Characterizing the residue level folding of the intrinsically unstructured IA3

Biochemistry

Volumn 45, Issue 45, 2006, Pages 13585-13596

  Ganesh, Omjoy K ^a   Green, Terry B ^b   Edison, Arthur S ^a   Hagen, Stephen J ^a,c  

^a UNIVERSITY OF FLORIDA   (United States)

^b CENTER FOR MEDICAL   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DECOMPOSITION; ETHANOL; FREQUENCY SHIFT KEYING; NUCLEAR MAGNETIC RESONANCE; YEAST;

RESIDUE LEVEL ANALYSIS; SINGULAR VALUE DECOMPOSITION (SVD); TRIFLUOROETHANOL (TFE); YEAST ASPARTIC PROTEINASE A (YPRA);

ENZYME INHIBITION;

ASPARTIC PROTEINASE; ASPARTIC PROTEINASE INHIBITOR; INHIBITOR PROTEIN; PROTEIN IA3; TRIFLUOROETHANOL; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CORRELATION ANALYSIS; DECOMPOSITION; ENZYME INHIBITOR COMPLEX; EQUILIBRIUM CONSTANT; MOLECULAR INTERACTION; NITROGEN 15 HETERONUCLEAR SINGLE QUANTUM CORRELATION; NONHUMAN; PHASE TRANSITION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTUM MECHANICS;

ASPARTIC ENDOPEPTIDASES; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE PROTEINS; THERMODYNAMICS; TRIFLUOROETHANOL;

EID: 33750978439     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061358w     Document Type: Article

References (54)

1. Green, T. B., Ganesh, O., Perry, K., Smith, L., Phylip, L. H., Logan, T. M., Hagen, S. J., Dunn, B. M., and Edison, A. S. (2004) IA3, an aspartic proteinase inhibitor from Saccharomyces cerevisiae, is intrinsically unstructured in solution, Biochemistry 43, 4071-4081.
2. Li, M., Phylip, L. H., Lees, W. E., Winther, J. R., Dunn, B. M., Wlodawer, A., Kay, J., and Gustchina, A. (2000) The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix, Nat. Struct. Biol. 7, 113-117.
3. 3 inhibitor and its target aspartic proteinase from Saccharomyces cerevisiae, J. Biol. Chem. 276, 2023-2030.
4. Wishart, D. S., and Sykes, B. D. (1994) Chemical shifts as a tool for structure determination, Methods Enzymol. 239, 363-392.
5. Pastore, A., and Saudek, V. (1990) The relationship between chemical shift and secondary structure in proteins, J. Magn. Reson. 90, 165-176.
6. Williamson, M. P. (1990) Secondary-structure dependent chemical shifts in proteins, Biopolymers 29, 1423-1431.
7. Matsuura, H., Shimotakahara, S., Sakuma, C., Tashiro, M., Shindo, H., Mochizuki, K., Yamagishi, A., Kojima, M., and Takahashi, K. (2004) Thermal unfolding of ribonuclease T1 studied by multidimensional NMR spectroscopy, Biol. Chem. 385, 1157-1164.
8. Sadqi, M., Fushman, D., and Munoz, V. (2006) Atom-by-atom analysis of global downhill protein folding, Nature 442, 317-321.
9. Zuiderweg, E. R. (2002) Mapping protein-protein interactions in solution by NMR spectroscopy, Biochemistry 41, 1-7.
10. Rajagopal, P., Waygood, E. B., Reizer, J., Saier, M. H., Jr., and Klevit, R. E. (1997) Demonstration of protein-protein interaction specificity by NMR chemical shift mapping, Protein Sci. 6, 2624-2627.
11. Baber, J. L., Levens, D., Libutti, D., and Tjandra, N. (2000) Chemical shift mapped DNA-binding sites and 15N relaxation analysis of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, Biochemistry 39, 6022-6032.
12. Lee, A. L., Volkman, B. F., Robertson, S. A., Rudner, D. Z., Barbash, D. A., Cline, T. W., Kanaar, R., Rio, D. C., and Wemmer, D. E. (1997) Chemical shift mapping of the RNA-binding interface of the multiple-RBD protein sex-lethal, Biochemistry 36, 14306-14317.
13. Henry, E. M., and Hofrichter, J. (1992) Singular value decomposition: application to the analysis of experimental data, Methods Enzymol. 210, 129-192.
14. 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects, J. Biomol. NMR 5, 67-81.
15. Piotto, M., Saudek, V., and Sklenar, V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions, J. Biomol. NMR 2, 661-665.
16. Bodenhausen, G., and Ruben, D. (1980) Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy, Chem. Phys. Lett. 69, 185-189.
17. Marion, D., Ikura, M., Tschudin, R., and Bax, A. (1989) Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins, J. Magn. Reson. 85, 393-399.
18. Grzesiek, S., and Bax, A. (1992) An efficient experiment for sequential backbone assignment of medium sized isotopically enriched proteins, J. Magn. Reson. 99, 201-207.
19. Grzesiek, S., and Bax, A. (1992) Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR, J. Am. Chem. Soc. 114, 6291-6293.
20. Grzesiek, S., and Bax, A. (1992) Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein, J. Magn. Reson. 96, 432-440.
21. Kay, L. E., Ikura, M., Tschudin, R., and Bax, A. (1990) Three-dimensional triple-resonance NMR-spectroscopy of isotopically enriched proteins, J. Magn. Reson. 89, 496-514.
22. Sattler, M., Schleucher, J., and Griesinger, C. (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients, Prog. Nucl. Magn. Reson. Spectrosc. 34, 93-158.
23. Palmer, A. G., Cavanagh, J., Wright, P. E., and Rance, M. (1991) Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy, J. Magn. Reson. (1969) 93, 151-170.
24. Kay, L., Keifer, P., and Saarinen, T. (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity, J. Am. Chem. Soc. 114, 10663-10665.
25. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR 6, 277-293.
26. Johnson, B., and Blevins, R. NMR View. A computer program for the visualization and analysis of NMR data, (1994) J. Biomol. NMR 4, 603-614.
27. Friedrichs, M. A model-free algorithm for the removal of baseline artifacts, (1995) J. Biomol. NMR 5, 147-153.
28. Schwarzinger, S., Kroon, G. J., Foss, T. R., Wright, P. E., and Dyson, H. J. (2000) Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView, J. Biomol. NMR 18, 43-48.
29. Schwarzinger, S., Kroon, G. J., Foss, T. R., Chung, J., Wright, P. E., and Dyson, H. J. (2001) Sequence-dependent correction of random coil NMR chemical shifts, J. Am. Chem. Soc. 123, 2970-2978.
30. Golub, G. H., and Reinsch, C. (1970) Singular value decomposition and least squares solution, Numer. Math. 14, 403-420.
31. Golub, G. H., and Van Loan, C. F. (1996) Matrix Computations, 3 ed., Johns Hopkins University Press, Baltimore, MA.
32. Nash, J. C. (1990) Compact Numerical Methods for Computers: Linear Algebra and Function Minimisation, 2 ed., Adam Hilger, England, New York.
33. Press, W., Flannery, B., Teukolsky, S., and Vetterling, W. (1992) Numerical Recipes in C: The Art of Scientific Computing, 2 ed., Cambridge University Press, New York.
34. Santoro, M. M., and Bolen, D. W. (1988) Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants, Biochemistry 27, 8063-8068.
35. Dobson, C. M., and Fersht, A. R. (1996) Protein Folding, Cambridge University Press, New York.
36. Goldstein, H., Poole, C., and Safko, J. (2002) Classical Mechanics, 3 ed., Addison Wesley, San Francisco, CA.
37. Demchenko, A. P. (2001) Concepts and misconcepts in the analysis of simple kinetics of protein folding, Curr. Protein Pept. Sci. 2, 73-98.
38. Asakura, T., Kazuhiro, T., Demura, M., and Williamson, M. P. (1995) The relationship between amide proton chemical shifts and secondary structure in proteins, J. Biomol. NMR 6, 227-236.
39. Wishart, D. S., Sykes, B. D., and Richards, F. M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure, J. Mol. Biol. 222, 311-333.
40. Wishart, D. S., and Case, D. A. (2001) Use of chemical shifts in macromolecular structure determination, Methods Enzymol. 338, 3-34.
41. Wishart, D. S., Sykes, B. D., and Richards, F. M. (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy, Biochemistry 31, 1647-1651.
42. Buck, M. (1998) Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins, Q. Rev. Biophys. 31, 297-355.
43. Fink, A. L. (2005) Natively unfolded proteins, Curr. Opin. Struct. Biol. 15, 35-41.
44. Matsuo, H., Walters, K. J., Teruya, K., Tanaka, T. T. G. G., Lippard, S. J., Kyogoku, Y., and Wagner, G. (1999) Identification by NMR spectroscopy of residues at contact surfaces in large, slowly exchanging macromolecular complexes, J. Am. Chem. Soc. 121, 9903-9904.
45. Edison, A. S., Espinoza, E., and Zachariah, C. (1999) Conformational ensembles: the role of neuropeptide structures in receptor binding, J. Neurosci. 19, 6318-6326.
46. Dossey, A. T., Reale, V., Chatwin, H., Zachariah, C., Debono, M., Evans, P. D., and Edison, A. S. (2006) NMR Analysis of Caenorhabditis elegans FLP-18 neuropeptides: implications for NPR-1 activation, Biochemistry 45, 7586-7597.
47. Santiveri, C. M., Pantoja-Uceda, D., Rico, M., and Jimenez, M. A. (2005) Beta-hairpin formation in aqueous solution and in the presence of trifluoroethanol: a (1)H and (13)C nuclear magnetic resonance conformational study of designed peptides, Biopolymers 79, 150-162.
48. Kemmink, J., and Creighton, T. E. (1995) Effects of trifluoroethanol on the conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor, Biochemistry 34, 12630-12635.
49. Bolin, K. A., Pitkeathly, M., Miranker, A., Smith, L. J., and Dobson, C. M. (1996) Insight into a random coil conformation and an isolated helix: structural and dynamical characterisation of the C-helix peptide from hen lysozyme, J. Mol. Biol. 261, 443-453.
50. Kentsis, A., and Sosnick, T. R. (1998) Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding, Biochemistry 37, 14613-14622.
51. 8-barrel N-(5′-phosphoribosyl)anthranilate isomerase from Escherichia coli, Biochemistry 33, 6350-6355.
52. Shiraki, K., Nishikawa, K., and Goto, Y. (1995) Trifluoroethanol-induced stabilization of the alpha-helical structure of beta-lactoglobulin: implication for non-hierarchical protein folding, J. Mol. Biol. 245, 180-194.
53. Luidens, M. K., Figge, J., Breese, K., and Vajda, S. (1996) Predicted and trifluoroethanol-induced alpha-helicity of polypeptides, Biopolymers 39, 367-376.
54. Iovino, M., Falconi, M., Marcellini, A., and Desideri, A. (2001) Molecular dynamics simulation of the antimicrobial salivary peptide histatin-5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect, J. Pept. Res. 58, 45-55.