The cyclic AMP receptor promoter DNA complex: A comparison of crystal and solution structure by quantitative molecular electrooptics

Journal of Molecular Biology

Volumn 269, Issue 5, 1997, Pages 842-850

  Meyer Almes, Franz Josef ^a   Porschke, Dietmar ^a,b  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b EVOTEC BioSystems GmbH   (Germany)

Author keywords

Bead model simulation; Calculation of electrooptical parameters; DNA bending; Electric dichroism; Gene activation

Indexed keywords

CYCLIC AMP BINDING PROTEIN; DNA FRAGMENT;

ARTICLE; CRYSTAL STRUCTURE; DIFFUSION COEFFICIENT; DNA HELIX; DNA STRUCTURE; IONIC STRENGTH; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; SIMULATION;

EID: 0031588024     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1086     Document Type: Article

References (38)

1. Antosiewicz J., Porschke D. Turn of promoter DNA by cAMP receptor protein characterized by bead model simulation of rotational diffusion. J. Biomol. Struct. Dynam. 5:1988;819-837.
2. Antosiewicz J., Porschke D. Volume corrections for bead model simulations of rotational friction coefficients of macromolecules. J. Phys. Chem. 93:1989;5301-5305.
3. Antosiewicz J., Grycuk T., Porschke D. Brownian dynamics simulation of electrooptical transients for solutions of rigid macromolecules. J. Chem. Phys. 95:1991;1354-1360.
4. Benoit H. Contribution a l'étude de effet kerr présenté par les solutions diluées de macromolécules rigides. Ann. de Phys. 6:1951;561-609.
5. Berg O. G., von Hippel P. H. Selection of DNA binding sites by regulatory proteins II: the binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200:1988;709-723.
6. Brierley I., Hoggett J. G. Binding of the cyclic AMP receptor protein of Escherichia coli and DNA bending at the P4 promoter of pBR322. Biochem. J. 285:1992;91-97.
7. 2+binding and its structural consequences at the transcription start site. Biochemistry. 34:1995;15624-15632.
8. Dripps D., Wartell R. M. DNA bending induced by the catabolite activator protein allows ring formation of a 144 bp DNA. J. Biomol. Struct. Dynam. 5:1987;1-13.
9. Ebright R. H., Ebright Y. W., Gunasekera A. Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac site. Nucl. Acids Res. 17:1989;10295-10305.
10. Fredericq E., Houssier C. Electric Dichroism and Electric Birefringence. 1973;Clarendon Press, Oxford.
11. Garcia De La Torre J., Bloomfield V. A. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Quart Rev. Biophys. 14:1981;81-139.
12. Ghosaini L. R., Brown A. M., Sturtevant J. M. Scanning calorimetric study of the thermal unfolding of catabolite activator protein from Escherichia coli in the absence and presence of cyclic mononucleotides. Biochemistry. 27:1988;5257-5261.
13. Harvey S. C., Garcia De La Torre J. Coordinate systems for modelling the hydrodynamic resistance and diffusion coefficients of irregularly shaped rigid macromolecules. Macromolecules. 13:1980;960-964.
14. Heyduk T., Lee J. C. Solution studies on the structure of bent DNA in the cAMP receptor protein- lac DNA complex. Biochemistry. 31:1992;5165-5171.
15. Kahn J. D., Crothers D. M. Protein-induced bending and DNA cyclization. Proc. Natl Acad. Sci. USA. 89:1992;6343-6347.
16. Kolb A., Spassky A., Chapon C., Blazy B., Buc H. On the different binding affinities of CRP at the lac, gal and mal T promoter regions. Nucl. Acids Res. 11:1983;7833-7852.
17. Kotlarz D., Fritsch A., Buc H. Variations of intramolecular ligation rates allow the detection of protein-induced bends in DNA. EMBO J. 5:1986;799-803.
18. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 11:1978;179-246.
19. McKay D. B., Steitz T. A. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature. 290:1981;744-749.
20. Meyer-Almes F. J., Heumann H., Porschke D. The structure of the RNA polymerase-promoter complex. DNA bending angle by quantitative electrooptics. J. Mol. Biol. 236:1994;1-6.
21. O'Konski C. T., Yoshioka K., Orttung W. H. Electric properties of macromolecules IV. Determination of electric and optical parameters from saturation of electric birefringence in solutions. J. Phys. Chem. 63:1959;1558-1565.
22. Parkinson G., Wilson C., Gunasekera A., Ebright Y. W., Ebright R. E., Berman H. M. Structure of the CAP-DNA complex at 2.5 Å resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260:1996;395-408.
23. Porschke D. Electric dichroism and bending amplitudes of DNA fragments according to a simple orientation function for weakly bent rods. Biopolymers. 28:1989;1383-1396.
24. Porschke D. Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations. Biophys. Chem. 40:1991;169-179.
25. Porschke D., Antosiewicz J. Permanent dipole moment of tRNAs and variation of their structure in solution. Biophys. J. 58:1990;403-411.
26. Porschke D., Jung M. The conformation of single stranded oligonucleotides and of oligonucleotide-peptide complexes from their rotation relaxation in the nanosecond time range. J. Biomol. Struct. Dynam. 2:1985;1173-1184.
27. Porschke D., Obst A. An electric field jump apparatus with ns time resolution for electro-optical measurements at physiological salt concentrations. Rev. Sci. Instr. 62:1991;818-820.
28. Porschke D., Hillen W., Takahashi M. The change of DNA structure by specific binding of the cAMP receptor from rotation diffusion and dichroism measurements. EMBO J. 3:1984;2873-2878.
29. Porschke D., Tovar K., Antosiewicz J. Structure of the Tet repressor and Tet repressor-operator complexes in solution from electrooptical measurements and hydrodynamic simulations. Biochemistry. 27:1988;4674-4679.
30. Record M. T. Jr, Anderson C. F., Lohman T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quart. Rev. Biophys. 11:1978;103-178.
31. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: The DNA is bent by 90° Science. 253:1991;1001-1007.
32. Takahashi M., Blazy B., Baudras A., Hillen W. Ligand-modulated binding of a gene regulatory protein to DNA. Quantitative analysis of cyclic-AMP induced binding of CRP from Escherichia coli to non-specific and specific DNA targets. J. Mol. Biol. 207:1989;783-796.
33. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes. Nucl. Acid Res. 16:1988;9687-9705.
34. Warwicker J., Engelman B. P., Steitz T. A. Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent. Proteins: Struct. Funct. Genet. 2:1987;283-289.
35. Weber I. T., Steitz T. A. Structure of a complex of catabolite gen activator protein and cyclic AMP refined at 2.5 Å resolution. J. Mol. Biol. 198:1987;311-326.
36. Wegener W. A., Dowben R. M., Koester V. J. Time-dependent birefringence, linear dichroism and optical rotation resulting from rigid-body rotational diffusion. J. Chem. Phys. 70:1979;622-632.
37. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 308:1984;509-513.
38. Zinkel S., Crothers D. M. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers. 29:1990;29-38.