Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics

Journal of Molecular Biology

Volumn 276, Issue 1, 1998, Pages 287-309

  Kahn, Jason D ^a   Crothers, Donald M ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

CAP; DNA bending; DNA twisting; Monte Carlo simulation; T4 ligase mediated cyclization

Indexed keywords

CURVED DNA; CYCLIC AMP BINDING PROTEIN;

ARTICLE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; DNA CONFORMATION; GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN DNA BINDING; RESTRICTION FRAGMENT; SYSTEM ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0032512613     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1515     Document Type: Article

References (93)

1. Bauer W.R., Lund R.A., White J.H. Twist and writhe of a DNA loop containing intrinsic bends. Proc. Natl Acad. Sci. USA. 90:1993;833-837
2. Bolshoy A., McNamara P., Harrington R.E., Trifonov E.N. Curved DNA without A-A experimental estimation of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA. 88:1991;2312-2316
3. 5promoter probed by singlet oxygen. EMBO J. 11:1992;2619-2625
4. Cacchione S., De Santis P., Savino M. Different flexibility of the upstream regulatory regions of two differently expressed pea rbc S genes studied by theoretical evaluation of DNA distortion energy and cyclization kinetics. FEBS Letters. 336:1993;293-298
5. Chirico G., Langowski J. Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys. J. 71:1996;955-971
6. Clendenning J.B., Schurr J.M. Circularization of small DNAs in the presence of ethidium a theoretical analysis. Biopolymers. 34:1994;849-868
7. Crothers D.M., Drak J., Kahn J.D., Levene S.D. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 212:1992;1-29
8. Dalma-Weiszhausz D.D., Gartenberg M.R., Crothers D.M. Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity. Nucl. Acids Res. 19:1991;611-616
9. De Santis P., Palleschi A., Savino M., Scipioni A. Theoretical prediction of the gel electrophoretic retardation changes due to point mutations in a tract of SV40 DNA. Biophys. Chem. 42:1992;147-152
10. De Santis P., Fuà M., Palleschi A., Savino M. Relationships between intrinsic and induced curvature in DNAs theoretical prediction of nucleosome positioning. Biophys. Chem. 46:1993;193-204
11. De Santis P., Fuà M., Savino M., Anselmi C., Bocchinfuso G. Sequence dependent circularization of DNAs a physical model to predict the DNA sequence dependent propensity to circularization and its changes in the presence of protein-induced bending. J. Phys. Chem. 100:1996;9968-9976
12. DiGabriele A.D., Sanderson M.R., Steitz T.A. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl Acad. Sci. USA. 86:1989;1816-1820
13. Douc-Rasy S., Kolb A., Prunell A. Protein-induced unwinding of DNA measurement by gel electrophoresis of complexes with DNA minicircles. Application to restriction endonuclease Eco RI, catabolite gene activator protein and lac repressor. Nucl. Acids Res. 17:1989;5173-5189
14. Drak J., Crothers D.M. Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proc. Natl Acad. Sci. USA. 88:1991;3074-3078
15. Drew H.R., Travers A.A. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:1985;773-790
16. Dripps D., Wartell R.M. DNA bending induced by the catabolite activator protein allows ring formation of a 144 bp DNA. J. Biomol. Struct. Dyn. 5:1987;1-13
17. Ferré-D'Amaré A.R., Prendergast G.C., Ziff E.B., Burley S.K. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature. 363:1993;38-45
18. Fisher D., Parent L.A., Sharp P.A. Myc/Max and other helix-loop-helix/leucine zipper proteins bend DNA toward the minor groove. Proc. Natl Acad. Sci. USA. 89:1992;11779-11783
19. Flory P.J., Suter U.W., Mutter M. Macrocyclization equilibria. I. Theory. J. Am. Chem. Soc. 98:1976;5733-5739
20. Gartenberg M.R., Crothers D.M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 333:1988;824-829
21. Gartenberg M.R., Ampe C., Steitz T.A., Crothers D.M. Molecular characterization of the GCN4-DNA complex. Proc. Natl Acad. Sci. USA. 87:1990;6034-6038
22. Ghosh G., Van Duyne G., Ghosh S., Sigler P.B. Structure of NF-κB p50 homodimer bound to a κB site. Nature. 373:1995;303-310
23. Glover J.N.M., Harrison S.C. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature. 373:1995;257-261
24. Goldstein H. Classical Mechanics. 2nd edit. :1980;Addison-Wesley Pub. Co, Reading, MA
25. Gorin A.A., Zhurkin V.B., Olson W.K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48
26. Hagerman P.J., Ramadevi V.A. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. Computational analysis. J. Mol. Biol. 212:1990;351-362
27. Haran T.E., Kahn J.D., Crothers D.M. Sequence elements responsible for DNA curvature. J. Mol. Biol. 244:1994;135-143
28. Heath P.J., Clendenning J.B., Fujimoto B.S., Schurr J.M. Effect of bending strain on the torsion elastic constant of DNA. J. Mol. Biol. 260:1996;718-730
29. 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
30. Hodges-Garcia Y., Hagerman P.J., Pettijohn D.E. DNA ring closure mediated by protein HU. J. Biol. Chem. 264:1989;14621-14623
31. Jacobson H., Stockmayer W.H. Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18:1950;1600-1606
32. Kabsch W., Sander C., Trifonov E.N. The ten helical twist angles of B-DNA. Nucl. Acids Res. 10:1982;1097-1104
33. Kahn J.D., Crothers D.M. Protein-induced bending and DNA cyclization. Proc. Natl Acad. Sci. USA. 89:1992;6343-6347
34. Kahn J.D., Crothers D.M. DNA bending in transcription initiation. Cold Spring Harbor Symp. Quant. Biol. 58:1993;115-122
35. Kahn J.D., Yun E., Crothers D.M. Detection of localized DNA flexibility. Nature. 368:1994;163-166
36. Kerppola T.K. Fos and Jun bend the AP-1 site effects of probe geometry on the detection of protein-induced DNA bending. Proc. Natl Acad. Sci. USA. 93:1996;10117-10122
37. Kerppola T.K., Curran T. DNA bending by Fos and Jun the flexible hinge model. Science. 254:1991;1210-1214
38. Kerppola T.K., Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations implications for transcription factor cooperativity. Cell. 66:1991;317-326
39. Klenin K.V., Frank-Kamenetskii M.D., Langowski J. Modulation of intramolecular interactions in superhelical DNA by curved sequences a Monte Carlo simulation study. Biophys. J. 68:1995;81-88
40. Kolb A., Buc H. Is DNA unwound by the cyclic AMP receptor protein? Nucl. Acids Res. 10:1982;473-485
41. Koo H.-S., Crothers D.M. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl Acad. Sci. USA. 85:1988;1763-1767
42. Koo H.-S., Drak J., Rice J.A., Crothers D.M. Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry. 29:1990;4227-4234
43. 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
44. Kremer W., Klenin K., Diekmann S., Langowski J. DNA curvature influences the internal motions of supercoiled DNA. EMBO J. 12:1993;4407-4412
45. Kuprash D.V., Rice N.R., Nedospasov S.A. Homodimer of p50 (NFκB1) does not introduce a substantial directed bend into DNA according to three different experimental assays. Nucl. Acids Res. 23:1995;427-433
46. Lavigne M., Kolb A., Yeramian E., Buc H. CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13:1994;4983-4990
47. Levene S.D., Crothers D.M. A computer graphics study of sequence-directed bending in DNA. J. Biomol. Struct. Dyn. 1:1983;429-435
48. Levene S.D., Crothers D.M. Ring closure probabilities for DNA fragments by Monte Carlo simulation. J. Mol. Biol. 189:1986;61-72
49. Levene S.D., Crothers D.M. Topological distributions and the torsional rigidity of DNA a Monte Carlo study of DNA circles. J. Mol. Biol. 189:1986;73-83
50. Levene S.D., Zimm B.H. Understanding the anomalous electrophoresis of bent DNA molecules a reptation model. Science. 245:1989;396-399
51. Liu-Johnson H.-N., Gartenberg M., Crothers D.M. The DNA binding domain and bending angle of E. coli CAP protein. Cell. 47:1986;995-1005
52. Lutter L.C., Halvorson H.R., Calladine C.R. Topological measurement of protein-induced DNA bend angles. J. Mol. Biol. 261:1996;620-633
53. Lyubchenko Y., Shlyakhtenko L., Chernov B., Harrington R.E. DNA bending induced by Cro protein binding as demonstrated by gel electrophoresis. Proc. Natl Acad. Sci. USA. 88:1991;5331-5334
54. Manning R.S., Maddocks J.H., Kahn J.D. A continuum rod model of sequence-dependent DNA structure. J. Chem. Phys. 105:1996;5626-5646
55. Marko J.F., Siggia E.D. Bending and twisting elasticity of DNA. Macromolecules. 27:1994;981-988
56. Maroun R.C., Olson W.K. Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains. Biopolymers. 27:1988;561-584
57. McCormick R.J., Badalina T., Fisher D.E. The leucine zipper may induce electrophoretic mobility anomalies without DNA bending. Proc. Natl Acad. Sci. USA. 93:1996;14434-14439
58. McNamara P.T., Bolshoy A., Trifonov E.N., Harrington R.E. Sequence-dependent kinks induced in curved DNA. J. Biomol. Struct. Dyn. 8:1990;529-538
59. Müller C.W., Rey F.A., Sodeoka M., Verdine G.L., Harrison S.C. Structure of the NF-κB p50 homodimer bound to DNA. Nature. 373:1995;311-317
60. Nardulli A.M., Shapiro D.J. Binding of the estrogen receptor DNA-binding domain to the estrogen response element induces DNA bending. Mol. Cell. Biol. 12:1992;2037-2042
61. Olson W.K., Marky N.L., Jernigan R.L., Zhurkin V.B. Influence of fluctuations on DNA curvature a comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232:1993;530-551
62. Onate S.A., Prendergast P., Wagner J.P., Nissen M., Reeves R., Pettijohn D.E., Edwards D.P. The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequence. Mol. Cell. Biol. 14:1994;3376-3391
63. Parkinson G., Wilson C., Gunasekera A., Ebright Y., Ebright R.H., 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
64. Parvin J.D., McCormick R.J., Sharp P.A., Fisher D.E. Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature. 373:1995;724-727
65. Passner J.M. Structural studies involving the E. coli catabolite gene activator protein. 1997;Yale University, CT. PhD thesis
66. Paull T.T., Haykinson M.J., Johnson R.C. The non-specific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev. 7:1993;1521-1534
67. Pil P.M., Chow C.S., Lippard S.J. High-mobility-group I protein mediates DNA bending as determined by ring closures. Proc. Natl Acad. Sci. USA. 90:1993;9465-9469
68. Press W.H., Flannery B.P., Teukolsky S.A., Vetterling W.T. Numerical Recipes The Art of Scientific Computing (FORTRAN Version). 1st edit. :1989;Cambridge University Press, Cambridge, UK
69. Ramstein J., Lavery R. Energetic coupling between DNA bending and base-pair opening. Proc. Natl Acad. Sci. USA. 85:1988;7231-7235
70. Sabbah M., Le Ricousse S., Redeuilh G., Baulieu E.-E. Estrogen receptor-induced bending of the Xenopus vitellogenin A2 gene hormone response element. Biochem. Biophys. Res. Commun. 185:1992;944-952
71. Sarai A., Mazur J., Nussinov R., Jernigan R.L. Sequence dependence of DNA conformational flexibility. Biochemistry. 28:1989;7842-7849
72. Sarai A., Jernigan R.L., Mazur J. Interdependence of conformational variables in double-helical DNA. Biophys. J. 71:1996;1507-1518
73. Schlick T., Olson W.K. Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223:1992;1089-1119
74. Schreck R., Zorbas H., Winnacker E.-L., Baeuerle P.A. The NF-κb transcription factor induces DNA bending which is modulated by its 65-kD subunit. Nucl. Acids Res. 18:1990;6497-6502
75. Schroth G.P., Cook G.R., Bradbury E.M., Gottesfeld J.M. Transcription factor IIIA induced bending of the Xenopus somatic 5 S gene promoter. Nature. 340:1989;487-488
76. 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
77. Schwabe J.W.R., Chapman L., Finch J.T., Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA how receptors discriminate between their response elements. Cell. 75:1993;567-578
78. Selvin P.R., Cook D.N., Pon N.G., Bauer W.R., Klein M.P., Hearst J.E. Torsional rigidity of positively and negatively supercoiled DNA. Science. 255:1992;82-85
79. Shimada J., Yamakawa H. Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules. 17:1984;689-698
80. Shore D., Baldwin R.L. Energetics of DNA twisting I. Relation between twist and cyclization probability. J. Mol. Biol. 170:1983;957-981
81. Shore D., Baldwin R.L. Energetics of DNA twisting II. Topoisomer analysis. J. Mol. Biol. 170:1983;983-1007
82. Shore D., Langowski J., Baldwin R.L. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl Acad. Sci. USA. 78:1981;4833-4837
83. Sitlani A., Crothers D.M. Fos and Jun do not bend the AP-1 recognition site. Proc. Natl Acad. Sci. USA. 93:1996;3248-3252
84. Taylor W.H., Hagerman P.J. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. Sodium chloride-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:1990;363-376
85. Thompson J.F., Landy A. Empirical estimation of protein-induced DNA bending angles applications to λ site-specific recombination complexes. Nucl. Acids Res. 16:1988;9687-9705
86. Ulanovsky L., Bodner M., Trifonov E.N., Choder M. Curved DNA design, synthesis and circularization. Proc. Natl Acad. Sci. USA. 83:1986;862-866
87. Wang J.C., Davidson N. On the probability of ring closure of lambda DNA. J. Mol. Biol. 19:1966;469-482
88. Warwicker J., Engelman B.P., Steitz T.A. Electrostatic calculations and model building suggest that CAP bound to DNA is sharply bent. Proteins: Struct. Funct. Genet. 2:1987;283-289
89. Wechsler D.S., Dang C.V. Opposite orientations of DNA bending by c-Myc and Max. Proc. Natl Acad. Sci. USA. 89:1992;7635-7639
90. Yang Y., Westcott T.P., Pedersen S.C., Tobias I., Olson W.K. Effects of localized bending on DNA supercoiling. Trends Biochem. Sci. 20:1995;313-319
91. Zhurkin V.B., Ulyanov N.B., Gorin A.A., Jernigan R.L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl Acad. Sci. USA. 88:1991;7046-7050
92. Zimm B.H. Mechanism of gel electrophoresis of DNA unexpected findings. Curr. Opin. Struct. Biol. 3:1993;373-376
93. Zinkel S.S., Crothers D.M. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers. 29:1990;29-38