Probing the role of water in the tryptophan repressor-operator complex

Protein Science

Volumn 8, Issue 6, 1999, Pages 1276-1285

  Brown, Martha P ^a   Grillo, Adeola O ^a   Boyer, Mireille ^b   Royer, Catherine A ^a,b,c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b INSERM   (France)

^c CENTRE DE BIOCHIMIE STRUCTURALE   (France)

Author keywords

DNA; Osmotic pressure; Tryptophan repressor protein; Water

Indexed keywords

DNA FRAGMENT; REPRESSOR PROTEIN; WATER;

ARTICLE; ESCHERICHIA COLI; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NONHUMAN; OPERATOR GENE; OSMOTIC PRESSURE; PRIORITY JOURNAL; PROTEIN DNA BINDING; REPRESSOR GENE;

EID: 0033030075     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.6.1276     Document Type: Article

References (49)

1. Arakawa T, Timasheff SN. 1985. The stabilization of proteins by osmolytes. Biophys J 47:411-414.
2. Bass S, Sugiono P, Arvidson DN, Gunsalus RP, Youderian P. 1987. DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes Dev 1:565-572.
3. Beechem JM, Gratton E, Ameloot M, Knutson JR, Brand L. 1989. In: Lakowicz JR, ed. Fluorescence spectroscopy: Principles and techniques, Vol I. New York: Plenum Press, pp 241-305.
4. Carey J, Lewis DEA, Lavoie TA, Yang J. 1991. How does trp repressor bind to its operator? J Biol Chem 266:24509-24513.
5. Colombo MF, Rau DC, Parsegian VA. 1992. Protein solvation in allosteric regulation: A water effect on hemoglobin. Science 256:655-657.
6. Fernando T, Royer CA. 1992. The role of protein-protein interactions in the regulation of transcription by trp repressor investigated by fluorescence spectroscopy. Biochemistry 31:3429-3441.
7. Garner MM, Rau DC. 1995. Water release associated with specific binding of gal repressor. EMBO J 14:1257-1263.
8. Grille A. 1999. Physical basis for trp repressor-operator recognition [PhD Dissertation]. Madison, Wisconsin: University of Wisconsin.
9. Grillo A, Brown MP, Royer CA. 1999. Probing the physical basis for trp repressor-operator recognition. J Mol Biol 287:539-554.
10. Gunsalus RP, Yanofsky C. 1980. Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci USA 77:7117-7121.
11. Haran TE, Joachumak A, Sigler PB. 1992. The DNA target of the trp repressor. EMBO J 11:3021-3030.
12. Haugland RP. 1996. In: Spence MTZ, ed. Handbook of fluorescent probes and research chemicals. Molecular Probes, Inc.
13. Joachimiak A, Haran TE, Sigler PB. 1994. Mutagenesis supports water mediated recognition in the trp repressor-operator system. EMBO J 13:367-372.
14. Joachimiak A, Kelley RL, Gunsalus RP, Yanofsky C, Sigler PB. 1983. Purification and characterization of trp aporepressor. Proc Natl Acad Sci USA 80:668-672.
15. Kelley RL, Yanofsky C. 1982. Trp aporepressor production is controlled by autogenous regulation and inefficient translation. Proc Natl Acad Sci USA 82:483-487.
16. Kornblatt JA, Hui Ban Hoa G. 1990. A nontraditional role for water in the cytochrome c oxidase reaction. Biochemistry 29:9370-9376.
17. Lawson CL, Carey J. 1993. Tandem binding in crystals of a trp repressor operator half-site complex. Nature 366:178-182.
18. LeTilly V, Royer CA. 1993. Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. Biochemistry 32:7753-7758.
19. Liu YC, Matthews KS. 1993. trp repressor mutations alter DNA complex stoichiometry. J Biol Chem 268:23239-23249.
20. Morton CJ, Ladbury JE. 1996. Water mediated protein-DNA interactions: The relationship of thermodynamics to structural detail. Protein Sci 5:2115-2118.
21. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB. 1988. Crystal structure of trp repressor/ operator complex at atomic resolution. Nature 335:321-329.
22. Parsegian VA, Rand RP, Rau DC. 1995. Macromolecules and water: Probing with osmotic stress. Methods Enzymol 259:43-94.
23. Prouty HS, Schechter AN, Parsegian VA. 1985. Chemical potential measurements of deoxyhemoglobin S polymerization. Determination of the phase diagram of an assembling protein. J Mol Biol 184:517-528.
24. Ptashne MA. 1986. Genetic switch. Cambridge, Massachusetts: Cell Press.
25. Rand RP, Fuller NL, Butko P, Francis G, Nicholls P. 1993. Measured change in protein solvation with substrate binding and turnover. Biochemistry 32:5925-5292.
26. Rand RP, Parsegian VA. 1989. Hydration forces between phospholipid bilayers. Biochim Biophys Acta 988:351-376.
27. Reedstrom RJ, Brown MP, Grillo A, Roen D, Royer CA. 1997. Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides. J Mol Biol 273:573-585.
28. Reid C, Rand RP. 1997. Probing protein hydration and conformational states in solution. Biophys J 72:1022-1030.
29. Robinson CR, Sligar SG. 1993. Molecular recognition mediated by bound water a mechanism for star activity of the restriction endonuclease EcoR1. J Mol Biol 234:302-306.
30. Robinson CR, Sugar SG. 1994. Hydrostatic pressure reverses osmotic pressure effect on the specificity of EcoR1-DNA interaction. Biochemistry 33:3787-3793.
31. Robinson CR, Sligar SG. 1995a. Hydrostatic and osmotic pressure as tools to study macromolecular recognition. Methods Enzymol 259:395-427.
32. Robinson CR, Sligar SG. 1995b. Heterogeneity in molecular recognition by restriction endonucleases: Osmotic and hydrostatic pressure effects on BamHI, PvuII and EcoRV specificity. Proc Natl Acad Sci USA 92:3444-3448.
33. Robinson CR, Sligar SG. 1996. Participation of water in Hin recombinase-DNA recognition. Protein Sci 5:2119-2124.
34. Robinson CR, Sligar SG. 1998. Changes in solvation during DNA binding and cleavage are critical to altered specificity of EcoRI endonuclease. Proc Natl Acad Sci USA 95:2186-2191.
35. Rose JK, Yanofsky C. 1973. Interaction of the operator of the tryptophan operator with repressor. Proc Natl Acad Sci USA 71:3134-3138.
36. Royer CA. 1993. Improvements in the numerical analysis of thermodynamic data from biomolecular complexes. Anal Biochem 210:91-97.
37. Royer CA, Beechem JM. 1992. Numerical analysis of binding data: Advantages, practical aspects, and implications. Methods Enzymol 210:481-505.
38. Royer CA, Smith WR, Beechem JM. 1990. Analysis of binding in macromolecular complexes: A generalized numerical approach. J Mol Biol 191:287-294.
39. Schevitz RW, Otwinowski Z, Joachimiak A, Lawson CL, Sigler PB. 1985. The three-dimensional structure of trp repressor. Nature 317:782-786.
40. Schwabe JWR. 1997. The role of water in protein-DNA interactions. Curr Opin Struct Biol 7:126-134.
41. Shakked Z, Guzikevich-Guerstein G, Frolow F, Rabinovich D, Joachimiak A, Sigler PB. 1994. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368:469-473.
42. Timasheff SN. 1993. The control of protein stability and association by weak interactions with water: How do solvents affect these processes? Anna Rev Biophys Biomol Struct 22:67-97.
43. Timasheff SN. 1998. In disperse solution, "osmotic stress" is a restricted case of preferential interactions. Proc Natl Acad Sci USA 95:7363-7367.
44. von Hippel PH, Berg OG. 1986. On the specificity of DNA-protein interactions. Proc Natl Acad Sci USA 83:1608-1612.
45. Vossen KM, Wolz K, Daugherty MA, Fried MG. 1997. Role of macromolecular hydration in the binding of the Escherichia coli cyclic AMP receptor to DNA. Biochemistry 36:11640-11647.
46. Weast RC, Astle MJ. 1983. Handbook of chemistry and physics. Boca Raton: CRC Press. pp D239-D240.
47. Yang J, Gunasekera A, Lavoie TA, Jin L, Lewis DEA, Carey J. 1996. In vivo and in vitro studies of TrpR-DNA interactions. J Mol Biol 258:37-52.
48. Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetsky O. 1994. The solution structures of the trp repressor-operator DNA complex. J Mol Biol 238:592-614.
49. Zurawski G, Gunsalus RP, Brown KD, Yanofsky C. 1981. Structure and regulation of aroH, the structural gene for the tryptophan-repressible 3-deoxy-D-arabinose-heptulosonic acid-7-phosphate-synthetase of Escherichia coli. J Mol Biol 145:47-73.