Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA

Biochemistry

Volumn 43, Issue 23, 2004, Pages 7273-7287

  Columbus, Linda ^a   Hubbell, Wayne L ^a  

^a JULES STEIN EYE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DIFFUSION; DNA; PROTEINS; RELAXATION PROCESSES;

MOBILITY GRADIENTS; SIDE CHAINS; SPECTRAL SIMULATION TECHNIQUES; SPIN LABELING;

BIOCHEMISTRY;

DNA; GLOBULAR PROTEIN; NITROXIDE; PROTEIN; PROTEIN GCN[4-58] BZIP; UNCLASSIFIED DRUG;

ARTICLE; DIFFUSION; DNA BINDING; DNA PROTEIN COMPLEX; ELECTRON SPIN RESONANCE; NITROGEN NUCLEAR MAGNETIC RESONANCE; PARAMETER; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; SPIN LABELING;

DIMERIZATION; DNA; DNA-BINDING PROTEINS; ELECTRON SPIN RESONANCE SPECTROSCOPY; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN KINASES; SACCHAROMYCES CEREVISIAE PROTEINS; SOLUTIONS; SPIN LABELS;

PTERIDIUM AQUILINUM;

EID: 2942527068     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0497906     Document Type: Article

References (35)

1. Carr, P. A., Erickson, H. P., and Palmer, A. G. (1997) Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin, Structure 5, 949-959.
2. Ishima, R., and Torchia, D. A. (2000) Protein dynamics from NMR, Nat. Struct. Biol. 7, 740-743.
3. Zuiderweg, E. R. (2002) Mapping protein-protein interactions in solution by NMR spectroscopy, Biochemistry 41, 1-7.
4. Wang, C., Pawley, N. H., and Nicholson, L. K. (2001) The role of backbone motions in ligand binding to the c-Src SH3 domain, J. Mol. Biol. 313, 873-887.
5. Stone, M. J., Gupta, S., Snyder, N., and Regan, L. (2001) Comparison of protein backbone entropy and β-sheet stability: NMR-derived dynamics of protein G B1 domain mutants, J. Am. Chem. Soc. 123, 185-186.
6. Yang, D., and Kay, L. E. (1996) Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding, J. Mol. Biol. 263, 369-382.
7. Parak, F. G. (2003) Proteins in action: the physics of structural fluctuations and conformational changes, Curr. Opin. Struct. Biol. 13, 552-557.
8. Hammes, G. G. (2002) Multiple conformational changes in enzyme catalyasis, Biochemistry 41, 8221-8228.
9. Gerstein, M., Lesk, A. M., and Chothia, C. (1994) Structural mechanisms for domain movements in proteins, Biochemistry 33, 6739-6749.
10. Hubbell, W. L., Gross, A., Langen, R., and Lietzow, M. A. (1998) Recent advances in site-directed spin labeling of proteins, Curr. Opin. Struct. Biol. 8, 649-656.
11. Hubbell, W. L., Cafiso, D. S., and Altenbach, C. (2000) Identifying conformational changes with site-directed spin labeling, Nat. Struct. Biol. 7, 735-739.
12. Columbus, L., Kalai, T., Jeko, J., Hideg, K., and Hubbell, W. L. (2001) Molecular motion of spin labeled side chains in α-helices: analysis by variation of side chain structure, Biochemistry 40, 3828-3846.
13. Columbus, L., and Hubbell, W. L. (2002) A new spin on protein dynamics, Trends Biochem. Sci. 27, 288-295.
14. Budil, D. E., Lee, S., Saxena, S., and Freed, J. H. (1996) Nonlinear-least-squares analysis of slow-motion EPR spectra in one and two dimensions using a modified Levenberg-Marquardt algorithm, J. Magn. Reson., Ser. A 120, 155-189.
15. Mchaourab, H. S., Lietzow, M. A., Hideg, K., and Hubbell, W. L. (1996) Motion of spin-labeled side chains in T4 lysozyme. correlation with protein structure and dynamics, Biochemistry 35, 7692-7704.
16. Langen, R., Oh, K. J., Cascio, D., and Hubbell, W. L. (2000) Crystal structures of spin labeled T4 lysozyme mutants: implications for the interpretation of EPR spectra in terms of structure, Biochemistry 39, 8396-8405.
17. Bracken, C., Carr, P. A., Cavanagh, J., and Palmer, A. G. (1999) Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA, J. Mol. Biol. 285, 2133-2146.
18. Ellenberger, T. E., Brandl, C. J., Struhl, K., and Harrison, S. C. (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex, Cell 71, 1223-1237.
19. Keller, W., Konig, P., and Richmond, T. J. (1995) Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition, J. Mol. Biol. 254, 657-667.
20. 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible, Biochemistry 31, 5269-5278.
21. Hill, D. E., Hope, I. A., Macke, J. P., and Struhl, K. (1986) Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein, Science 234, 451-457.
22. Weiss, M. A., Ellenberger, T., Wobbe, C. R., Lee, J. P., Harrison, S. C., and Struhl, K. (1990) Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA, Nature 347, 575-578.
23. Hubbell, W. H., Froncisz, W., and Hyde, J. S. (1987) Continuous and stopped flow EPR Spectrometer based on a loop gap resonator, Rev. Sci. Instrum. 58, 1879-1886.
24. Langen, R., Cai, K., Altenbach, C., Khorana, H. G., and Hubbell, W. L. (1999) Structural features of the C-terminal domain of bovine rhodopsin: a site-directed spin-labeling study, Biochemistry 38, 7918-7924.
25. Bales, B. L. (1989) Inhomogenously broadened spin-label spectra, in Biological Magnetic Resonance: Spin Labeling Theory and Applications (Berliner, L. J., and Reuben, J., Eds.) pp 77-126, Plenum Press, New York.
26. Robinson, B. H., Mailer, C., and Reese, A. W. (1999) Linewidth analysis of spin labels in liquids I. theory and data analysis, J. Magn. Reson. 138, 199-209.
27. Stone, T. J., Buckman, T., Nordio, P. L., and McConnell, H. M. (1965) Spin-labeled biomolecules, Proc. Natl. Acad. Sci. U.S.A. 54, 1010-1017.
28. Freed, J. H. (1976) Theory of slow tumbling ESR spectra for nitroxides, in Spin Labeling Theory and Applications (Berliner, L. J., Ed.) pp 53-132, Academic Press, New York.
29. Alber, T. (1993) How GCN4 binds DNA, Curr. Opin. Struct. Biol. 3, 182-184.
30. Altenbach, C., Oh, K. J., Trabanino, R. J., Hideg, K., and Hubbell, W. H. (2001) Estimation of interresidue distances in spin labeled proteins at physiological temperatures: experimental strategies and practical limitations, Biochemistry 40, 15471-15482.
31. Mchaourab, H. S., Oh, K. J., Fang, C. J., and Hubbell, W. L. (1997) Conformation of T4 lysozyme in solution, hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling, Biochemistry 36, 307-316.
32. Barnes, J. P., Liang, Z., McHaourab, H. S., Freed, J. H., and Hubbell, W. L. (1999) A multifrequency electron spin resonance study of T4 lysozyme dynamics, Biophys. J. 76, 3298-3306.
33. Saudek, V., Pasley, H. S., Gibson, T., Gausepohl, H., Frank, R., and Pastore, A. (1991) Solution structure of the basic region from the transcriptional activator GCN4, Biochemistry 30, 1310-1317.
34. Saudek, V., Pastore, A., Morelli, M. A., Frank, R., Gausepohl, H., and Gibson, T. (1991) The solution structure of a leucine-zipper motif peptide, Protein Eng. 4, 519-529.
35. Griffith, O. H., and Jost, P. C. (1976) Lipid spin labels in biological membranes, in Spin Labeling Theory and Applications (Berliner, L. J., Ed.) pp 454-523, Academic Press, New York.