. R., Pontiggia A., Goodfellow P. N., Lovell-Badge R., Bianchi M. E. SRY, like HMG1, recognizes sharp angles in DNA. EMBO J. 11:1992;4497-4506.
11. Hardman C. H., Broadhurst R. H., Raine A. R. C., Grasser K. D., Thomas J. O., Laue E. D. Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three and four dimensional NMR spectroscopy. Biochemistry. 34:1995;16596-16607.
12. Jamieson E. R., Jacobson M. P., Barnes C. M., Chow C. S., Lippard S. J. Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B. J. Biol. Chem. 274:1999;12346-12354.
13. Jones D. N. M., Searles M. A., Shaw G. L., Churchill M. E. A., Ner S. S., Keeler J., Travers A. A., Neuhaus D. The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster. Structure. 2:1994;609-627.
14. Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6:1988;63-91.
15. Lorenz M., Hillisch A., Payet D., Buttinelli M., Travers A., Diekmann S. DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer (FRET). Biochemistry. 38:1999;12150-12158.
16. Love J. J., Xiang L., 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.
17. Ohndorf U.-M., Rould M. A., He Q., Pabo C., Lippard S. J. Basis of cis-platin modified DNA by high-mobility-group proteins. Nature. 399:1999;708-712.
18. Paull T. T., Haykinson M. J., Johnson R. C. The nonspecific DNA-binding and DNA-bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev. 7:1993;1521-1534.
19. Payet D., Travers A. The acidic tail of the high mobility group protein HMG-D modulates the structural specificity of DNA binding. J. Mol. Biol. 266:1997;66-75.
20. Pearlman D. A., Case D. A., Caldwell J. W., Ross W. S., Cheatham T. E. III. AMBER 4.1. 1995;University of San Francisco.
21. Peters R., King C. Y., Ukiyama E., Falsafi S., Donahue P. K., Weiss M. A. An SRY mutation causing human sex reversal resolves a general mechanism of structure-specific DNA recognition: application to the four-way junction. Biochemistry. 34:1995;4569-4576.
22. Pil P. M., Lippard S. J. Specific binding of chromosomal protein HMG1 to DNA damaged by the anticancer drug cisplatin. Science. 256:1992;234-237.
23. Pil P. M., Chow C. S., Lippard S. J. High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc. Natl Acad. Sci. USA. 90:1993;9465-9469.
24. Pohler J. R. G., Norman D. G., Bramham J., Bianchi M. E., Lilley D. M. J. HMG box proteins bind to four-way DNA junctions in their open conformation. EMBO J. 17:1998;817-826.
25. Read C. M., Cary P. D., Crane-Robinson C., Driscoll P. C., Norman D. G. Solution structure of a DNA-binding domain from HMG1. Nucl. Acids Res. 21:1993;3427-3436.
26. n-bulge loops in DNA duplexes - intrahelical stacking of A, A-A, and A-A-A bulge loops. Biochemistry. 31:1992a;4004-4014.
27. Rosen M. A., Shapiro L., Patel D. J. Solution structure of a trinucleotide A-T-A-bulge loop within a DNA duplex. Biochemistry. 31:1992b;4015-4026.
28. Sheflin L. G., Spaulding S. W. High mobility group protein 1 preferentially conserves torsion in negatively supercoiled DNA. Biochemistry. 28:1989;5658-5664.
29. Sheflin L. G., Fucile N. W., Spaulding S. W. The specific interactions of HMG1 and 2 with negatively supercoiled DNA are modulated by their acidic C-terminal domains and involve cysteine residues in their HMG1/2 boxes. Biochemistry. 32:1993;3238-3248.
30. Strauss J. K., Maher L. J. III. DNA bending by asymmetric phosphate neutralization. Science. 266:1994;1829-1834.
31. Teo S.-H., Grasser K. D., Hardman C. H., Broadhurst R. W., Laue E. D., Thomas J. O. Two mutations in the HMG-box with very different structural consequences provide insights into the nature of binding to 4-way junction DNA. EMBO J. 14:1995a;3844-3853.
32. Teo S.-H., Grasser K. D., Thomas J. O. Differences in the DNA-binding properties of the HMG-box domains of HMG1 and the sex-determining factor SRY. Eur. J. Biochem. 230:1995b;943-950.
33. Tripos Inc. SYBYL 6.4. 1997;1699 S. Hanley Road, MO 63144-2913, Suite 303, St. Louis.
34. Vallis Y., Wigge P., Marks B., Evans P. R., McMahon H. T. Importance of the pleckstrin homology domain of dynamin in clathrin-mediated endocytosis. Curr. Biol. 9:1999;257-260.
35. Van Houte L. P. A., Chuprina V. P., Van der Wetering M., Boelens R., Kaptein R., Clevers H. Solution structure of the sequence -specific HMG box of the lymphocyte transcriptional activator Sox-4. J. Biol. Chem. 270:1995;30516-30524.
36. von Kitzing E., Lilley D. M. J., Diekmann S. The stereochemistry of a four-way DNA junction: a theoretical study. Nucl. Acids Res. 18:1990;2671-2683.
37. Webb M., Thomas J. O. Structure-specific binding of the two tandem HMG boxes of HMG1 to four-way junction DNA is mediated by the A domain. J. Mol. Biol. In the press:1999.
38. Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A. An all atom force-field for simulations of proteins and nucleic-acids. J. Comp. Chem. 7:1986;230-252.
39. Weir H. M., Kraulis P. J., Hill C. S., Raine A. R. C., Laue E. D., Thomas J. O. Structure of the HMG box motif in the B-domain of HMG1. EMBO J. 12:1993;1311-1319.
40. 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.
41. Wolfe S. A., Ferentz A. E., Grantchavora V., Churchill M. E. A., Verdine G. L. Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend. Chem. Biol. 2:1995;213-221.
42. Yang D., van Boom S. S., Reedijk J., van Boom J. H., Wang A. H. J. Structure and isomerization of an intrastrand cisplatin-cross-linked octamer DNA duplex by NMR analysis. Biochemistry. 34:1995;12912-12920.