Profiling the dynamic interfaces of fluorinated transcription complexes for ligand discovery and characterization

ACS Chemical Biology

Volumn 7, Issue 8, 2012, Pages 1345-1350

  Pomerantz, William C ^a   Wang, Ningkun ^a   Lipinski, Ashley K ^a   Wang, Rurun ^a   Cierpicki, Tomasz ^a,b   Mapp, Anna K ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC AMINO ACID; LIGAND;

ARTICLE; BINDING AFFINITY; BINDING SITE; CIRCULAR DICHROISM; FLUORINATION; HEMATOPOIESIS; MOLECULAR WEIGHT; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ONCOGENE C MYB; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; SCREENING;

ALLOSTERIC SITE; ANIMALS; BINDING SITES; BIOCHEMISTRY; COMPUTATIONAL BIOLOGY; FLUORINE; HUMANS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84865263199     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb3002733     Document Type: Article

References (42)

1. Koehler, A. N. (2010) A complex task? Direct modulation of transcription factors with small molecules Curr. Opin. Chem. Biol. 14, 331-340
2. Lee, L. W. and Mapp, A. K. (2010) Transcriptional switches: Chemical approaches to gene regulation J. Biol. Chem. 285, 11033-11038
3. Fuxreiter, M., Tompa, P., Simon, I., Uversky, V. N., Hansen, J. C., and Asturiase, F. J. (2008) Malleable machines take shape in eukaryotic transcriptional regulation, Targeting intrinsically disordered proteins in neurodegenerative and protein dysfunction diseases: another illustration of the D(2) concept Nat. Chem. Biol. 4, 728-37
4. Uversky, V. N. (2010) Expert Rev. Proteomics 7, 543-564
5. Dyson, H. J. and Wright, P. E. (2005) Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell. Biol. 6, 197-208
6. Goto, N. K., Zor, T., Martinez-Yamout, M., Dyson, H. J., and Wright, P. E. (2002) Cooperativity in transcription factor binding to the coactivator CREB-binding protein (CBP). The mixed lineage leukemia protein (MLL) activation domain binds to an allosteric site on the KIX domain J. Biol. Chem. 277, 43168-43174
7. Hallam, T. M. and Bourtchouladze, R. (2006) Rubinstein-Taybi syndrome: Molecular findings and therapeutic approaches to improve cognitive dysfunction Cell. Mol. Life Sci. 63, 1725-1735
8. Sakamoto, K. M. and Frank, D. A. (2009) CREB in the pathophysiology of cancer: Implications for targeting transcription factors for cancer therapy Clin. Cancer Res. 15, 2583-2587
9. Ramirez, J. A. and Nyborg, J. K. (2007) Molecular characterization of HTLV-1 tax interaction with the KIX domain of CBP/p300 J. Mol. Biol. 372, 958-969
10. De Guzman, R. N., Goto, N. K., Dyson, H. J., and Wright, P. E. (2006) Structural basis for cooperative transcription factor binding to the CBP coactivator J. Mol. Biol. 355, 1005-1013
11. Radhakrishnan, I., PerezAlvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., and Wright, P. E. (1997) Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: A model for activator:coactivator interactions Cell 91, 741-752
12. Zor, T., De Guzman, R. N., Dyson, H. J., and Wright, P. E. (2004) Solution structure of the KIX domain of CBP bound to the transactivation domain of c-Myb J. Mol. Biol. 337, 521-534
13. Best, J. L., Amezcua, C. A., Mayr, B., Flechner, L., Murawsky, C. M., Emerson, B., Zor, T., Gardner, K. H., and Montminy, M. (2004) Identification of small-molecule antagonists that inhibit an activator: coactivator interaction Proc. Natl. Acad. Sci. U.S.A. 101, 17622-17627
14. Bates, C. A., Pomerantz, W. C., and Mapp, A. K. (2011) Transcriptional tools: Small molecules for modulating CBP KIX-dependent transcriptional activators Biopolymers 95, 17-23
15. Li, B. B. X. and Xiao, X. S. (2009) Discovery of a small-molecule inhibitor of the KIX-KID Interaction ChemBioChem 10, 2721-2724
16. Alluri, P., Liu, B., Yu, P., Xiao, X. S., and Kodadek, T. (2006) Isolation and characterization of coactivator- binding peptoids from a combinatorial library Mol. Biosyst. 2, 568-79
17. Rutledge, S. E., Volkman, H. M., and Schepartz, A. (2003) Molecular recognition of protein surfaces: High affinity ligands for the CBPKIX domain J. Am. Chem. Soc. 125, 14336-14347
18. For example see: Bruschweiler, S., Schanda, P., Kloiber, K., Brutscher, B., Kontaxis, G., Konrat, R., and Tollinger, M. (2009) Direct observation of the dynamic process underlying allosteric signal transmission J. Am. Chem. Soc. 131, 3063-3068
19. Najmanovich, R., Kuttner, J., Sobolev, V., and Edelman, M. (2000) Side-chain flexibility in proteins upon ligand binding Proteins 39, 261-268
20. 19F nuclear spin relaxation mechanism in proteins J. Mol. Biol. 98, 121-153
21. Frieden, C., Hoeltzli, S. D., and Bann, J. G. (2004) The preparation of F-19-labeled proteins for NMR studies Methods Enzymol. 380, 400-415
22. 19F NMR to studies of protein structure and dynamics Prog. Nucl. Magn. Reson. Spectrosc. 62, 1-33
23. Bogan, A. A. and Thorn, K. S. (1998) Anatomy of hot spots in protein interfaces J. Mol. Biol. 280, 1-9
24. Bullock, B. N., Jochim, A. L., and Arora, P. S. (2011) Assessing helical protein interfaces for inhibitor design J. Am. Chem. Soc. 133, 14220-14223
25. For examples see references 24-28: Salopek-Sondi, B., Vaughan, M. D., Skeels, M. C., Honek, J. F., and Luck, L. A. (2003) F-19 NMR studies of the leucine-isoleucine-valine binding protein: Evidence that a closed conformation exists in solution J. Biomol. Struct. Dyn. 21, 235-246
26. 19F]tryptophan-labeled Escherichia coli dihydrofolate reductase: equilibrium folding and ligand binding studies Biochemistry 33, 5502-5509
27. Evanics, F., Kitevski, J. L., Bezsonova, I., Forman-Kay, J., and Prosser, R. S. (2007) F-19 NMR studies of solvent exposure and peptide binding to an SH3 domain Biochim. Biophys. Acta, Gen. Subj. 1770, 221-230
28. 19F-NMR Science 335, 1106-1110
29. Cellitti, S. E., Jones, D. H., Lagpacan, L., Hao, X. S., Zhang, Q., Hu, H. Y., Brittain, S. M., Brinker, A., Caldwell, J., Bursulaya, B., Spraggon, G., Brock, A., Ryu, Y., Uno, T., Schultz, P. G., and Geierstanger, B. H. (2008) In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy J. Am. Chem. Soc. 130, 9268-9281
30. Dalvit, C., Fagerness, P. E., Hadden, D. T. A., Sarver, R. W., and Stockman, B. J. (2003) Fluorine-NMR experiments for high-throughput screening: Theoretical aspects, practical considerations, and range of applicability J. Am. Chem. Soc. 125, 7696-7703
31. Dalvit, C. (2007) Ligand- and substrate-based 19F NMR screening: Principles and applications to drug discovery Prog. Nucl. Magn. Reson. Spectrosc. 51, 243-271
32. Li, C., Charlton, L. M., Lakkavaram, A., Seagle, C., Wang, G., Young, G. B., Macdonald, J. M., and Pielak, G. J. (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: Implications, for in-cell NMR spectroscopy J. Am. Chem. Soc. 130, 6310-6311
33. Wei, Y., Horng, J. C., Vendel, A. C., Raleigh, D. P., and Lumb, K. J. (2003) Contribution to stability and folding of a buried polar residue at the CARM1 methylation site of the KIX domain of CBP Biochemistry 42, 7044-7049
34. Zor, T., Mayr, B. M., Dyson, H. J., Montminy, M. R., and Wright, P. E. (2002) Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators J. Biol. Chem. 277, 42241-42248
35. Sugase, K., Dyson, H. J., and Wright, P. E. (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein Nature 447, 1021-1025
36. For a discussion of disulfide tethering see Erlanson, D. A., Wells, J. A., and Braisted, A. C. (2004) Tethering: fragment-based drug discovery Annu. Rev. Biophys. Biomol. Struct. 33, 199-223. Details of the assay format will be discussed in subsequent report
37. Hajduk, P. J. and Greer, J. (2007) A decade of fragment-based drug design: strategic advances and lessons learned Nat. Rev. Drug Discovery 6, 211-219
38. Deng, X. M., Okram, B., Ding, Q. A., Zhang, J. M., Choi, Y. M., Adrian, F. J., Wojciechowski, A., Zhang, G. B., Che, J. W., Bursulaya, B., Cowan-Jacob, S. W., Rummel, G., Sim, T., and Gray, N. S. (2010) Expanding the diversity of allosteric Bcr-Abl inhibitors J. Med. Chem. 53, 6934-6946
39. Yu, L. P., Hajduk, P. J., Mack, J., and Olejniczak, E. T. (2006) Structural studies of Bcl-xL/ligand complexes using F-19 NMR J. Biomol. NMR 34, 221-227
40. Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W. (1996) Discovering high-affinity ligands for proteins: SAR by NMR Science 274, 1531-1534
41. Buhrlage, S. J., Bates, C. A., Rowe, S. P., Minter, A. R., Brennan, B. B., Majmudar, C. Y., Wemmer, D. E., Al-Hashimi, H., and Mapp, A. K. (2009) Small molecule transcriptional activation domains interact with endogenous coactivators ACS Chem. Biol. 4, 335-344
42. Muchmore, D. C., McIntosh, L. P., Russell, C. B., Anderson, D. E., and Dahlquist, F. W. (1989) Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance Methods Enzymol. 177, 44-73