Determining Structural Ensembles for Intrinsically Disordered Proteins

Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation

Volumn , Issue , 2010, Pages 107-129

  Daughdrill, Gary W ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

Determining structural ensembles for intrinsically disordered proteins; Intrinsically disordered proteins (IDPs) ensembles of structures, range of compactness, secondary structure content and conformational dynamics; Validation, analysis and interpretation of structural ensembles

Indexed keywords

EID: 84865333470     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470602614.ch5     Document Type: Chapter

References (61)

1. Abramova, N. A., J. Russell, M. Botchan, and R. Li. 1997. Interaction between replication protein A and p53 is disrupted after UV damage in a DNA repair - dependent manner. Proc Natl Acad Sci U S A 94: 7186-91.
2. Ackerman, M. S., and D. Shortle. 2002. Molecular alignment of denatured states of staphylococcal nuclease with strained polyacrylamide gels and surfactant liquid crystalline phases. Biochemistry 41: 3089-95.
3. Al - Lazikani, B., J. Jung, Z. Xiang, and B. Honig. 2001. Protein structure prediction. Curr Opin Chem Biol 5: 51-6.
4. Baker, D., and A. Sali. 2001. Protein structure prediction and structural genomics. Science 294: 93-6.
5. Bargonetti, J., and J. J. Manfredi. 2002. Multiple roles of the tumor suppressor p53. Curr Opin Oncol 14: 86-91.
6. Battiste, J. L., and G. Wagner. 2000. Utilization of site - directed spin labeling and high - resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. Biochemistry 39: 5355-65.
7. Bax, A. 2003. Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12: 1-16.
8. Bax, A., G. Kontaxis, and N. Tjandra. 2001. Dipolar couplings in macromolecular structure determination. Methods Enzymol 339: 127-74.
9. Bell, S., C. Klein, L. Muller, S. Hansen, and J. Buchner. 2002. p53 contains large unstructured regions in its native state. J Mol Biol 322: 917-27.
10. Bernado, P., C. W. Bertoncini, C. Griesinger, M. Zweckstetter, and M. Blackledge. 2005. Defining long - range order and local disorder in native alpha - synuclein using residual dipolar couplings. J Am Chem Soc 127: 17968-9.
11. Bernado, P., L. Blanchard, P. Timmins, D. Marion, R. W. Ruigrok, and M. Blackledge. 2005. A structural model for unfolded proteins from residual dipolar couplings and small - angle x - ray scattering. Proc Natl Acad Sci U S A 102: 17002-7.
12. Bochkareva, E., L. Kaustov, A. Ayed, G. S. Yi, Y. Lu, A. Pineda - Lucena, J. C. Liao, A. L. Okorokov, J. Milner, C. H. Arrowsmith, and A. Bochkarev. 2005. Single - stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A. Proc Natl Acad Sci U S A 102: 15412-7.
13. Buevich, A. V., U. P. Shinde, M. Inouye, and J. Baum. 2001. Backbone dynamics of the natively unfolded pro - peptide of subtilisin by heteronuclear NMR relaxation studies. J Biomol NMR 20: 233-49.
14. Chi, S. W., S. H. Lee, D. H. Kim, M. J. Ahn, J. S. Kim, J. Y. Woo, T. Torizawa, M. Kainosho, and K. H. Han. 2005. Structural details on mdm2 - p53 interaction. J Biol Chem 280: 38795-802.
15. Chothia, C., and A. M. Lesk. 1987. The evolution of protein structures. Cold Spring Harb Symp Quant Biol 52: 399-405.
16. Chothia, C., and A. M. Lesk. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-6.
17. Clore, G. M., C. Tang, and J. Iwahara. 2007. Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol 17: 603-16.
18. Daughdrill, G. W., G. J. Pielak, V. N. Uversky, M. S. Cortese, and A. K. Dunker. 2005. Natively disordered proteins, pp. 275-357. In J. Buchner and T. Kiefhaber (eds.), Protein Folding Handbook, vol. 3. Wiley - VCH, Darmstadt, Germany.
19. Dawson, R., L. Muller, A. Dehner, C. Klein, H. Kessler, and J. Buchner. 2003. The N - terminal domain of p53 is natively unfolded. J Mol Biol 332: 1131-41.
20. De Gennes, P. G. 1979. Scaling Concepts in Polymer Physics. Cornell University Press, Ithaca, NY.
21. Dedmon, M. M., K. Lindorff - Larsen, J. Christodoulou, M. Vendruscolo, and C. M. Dobson. 2005. Mapping long - range interactions in alpha - synuclein using spin - label NMR and ensemble molecular dynamics simulations. J Am Chem Soc 127: 476-7.
22. Dosztanyi, Z., V. Csizmok, P. Tompa, and I. Simon. 2005. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 347: 827-39.
23. Dunker, A. K., J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero, J. S. Oh, C. J. Oldfield, A. M. Campen, C. M. Ratliff, K. W. Hipps, J. Ausio, M. S. Nissen, R. Reeves, C. Kang, C. R. Kissinger, R. W. Bailey, M. D. Griswold, W. Chiu, E. C. Garner, and Z. Obradovic. 2001. Intrinsically disordered protein. J Mol Graph Model 19: 26-59.
24. Dyson, H. J., and P. E. Wright. 2005. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
25. Ferreira, M. E., S. Hermann, P. Prochasson, J. L. Workman, K. D. Berndt, and A. P. Wright. 2005. Mechanism of transcription factor recruitment by acidic activators . J Biol Chem 280: 21779-84.
26. Fieber, W., S. Kristjansdottir, and F. M. Poulsen. 2004. Short - range, long - range and transition state interactions in the denatured state of ACBP from residual dipolar couplings. J Mol Biol 339: 1191-9.
27. Flory, P. J. 1953. Principles of Polymer Chemistry. Cornell University Press, Ithaca, NY.
28. Gillespie, J. R., and D. Shortle. 1997. Characterization of long - range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. J Mol Biol 268: 158-69.
29. Gillespie, J. R., and D. Shortle. 1997. Characterization of long - range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. J Mol Biol 268: 170-84.
30. Hermann, S., K. D. Berndt, and A. P. Wright. 2001. How transcriptional activators bind target proteins. J Biol Chem 276: 40127-32.
31. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J Mol Graph 14: 27-8, 33-8.
32. Iwahara, J., C. D. Schwieters, and G. M. Clore. 2004. Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126: 5879-96.
33. Jacobs, D. M., A. S. Lipton, N. G. Isern, G. W. Daughdrill, D. F. Lowry, X. Gomes, and M. S. Wold. 1999. Human replication protein A: global fold of the N - terminal RPA - 70 domain reveals a basic cleft and flexible C - terminal linker. J Biomol NMR 14: 321-31.
34. Jha, A. K., A. Colubri, K. F. Freed, and T. R. Sosnick. 2005. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc Natl Acad Sci U S A 102: 13099-104.
35. Kaustov, L., G. S. Yi, A. Ayed, E. Bochkareva, A. Bochkarev, and C. H. Arrowsmith. 2006. p53 transcriptional activation domain: a molecular chameleon? Cell Cycle 5: 489-94.
36. Kussie, P. H., S. Gorina, V. Marechal, B. Elenbaas, J. Moreau, A. J. Levine, and N. P. Pavletich. 1996. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274: 948-53.
37. Lee, H., K. H. Mok, R. Muhandiram, K. H. Park, J. E. Suk, D. H. Kim, J. Chang, Y. C. Sung, K. Y. Choi, and K. H. Han. 2000. Local structural elements in the mostly unstructured transcriptional activation domain of human p53. J Biol Chem 275: 29426-32.
38. Lesk, A. M., and C. Chothia. 1980. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136: 225-70.
39. Lesk, A. M., M. Levitt, and C. Chothia. 1986. Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng 1: 77-8.
40. Lindorff - Larsen, K., S. Kristjansdottir, K. Teilum, W. Fieber, C. M. Dobson, F. M. Poulsen, and M. Vendruscolo. 2004. Determination of an ensemble of structures representing the denatured state of the bovine acyl - coenzyme a binding protein. J Am Chem Soc 126: 3291-9.
41. Lowry, D. F., A. C. Hausrath, and G. W. Daughdrill. 2008. A robust approach for analyzing a heterogeneous structural ensemble. Proteins (in press).
42. Lowry, D. F., A. Stancik, R. M. Shresta, and G. W. Daughdrill. 2007. Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53. Proteins (in press).
43. Mohana - Borges, R., N. K. Goto, G. J. Kroon, H. J. Dyson, and P. E. Wright. 2004. Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J Mol Biol 340: 1131-42.
44. Petsko, G. A., and D. Ringe. 2004. Protein Structure and Function. New Science Press Ltd., London.
45. Prestegard, J. H., H. M. al - Hashimi, and J. R. Tolman. 2000. NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q Rev Biophys 33: 371-424.
46. Ruckert, M., and G. Otting. 2000. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122: 7793-7.
47. Schon, O., A. Friedler, M. Bycroft, S. M. Freund, and A. R. Fersht. 2002. Molecular mechanism of the interaction between MDM2 and p53. J Mol Biol 323: 491-501.
48. Schwieters, C. D., Kuszewski, J. J., N. Tjandra, N., and Clore, G. M. 2003. The Xplor - NIH NMR Molecular Structure Determination Package. J Magn Res 160: 66-74.
49. Schwieters, C. D., Kuszewski, J. J., and Clore, G. M. 2006. Using Xplor - NIH for NMR molecular structure determination. Progr NMR Spectroscopy 48: 47-62.
50. Shortle, D., and M. S. Ackerman. 2001. Persistence of native - like topology in a denatured protein in 8 M urea. Science 293: 487-9.
51. Tompa, P. 2002. Intrinsically unstructured proteins. Trends Biochem Sci 27: 527-33.
52. Uversky, V. N. 2002. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 11: 739-56.
53. Uversky, V. N. 1993. Use of fast protein size - exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule. Biochemistry 32: 13288-98.
54. Uversky, V. N. 2002. What does it mean to be natively unfolded? Eur J Biochem 269: 2-12.
55. Vendruscolo, M. 2007. Determination of conformationally heterogeneous states of proteins. Curr Opin Struct Biol 17: 15-20.
56. Vise, P., B. Baral, A. Stancik, D. F. Lowry, and G. W. Daughdrill. 2007. Identifying long - range structure in the intrinsically unstructured transactivation domain of p53. Proteins 67: 526-30.
57. Vise, P. D., B. Baral, A. J. Latos, and G. W. Daughdrill. 2005. NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain. Nucleic Acids Res 33: 2061-77.
58. von Ossowski, I., J. T. Eaton, M. Czjzek, S. J. Perkins, T. P. Frandsen, M. Schulein, P. Panine, B. Henrissat, and V. Receveur - Brechot. 2005. Protein disorder: conformational distribution of the flexible linker in a chimeric double cellulase. Biophys J 88: 2823-32.
59. Wells, M., H. Tidow, T. J. Rutherford, P. Markwick, M. R. Jensen, E. Mylonas, D. I. Svergun, M. Blackledge, and A. R. Fersht. 2008. Structure of tumor suppressor p53 and its intrinsically disordered N - terminal transactivation domain. Proc Natl Acad Sci U S A 105: 5762-7.
60. Woods, D. B., and K. H. Vousden. 2001. Regulation of p53 function. Exp Cell Res 264: 56-66.
61. Wright, P. E., and H. J. Dyson. 1999. Intrinsically unstructured proteins: re - assessing the protein structure - function paradigm. J Mol Biol 293: 321-31.