Cooperative non-specific DNA binding by octamerizing λ cl repressors: A site-specific thermodynamic analysis

Journal of Molecular Biology

Volumn 282, Issue 5, 1998, Pages 947-958

  Pray, Todd R ^a   Burz, David S ^a   Ackers, Gary K ^a  

^a Washington University   (United States)

Author keywords

DNase footprinting; Ising lattice; Multivalent binding

Indexed keywords

BACTERIOPHAGE DNA;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIOPHAGE LAMBDA; DNA BINDING; DNA FOOTPRINTING; ENERGY; NONHUMAN; PRIORITY JOURNAL; REPRESSOR GENE; THERMODYNAMICS;

BACTERIOPHAGE LAMBDA; UNIDENTIFIED BACTERIOPHAGE;

EID: 0032500562     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2056     Document Type: Article

References (53)

1. Ackers G.K., Johnson A.D., Shea M.A. Quantitative model for gene regulation by λ phage repressor. Proc. Natl Acad. Sci. USA. 79:1982;1129-1133
2. Ackers G.K., Shea M.A., Smith F.R. Free energy coupling within macromolecules the chemical work of ligand binding at the individual sites in cooperative systems. J. Mol. Biol. 170:1983;223-242
3. Amann E., Brosius J., Ptashne M. Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli. Gene. 25:1983;167-178
4. Backman K.C., Ptashne M., Gilbert W. Construction of plasmids carrying the cI gene of bacteriophage λ Proc. Natl Acad. Sci. USA. 73:1976;4174-4178
5. Bain D.L., Ackers G.K. Self-association and DNA binding of lambda cI repressor N-terminal domains reveal linkage between sequence-specific binding and the C-terminal cooperativity domain. Biochemistry. 33:1994;14679-14689
6. Beckett D., Koblan K.S., Ackers G.K. Qualitative study of protein association at picomolar concentrations the λ phage cI repressor. Anal. Biochem. 196:1991;69-75
7. Beckett D., Burz D.S., Ackers G.K., Sauer R.T. Isolation of λ repressor mutants with defects in cooperative operator binding. Biochemistry. 32:1993;9073-9079
8. Benson N., Adams C., Youderian P. Genetic selection for mutations that impair the co-operative binding of lambda repressor. Mol. Microbiol. 11:1994;567-579
9. Brenowitz M., Senear D.F., Shea M.A., Ackers G.K. Quantitative DNase footprint titration a method for studying protein-DNA interactions. Methods Enzymol. 130:1986;132-181
10. Brenowitz M., Senear D.F., Shea M.A., Ackers G.K. "Footprint" titrations yield valid thermodynamic isotherms. Proc. Natl Acad. Sci. USA. 83:1986;8462-8466
11. Bujalowski W., Lohman T.M. On the cooperative binding of large ligands to a one-dimensional homogenous lattice the generalized three-state model. Biopolymers. 28:1989;1637-1643
12. R. Biochemistry. 33:1994;8406-8416
13. Burz D.S., Ackers G.K. Cooperativity mutants of λcI repressor temperature dependence of self-assembly. Biochemistry. 35:1996;3341-3350
14. Burz D.S., Beckett D., Benson N., Ackers G.K. Self-assembly of bacteriophage λcI repressor effects of single-site mutations on the monomer-dimer equilibrium. Biochemistry. 33:1994;8399-8405
15. Clore G.M., Groneenborn A.M., Davies R.W. Theoretical aspects of specific and non-specific binding of proteins to DNA as studied by the nitrocellulose filter binding assay. J. Mol. Biol. 155:1982;447-466
16. Crothers D.M. Calculation of binding isotherms for heterogeneous polymers. Biopolymers. 6:1968;575-584
17. Di Cera E. Thermodynamic Theory of Site-specific Binding Processes in Biological Macromolecules. 1995;Cambridge University Press, Cambridge, UK
18. Di Cera E., Kong Y. Theory of multivalent binding in one and two-dimensional lattices. Biophys. Chem. 61:1996;107-124
19. Epstein I.D. Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys. Chem. 8:1978;327-339
20. Gimble F.S., Sauer R.T. Lambda repressor mutants that are better substrates for RecA-mediated cleavage. J. Mol. Biol. 206:1989;29-39
21. Hill T.L. Cooperativity Theory in Biochemistry. 1985;Springer-Verlag, New York
22. Johnson A.D., Pabo C.O., Sauer R.T. Bacteriophage lambda repressor and cro protein interactions with operator DNA. Methods Enzymol. 65:1980;839-856
23. Johnson A.D., Poteete A.R., Lauer G., Sauer R.T., Ackers G.K., Ptashne M. λ repressor and cro-components of an efficient molecular switch. Nature. 294:1981;217-233
24. Koblan K.S., Ackers G.K. Energetics of subunit dimerization in bacteriophage λcI repressor linkage to protons, temperature, and KCl. Biochemistry. 30:1991;7817-7821
25. R. Biochemistry. 30:1991;7822-7827
26. R. Biochemistry. 31:1992;57-65
27. Koblan K.S., Bain D.L., Beckett D., Shea M.A., Ackers G.K. Analysis of site-specific interaction parameters in protein-DNA complexes. Methods Enzymol. 210:1992;405-425
28. Kowalczykowski S.C., Paul L.S., Lonberg N., Newport J.W., McSwiggen J.A., von Hippel P.H. Cooperative and noncooperative binding of protein ligands to nucleic acid lattices experimental approaches to the determination of thermodynamic parameters. Biochemistry. 25:1986;1226-1240
29. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:1970;680-685
30. Ling G.N. The theory of allosteric control of cooperative adsorption. Karreman G. Cooperative Phenomena in Biology. 1980;39-70 Pergamon Press, Oxford, UK
31. Lohman T.M., Bujalowski W. Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions spectroscopic approaches to monitor binding. Methods Enzymol. 208:1991;258-290
32. Lohman T.M., Ferrari M.E. Escherichia coli single-stranded binding protein multiple DNA binding modes and cooperatives. Annu. Rev. Biochem. 63:1994;527-570
33. R3 and autogenous negative control by repressor. J. Mol. Biol. 139:1980;147-161
34. McGhee J.D., von Hippel P.H. Theoretical aspects of DNA-protein interactions cooperative and noncooperative binding of large ligands to a one-dimensional homogenous lattice. J. Mol. Biol. 86:1974;469-489
35. Merabet E., Ackers G.K. Calorimetric analysis of λcI repressor binding to DNA operator sites. Biochemistry. 34:1995;8554-8563
36. Merabet E., Burz D.S., Ackers G.K. Thermal melting properties of C-terminal domain mutants of bacteriophage λcI repressor. Methods Enzymol. 295:1998;450-467
37. R3 their roles in mediating the effects of repressor and cro. J. Mol. Biol. 139:1980;163-194
38. Perini L.T., Doherty E.A., Werner E., Senear D.F. Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein. J. Biol. Chem. 271:1996;33242-33255
39. Ptashne M. A Genetic Switch. 2nd edit.:1992;Cell Press and Blackwell Scientific Publications, Cambridge, MA
40. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edit.:1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
41. Sauer R.T., Anderegg R. Primary structure of the lambda repressor. Biochemistry. 17:1978;1092-1100
42. R. Biochemistry. 29:1990;6568-6577
43. Senear D.F., Batey R. Comparison of operator-specific and nonspecific DNA binding of the λcI repressor [KCl] and pH effects. Biochemistry. 30:1991;6677-6688
44. Senear D.F., Brenowitz M. Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J. Biol. Chem. 21:1991;13661-13671
45. Senear D.F., Dalma-Weishausz D.D., Brenowitz M. Effects of anomalous migration and DNA to protein ratios on resolution of equilibrium constants from gel mobility-shift assays. Electrophoresis. 14:1993;704-712
46. Senear D.F., Laue T.M., Ross J.B.A., Waxman E., Eaton S., Rusinova E. The primary self-assembly reaction of λcI repressor dimers is to octamer. Biochemistry. 32:1993;6179-6189
47. Rcontrol system of bacteriophage lambda - a physical-chemical model for gene regulation. J. Mol. Biol. 181:1985;211-230
48. Thompson C.J. Models for hemoglobin and allosteric enzymes. Biopolymers. 6:1968;1101-1118
49. Vipond I.B., Halford S.E. Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry. 34:1995;1113-1119
50. von Hippel P.H., Berg O.G. Facilitated target location in biological systems. J. Biol. Chem. 264:1989;675-678
51. von Hippel P.H., Revzin A., Gross C.A., Wang A.C. Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects. Proc. Natl Acad. Sci. USA. 71:1974;4808-4812
52. Waldburger C.D., Sauer R.T. Domains of mnt repressor - roles in tetramer formation, protein stability, and operator DNA binding. Biochemistry. 34:1995;13109-13116
53. Woodbury C.P. Jr, von Hippel P.H. On the determination of deoxyribonucleic acid-protein interaction parameters using the nitrocellulose filter-binding assay. Biochemistry. 22:1983;4730-4737