Direct Demonstration of Structural Similarity between Native and Denatured Eglin C

Biochemistry

Volumn 43, Issue 14, 2004, Pages 4064-4070

  Ohnishi, Satoshi ^a   Lee, Andrew L ^b   Edgell, Marshall H ^c   Shortle, David ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENZYME KINETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH EFFECTS; PROTEINS; TOPOLOGY; UREA;

FIBRILS; RESIDUAL DIPOLAR COUPLINGS (RDC);

BIOCHEMISTRY;

AMYLOID; EGLIN C; NUCLEASE;

ARTICLE; CHEMICAL BOND; COMPUTER SIMULATION; DIPOLE; KINETICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; STAPHYLOCOCCUS;

ANIMALS; COMPUTER SIMULATION; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; RECOMBINANT PROTEINS; SERPINS; SOLUBILITY; THERMODYNAMICS; UREA;

STAPHYLOCOCCUS;

EID: 1842426942     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049879b     Document Type: Article

References (46)

1. Matthews, C. R., and Westmoreland, D. G. (1975) Nuclear magnetic resonance studies of residual structure in thermally unfolded ribonuclease A. Biochemistry 14, 4532-4538.
2. 15N nuclear magnetic resonance as a probe of residual structure in the backbone of unfolded hemoglobin. J. Am. Chem. Soc. 99, 5489-5490.
3. Neri, D., Billeter, M., Wider, G., and Wuthrich, K. (1992) NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science 257, 1559-1563.
4. Blanco, F. J., Serrano, L., and Forman-Kay, J. D. (1998) High populations of non-native structures in the denatured state are compatible with the formation of the native folded state. J. Mol. Biol. 284, 1153-1164.
5. Buck, M., Radford, S. E., and Dobson, C. M. (1994) Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea. J. Mol. Biol. 237, 247-254.
6. Shortle, D. (1996) Structural analysis of non-native states of proteins by NMR methods. Curr. Opin. Struct. Biol. 6, 24-30.
7. Dyson, H. J., and Wright, P. E. (1998) Equilibrium NMR studies of unfolded and partially folded proteins. Nat. Struct. Biol. 5 Suppl, 499-503.
8. Alexandrescu, A. T., and Shortle, D. (1994) Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease. J. Mol. Biol. 242, 527-546.
9. Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. E. (1997) Characterization of the backbone dynamics of folded and denatured states of an SH3 domain. Biochemistry 36, 2390-2402.
10. Buevich, A. V., Shinde, U. P., Inouye, M., and Baum, J. (2001) Backbone dynamics of the natively unfolded pro-peptide of subtilisin by heteronuclear NMR relaxation studies. J. Biomol. NMR. 20, 233-249.
11. Yao, J., Chung, J., Eliezer, D., Wright, P. E., and Dyson, H. J. (2001) NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding. Biochemistry 40, 3561-3571.
12. Buevich, A. V., and Baum, J. (1999) Dynamics of unfolded proteins: Incorporation of distributions of correlation times in the model free analysis of NMR relaxation data. J. Am. Chem. Soc. 121, 8671-8672.
13. Ohnishi, S., and Shortle, D. (2003) Effects of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nuclease. Protein Sci. 12, 1530-1537.
14. Gillespie, J. R., and Shortle, D. (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, 158-169.
15. Gillespie, J. R., and Shortle, D. (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, 170-184.
16. Yi, Q., Scalley-Kim, M. L., Alm, E. J., and Baker, D. (2000) NMR characterization of residual structure in the denatured state of protein L. J. Mol. Biol. 299, 1341-1351.
17. Lietzow, M. A., Jamin, M., Dyson, H. J., and Wright, P. E. (2002) Mapping long-range contacts in a highly unfolded protein. J. Mol. Biol. 322, 655-662.
18. Bax, A. (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci. 12, 1-16.
19. Prestegard, J. H., al-Hashimi, H. M., and Tolman, J. R. (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys. 33, 371-424.
20. Ackerman, M. S., and Shortle, D. (2002) Molecular alignment of denatured states of staphylococcal nuclease with strained polyacrylamide gels and surfactant liquid crystalline phases. Biochemistry 41, 3089-3095.
21. Ackerman, M. S., and Shortle, D. (2002) Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence. Biochemistry 41, 13791-13797.
22. Shortle, D., and Ackerman, M. S. (2001) Persistence of nativelike topology in a denatured protein in 8 M urea. Science 293, 487-489.
23. Hyberts, S. G., Goldberg, M. S., Havel, T. F., and Wagner, G. (1992) The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci. 1, 736-751.
24. Bode, W., Papamokos, E., and Musil, D. (1987) The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry. Eur. J. Biochem. 166, 673-692.
25. Hu, H., Clarkson, M. W., Hermans, J., and Lee, A. L. (2003) Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations. Biochemistry 42, 13856-13868.
26. Muhandiram, D. R., and Kay, L. E. (1994) Gradient-enhanced triple-resonance three-dimensional NMR experiments with improved sensitivity. J. Magn. Reson. B 103, 203-216.
27. Ottiger, M., Delaglio, F., and Bax, A. (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 373-378.
28. 13C labeled proteins. J. Biomol. NMR 12, 325-332.
29. Delaglio, F., Kontaxis, G., and Bax, A. (2000) Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122, 2142-2143.
30. Tycko, R., Blanco, F. J., and Ishii, Y. (2000) Alignment of biopolymers in strained gels: a new way to create detectable dipole-dipole couplings in high-resolution biomolecular NMR. J. Am. Chem. Soc. 122, 9340-9341.
31. Sass, H. J., Musco, G., Stahl, S. J., Wingfield, P. T., and Grzesiek, S. (2000) Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes. J. Biomol. NMR. 18, 303-309.
32. Louhivuori, M., Paakkonen, K., Fredriksson, K., Permi, P., Lounila, J., and Annila, A. (2003) On the origin of residual dipolar couplings from denatured proteins. J. Am. Chem. Soc. 125, 15647-15650.
33. Manly, B. F. J. (1997) in Randomization, Bootstrap and Monte Carlo Methods in Biology, Chapman & Hall, Boca Raton, FL.
34. Tolman, J. R. (2002) A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J. Am. Chem. Soc. 124, 12020-12030.
35. Flory, P. (1969) in Statistical Mechanics of Chain Molecules, Wiley, New York.
36. Clore, G. M., Gronenborn, A. M., and Bax, A. (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Magn. Reson. 133, 216-221.
37. Ding, K., Louis, J. M., and Gronenborn, A. M. (2004) Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR. J. Mol. Biol. 335, 1299-1307.
38. Ohnishi, S., and Shortle, D. (2003) Observation of residual dipolar couplings in short peptides. Proteins 50, 546-551.
39. Alexandrescu, A. T., and Kammerer, R. A. (2003) Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings. Protein Sci. 12, 2132-2140.
40. Nomura, K., and Kainosho, M. (2002) Graphical analysis of the relative orientation of molecular alignment tensors for a protein dissolved in two different anisotropic media. J. Magn. Reson. 154, 146-153.
41. Briggman, K. B., and Tolman, J. R. (2003) De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy. J. Am. Chem. Soc. 125, 10164-10165.
42. Zagrovic, B., Snow, C. D., Khaliq, S., Shirts, M. R., and Pande, V. S. (2002) Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323, 153-164.
43. Vendruscolo, M., Paci, E., Karplus, M., and Dobson, C. M. (2003) Structures and relative free energies of partially folded states of proteins. Proc. Natl. Acad. Sci. U.S.A. 100, 14817-14821.
44. Bu, Z., Cook, J., and Callaway, D. J. (2001) Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin. J. Mol. Biol. 312, 865-873.
45. Klein-Seetharaman, J., Oikawa, M., Grimshaw, S. B., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L. J., Dobson, C. M., and Schwalbe, H. (2002) Long-range interactions within a normative protein. Science 295, 1719-1722.
46. Harlow, E., Lane, D. (1999) in Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.