Analysis of Transcription Factor Interactions at Sedimentation Equilibrium

Methods in Enzymology

Volumn 370, Issue , 2003, Pages 349-369

  Daugherty, Margaret A ^a   Fried, Michael G ^b  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

^b PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; COMPUTER PROGRAM; EQUILIBRIUM CONSTANT; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; MATHEMATICAL ANALYSIS; MATHEMATICAL PARAMETERS; MODEL; NONHUMAN; PH; PRIORITY JOURNAL; TATA BOX; TEMPERATURE DEPENDENCE; YEAST;

ESCHERICHIA COLI;

EID: 0346120326     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(03)70031-7     Document Type: Article

References (71)

1. A. Hochschild and S. L. Dove, Cell 92, 597 (1998).
2. T. I. Li and R. A. Young, Annu. Rev. Genet. 34, 77 (2000).
3. D. Beckett, J. Mol. Biol. 314, 335 (2001).
4. A. Dvir, J. W. Conaway, and R. C. Conaway, Curr. Opin. Genet. Dev. 11, 209 (2001).
5. G. Gill, Essays Biochem. 37, 33 (2001).
6. T. Svedburg and K. O. Pedersen, "The Ultracentrifuge." Johnson Reprint Corp., New York, 1956.
7. D. K. McRorie and P. J. Voelker, "Self-associating Systems in the Analytical Ultracentrifuge" Beckman Instruments, Inc., Palo Alto, CA, 1993.
8. J. C. Hansen, J. Lebowitz, and B. Demeler, Biochemistry 33, 13155 (1994).
9. T. M. Laue, Methods Enzymol. 259, 427 (1995).
10. A. P. Minton, Progr. Colloid Polym. Sci. 107, 11 (1997).
11. G. Rivas, W. F. Stafford III, and A. P. Minton, Methods 19, 194 (1999).
12. T. M. Laue and W. F. Stafford III, Annu. Rev. Biophys. Biomol. Struct. 28, 75 (1999).
13. J. Lebowitz, M. Lewis, and P. Schuck, Protein Sci. 11, 2067 (2002).
14. H. K. Schachman, "Ultracentrifugation in Biochemistry" Academic Press, New York, 1959.
15. J. W. Williams, "Ultracentrifugation of Macromolecules" Academic Press, New York, 1972.
16. D. C. Teller, Methods Enzymol. 27, 346 (1973).
17. D. F. Senear, J. B. Ross, and T. M. Laue, Methods 16, 3 (1998).
18. i defined in the text and requires inclusion of an additional factor of 1/2 in Eq. (1). Often data will contain a concentration-independent component due to a constant absorbance or refractive index difference between reference and sample sectors. For this reason, expressions describing absorbance or refractive index gradients commonly contain an additional constant "baseline offset" term.
19. Typically ≤3, although under favorable conditions, systems containing more species are amenable to analysis.
20. n does not change the number of adjustable parameters.
21. M. A. Daugherty, M. Brenowitz, and M. G. Fried, J. Mol. Biol. 285, 1389 (1999).
22. M. A. Daugherty, M. Brenowitz, and M. G. Fried, Biochemistry 39, 4869 (2000).
23. TBP) is unchanged by self-association. If σ is allowed to float, there are four adjustable parameters. This can be reduced to three if the value of σ is fixed at the known monomer molecular weight.
24. R. A. Coleman, A. K. P. Taggart, L. R. Benjamin, and B. F. Pugh, J. Biol. Chem. 270, 13842 (1995).
25. A. K. P. Taggart and B. F. Pugh, Science 272, 1331 (1996).
26. K. M. Campbell, R. T. Ranallo, L. A. Stargell, and K. J. Lumb, Biochemistry 39, 2633 (2000).
27. Two optical path lengths are common: that of standard cells is 1.2 cm and that of short optical path cells is 0.3 cm.
28. For proteins, the refractive increment dn/dc is equivalent to ∼3.33 fringes ml/mg using light of 670 nm and a 1.2-cm optical path length 4.
29. H. Durschlag, in "Thermodynamic Data for Biochemistry and Biotechnology" (H.-J. Hinz, ed.), p. 45. Springer-Verlag, Berlin, 1986.
30. D. Dyckman and M. G. Fried, J. Biol. Chem. 277, 19064 (2002).
31. C. Y. Huang, Methods Enzymol. 87, 509 (1982).
32. obs while minimizing the number of adjustable species in the fit.
33. Under dilute solution conditions. In concentrated solutions, steric interactions and other nonideal effects can prevent independent sedimentation.
34. The presence of inactive species increases the number of adjustable terms in the sedimentation equation that must be evaluated by fitting. Because acquiring a meaningful fit becomes more difficult as the number of species increases, systems containing several inactive species should be purified further before a detailed SE analysis is attempted.
35. J. Wyman and S. J. Gill, "Binding and Linkage," University Science Books, Mill Valley, CA, 1990.
36. M. G. Fried and M. A. Daugherty, J. Biol. Chem. 276, 11226 (2001).
37. For the reaction shown in Eq. (12), net cAMP uptake will yield n > 0, net release n < 0, and a cAMP-independent reaction, n = 0.
38. T. Takahashi, B. Blazy, and A. Baudras, Biochemistry 19, 5124 (1980).
39. For accurate measurements, the operating temperature of the centrifuge should be calibrated as described by S. Liu and W. F. Stafford III, Anal. Biochem. 224, 199 (1995).
40. R. S. Spolar, J.-H. Ha, and M. T. Record, Jr., Proc. Natl. Acad. Sci. USA 86, 8382 (1989).
41. E. C. W. Clarke and D. N. Glew, Trans. Faraday Soc. 62, 539 (1966).
42. J. J. Correia and D. A. Yphantis, in "Analytical Ultracentrifuation in Biochemistry and Polymer Science" (S. E. Harding, A. J. Rowe, and J. C. Horton, eds.), p. 237. Royal Society of Chemistry, Cambridge, 1992.
43. T. M. Laue, Technical Information, Vol. DS-835, Beckman Instruments, Palo Alto, CA, 1992.
44. G. Ralston, "Introduction to Analytical Ultracentrifugation." Beckman Instruments, Inc, Fullerton, 1993.
45. T. M. Laue, D. F. Senear, S. Eaton, and J. B. Ross, Biochemistry 32, 2469 (1993).
46. M. S. Lewis, R. I. Shrager, and S. J. Kim, in "Modern Analytical Ultracentrifugation" (T. M. Schuster and T. M. Laue, eds.), p. 94, Birkhauser, Boston, 1994.
47. P. Schuck, M. A. Perugini, N. R. Gonzales, G. J. Howlett, and D. Schubert, Biophys. J. 82, 1096 (2002).
48. J. J. Correia, Methods Enzymol. 321, 81 (2000).
49. L. M. Carruthers, V. R. Schirf, B. Demeler, and J. C. Hansen, Methods Enzymol. 321, 66.
50. E. F. Casassa and H. Eisenberg, Adv. Prot. Chem. 19, 287 (1964).
51. H. S. Penefsky, Methods Enzymol. 56, 527 (1979).
52. K. Struhl, in "Current Protocols in Molecular Biology" (F. M. Ausubel et al., eds.), p. 3.4.8, Wiley, New York, 1989.
53. C. H. Chervenka, "A Manual of Methods for the Analytical Ultracentrifuge," Spinco Division, Beckman Instruments, Palo Alto, CA 1969.
54. M. L. Johnson, J. J. Correia, D. A. Yphantis, and H. R. Halvorson, Biophys. J. 36, 575 (1981).
55. The program MATCH by D. Yphantis and J. Lary (available on the web at ftp://rasmb.bbri.org) facilitates this comparison.
56. D. E. Roark, Biophys. Chem. 5, 185 (1976).
57. T. M. Laue, B. D. Shah, T. M. Ridgeway, and S. L. Pelletier, in "Analytical Ultracentrifugation in Biochemistry and Polymer Science" (S. E. Harding, A. J. Rowe, and J. C. Harding, eds.), p. 90. The Royal Society of Chemistry, Cambridge, England, 1992.
58. O. Kratky, H. Leopold, and H. Stabinger, Methods Enzymol. 27, 98 (1973).
59. E. J. Cohn and J. T. Edsall, "Proteins, Amino Acids and Peptides as Ions and Dipolar Ions," Reinhold, New York, 1943.
60. S. J. Edelstein and H. K. Schachman, Methods Enzymol. 27, 82 (1973).
61. This calculation ignores changes in M that result from H-D exchange, which will depend on the identity of amino acids and nonprotein components of the molecule(s) in question.
62. D. E. Roark and D. A. Yphantis, Ann. N.Y. Acad. Sci. 164, 245 (1969).
63. R. H. Haschemeyer and W. F. Bowers, Biochemistry 9, 435 (1970).
64. G. J. Howlett, Chemtracts-Biochem. Mol. Biol. 11, 950 (1998).
65. D. J. Winzor and P. R. Wills, in "Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems" (T. M. Schuster and T. M. Laue, eds.), p. 66. Birkhauser, Boston, 1994.
66. D. J. Winzor, M. P. Jacobsen, and P. R. Wills, Biochemistry 37, 2226 (1998).
67. M. L. Johnson and M. Straume, in "Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems" (T. M. Schuster and T. M. Laue, eds.), p. 37, Birkhauser, Boston, 1994.
68. M. L. Johnson, Anal. Biochem. 206, 215 (1992).
69. T. M. Laue, A. L. Anderson, and B. J. Weber, in "Ultrasensitive Clinical Laboratory Diagnostics" (G. Cohn, ed.), Vol. 2985, p. 196. SPIE, Bellingham, WA, 1997.
70. J. B. Ross, D. F. Senear, E. Waxman, B. B. Kombo, E. Rusinova, Y. T. Huang, W. R. Laws, and C. A. Hasselbacher, Proc. Natl. Acad. Sci. USA 89, 12023 (1992).
71. S. Darawashe and A. P. Minton, Anal. Biochem. 220, 1 (1994).