An analysis of the relationship between hydration and protein-DNA interactions

Biophysical Journal

Volumn 75, Issue 5, 1998, Pages 2170-2177

  Woda, Juliana ^a   Schneider, Bohdan ^c   Patel, Ketan ^a   Mistry, Kavin ^a   Berman, Helen M ^a,b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BASE; PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; DNA SEQUENCE; HYDRATION; MOLECULAR RECOGNITION; PROTEIN DNA INTERACTION;

EID: 0031722426     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77660-X     Document Type: Article

References (24)

1. Aggarwal, A. K., D. W. Rodgers, M. Drottar, M. Ptashne, and S. C. Harrison. 1988. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science. 242:899-907.
2. Beamer, L. J., and C. O. Pabo. 1992. Refined 1.8 Å crystal structure of the λ repressor-operator complex. J. Mol. Biol. 227:177-196.
3. Berman, H. M. 1991. Hydration of DNA. Curr. Opin. Struct. Biol. 1:423-427.
4. Berman, H. M. 1994. Hydration of DNA: take 2. Curr. Opin. Struct. Biol. 4:345-350.
5. Carrell, H. L. 1979. BANG: a computer program for the rapid calculation of bond lengths and angles. The Institute of Cancer Research, Fox Chase Cancer Center, Philadelphia.
6. Cohen, D., K. Vadaparty, and B. Dickinson. 1995. Efficient algorithms for geometric queries in macromolecular structure databases. University of Pittsburgh, Pittsburgh.
7. Franklin, R. E., and R. G. Gosling. 1953. Molecular configuration in sodium thymonucleate. Nature. 171:740-741.
8. Harrison, S. C., J. E. Anderson, G. B. Koudelka, A. Mondragon, S. Subbiah, R. P. Wharton, C. Wolberger, and M. Ptashne. 1988. Recognition of DNA sequences by the repressor of bacteriophage 434. Biophys. Chem. 29:31-37.
9. Kissinger, C. R., B. S. Liu, E. Martinblanco, T. B. Kornberg, and C. O. Pabo. 1990. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: a framework for understanding homeodomain-DNA interactions. Cell. 63:579-590.
10. Langley, R. 1971. Practical Statistics. Dover Publications, New York.
11. Marmorstein, R., M. Carey, M. Ptashne, and S. C. Harrison. 1992. DNA recognition by Gal4: structure of a protein-DNA complex. Nature. 356:408-414.
12. Otwinowski, Z., R. W. Schevitz, R.-G. Zhang, C. L. Lawson, A. Joachimiak, R. Q. Marmorstein, B. F. Luisi, and P. B. Sigler. 1988. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335:321-329.
13. Parkinson, G., A. Gunasekera, J. Vojtechovsky, X. Zhang, T. A. Kunkel, H. Berman, and R. H. Ebright. 1996b. Aromatic hydrogen bond in sequence-specific protein-DNA recognition. Nature Struct. Biol. 3:837-841.
14. Parkinson, G., C. Wilson, A. Gunasekera, Y. Ebright, R. H. Ebright, and H. M. Berman. 1996a. Structure of the CAP-DNA complex at 2.5 angstrom resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 259:395-408.
15. Pavletich, N. P., and C. O. Pabo. 1991. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science. 252: 809-817.
16. Sack, J. S. 1988. CHAIN: a crystallographic modeling program. J. Mol. Graphics. 6:224-225.
17. Schneider, B., and H. M. Berman. 1995. Hydration of the DNA bases is local. Biophys. J. 69:2661-2669.
18. Schneider, B., D. M. Cohen, L. Schleifer, A. R. Srinivasan, W. K. Olson, and H. M. Berman. 1993. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65:2291-2303.
19. Schneider, B., K. Patel, and H. M. Berman. 1998. Hydration of the phosphate group in double helical DNA. Biophys. J. 75:2422-2434.
20. Seeman, N. C., J. M. Rosenberg, and A. Rich. 1976. Sequence specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA. 73:804-808.
21. Shakked, Z., G. Guzikevich-Guerstein, F. Frolow, D. Rabinovich, A. Joachimiak, and P. B. Sigler. 1994. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature. 368:469-473.
22. R2/R1-69 complex at 2.5 Å resolution. J. Mol. Biol. 232:826-838.
23. Westhof, E. 1993. Structural Water Bridges in Nucleic Acids. Water and Biological Macromolecules. CRC Press, Boca Raton.
24. Wolberger, C., A. K. Vershon, B. Liu, A. D. Johnson, and C. O. Pabo. 1991. Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell. 67:517-528.