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Hydrophobic Core Variant Ubiquitin Forms a Molten Globule Conformation at Acidic pH

  • Park, Soon-Ho (Department of Dentistry, College of Dentistry, Kangnung National University)
  • Published : 2004.11.30
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Abstract

The conformational properties of hydrophobic core variant ubiquitin (Val26 to Ala mutation) in an acidic solution were studied. The intrinsic tryptophan fluorescence emission spectrum, far-UV and near-UV circular dichroic spectra, the fluorescence emission spectrum of 8-anilinonaphthalene-1-sulfonic acid in the presence of V26A ubiquitin, and urea-induced unfolding measurements indicate this variant ubiquitin to be in the partially folded molten globule conformation in solution at pH 2. The folding kinetics from molten globule to the native state was nearly identical to those from the unfolded state to the native state. This observation suggests that the equilibrium molten globule state of hydrophobic core variant ubiquitin is an on-pathway folding intermediate.

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References

  1. Anfinsen, C. B. (1973) Principles that govern the folding of protein chains. Science 181, 223-229. https://doi.org/10.1126/science.181.4096.223
  2. Arai, M. and Kuwajima, K. (1996) Rapid formation of a molten globule intermediate in refolding of $\alpha$-lactalbumin. Fold. Des. 1, 275-287. https://doi.org/10.1016/S1359-0278(96)00041-7
  3. Azzi, A. (1974) The use of fluorescent probes for the study of membranes. Methods Enzymol. 32, 234-246. https://doi.org/10.1016/0076-6879(74)32024-1
  4. Briggs, M. S. and Roder, H. (1992) Early hydrogen-bonding events in the folding reaction of ubiquitin. Proc. Natl. Acad. Sci. USA 89, 2017-2021. https://doi.org/10.1073/pnas.89.6.2017
  5. Cox, J. P. L., Evans, P. A., Packman, L. C., Williams, D. H. and Woolfson, D. N. (1993) Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin. J. Mol. Biol. 234, 483-492. https://doi.org/10.1006/jmbi.1993.1600
  6. Dabora, J. M., Pelton, J. G. and Marqusee, S. (1996) Structure of the acid state of Escherichia coli ribonuclease H1. Biochemistry 35, 11951-11958. https://doi.org/10.1021/bi9611671
  7. Dobson, C. M. (2004) Principles of protein folding, misfolding and aggregation. Semin. Cell Dev. Biol. 15, 3-16. https://doi.org/10.1016/j.semcdb.2003.12.008
  8. Edelhoch, H. (1967) Spectroscopic Determination of Tryptophan and Tyrosine in Proteins. Biochemistry 6, 1948-1954. https://doi.org/10.1021/bi00859a010
  9. Fersht, A. R. (1995) Characterizing transition states in protein folding: an essential step in the puzzle. Curr. Opin. Struct. Biol. 5, 79-84 https://doi.org/10.1016/0959-440X(95)80012-P
  10. Fink, A. L. (1998) Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold. Des. 3, R9-23. https://doi.org/10.1016/S1359-0278(98)00002-9
  11. Fink, A. L., Calciano, L. J., Goto, Y., Kurotsu, T. and Palleros, D. R. (1994) Classification of Acid Denaturation of Proteins: Intermediates and Unfolded States. Biochemistry 33, 12504-12511. https://doi.org/10.1021/bi00207a018
  12. Gladwin, S. T. and Evans, P. A. (1996) Structure of very early protein folding intermediates: new insights through a variant of hydrogen exchange labelling. Fold. Des. 1, 407-417. https://doi.org/10.1016/S1359-0278(96)00057-0
  13. Goto, Y., Calciano, L. J. and Fink, A. L. (1990) Acid-induced folding of proteins. Proc. Natl. Acad. Sci. USA 87, 573-577. https://doi.org/10.1073/pnas.87.2.573
  14. Goto, Y. and Fink, A. L. (1989) Conformational states of $\beta$- lactamase: molten-globule states at acidic and alkaline pH with high salt. Biochemistry 28, 945-952. https://doi.org/10.1021/bi00429a004
  15. Greenfield, N. and Fasman, G. D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8, 4108-4116. https://doi.org/10.1021/bi00838a031
  16. Heidary, D. K., Gross, L. A., Roy, M. and Jennings, P. A. (1997) Evidence for an obligatory intermediate in the folding of interleukin-1$\beta$. Nat. Struct. Biol. 4, 725-731. https://doi.org/10.1038/nsb0997-725
  17. Khorasanizadeh, S., Peters, I. D., Butt, T. R. and Roder, H. (1993) Stability and folding of a tryptophan-containing mutant of ubiquitin. Biochemistry 32, 7054-7063. https://doi.org/10.1021/bi00078a034
  18. Khorasanizadeh, S., Peters, I. D., Butt, T. R. and Roder, H. (1993) Stability and folding of a tryptophan-containing mutant of ubiquitin. Biochemistry 32, 7054-7063. https://doi.org/10.1021/bi00078a034
  19. Kim, P. S. and Baldwin, R. L. (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu. Rev. Biochem. 51, 459-489. https://doi.org/10.1146/annurev.bi.51.070182.002331
  20. Kim, P. S. and Baldwin, R. L. (1990) Intermediates in the folding reactions of small proteins. Annu. Rev. Biochem. 59, 631-660. https://doi.org/10.1146/annurev.bi.59.070190.003215
  21. Kuwajima, K., Hiraoka, Y., Ikeguchi, M. and Sugai, S. (1985) Comparison of the transient folding intermediates in lysozyme and $\alpha$-lactalbumin. Biochemistry 24, 874-881. https://doi.org/10.1021/bi00325a010
  22. Laub, P. B., Khorasanizadeh, S. and Roder, H. (1995) Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints. Protein Sci. 4, 973-982.
  23. Luo, Y., Kay, M. S. and Baldwin, R. L. (1997) Cooperativity of folding of the apomyoglobin pH 4 intermediate studied by glycine and proline mutations. Nat. Struct. Biol. 4, 925-930. https://doi.org/10.1038/nsb1197-925
  24. Matthews, C. R. (1993) Pathways of protein folding. Annu. Rev. Biochem. 62, 653-683. https://doi.org/10.1146/annurev.bi.62.070193.003253
  25. Mizuguchi, M., Arai, M., Ke, Y., Nitta, K. and Kuwajima, K. (1998) Equilibrium and kinetics of the folding of equine lysozyme studied by circular dichroism spectroscopy. J. Mol. Biol. 283, 265-277. https://doi.org/10.1006/jmbi.1998.2100
  26. Ptitsyn, O. B. (1995) Molten globule and protein folding. Adv. Protein Chem. 47, 83-229. https://doi.org/10.1016/S0065-3233(08)60546-X
  27. Raschke, T. M. and Marqusee, S. (1997) The kinetic folding intermediate of ribonuclease H1 resembles the acid molten globule and partially unfolded molecules detected under native conditions. Nat. Struct. Biol. 4, 298-304. https://doi.org/10.1038/nsb0497-298
  28. Semisotnov, G. V., Rodionova, N. A., Razgulyaev, O. I., Uversky, V. N., Gripas, A. F. and Gilmanshin, R. I. (1991) Study of the molten globule intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers 31, 119-128. https://doi.org/10.1002/bip.360310111
  29. Stryer, L. (1968) Fluorescence Spectroscopy of Proteins. Science 162, 526-533. https://doi.org/10.1126/science.162.3853.526
  30. Uversky, V. N. (2002) Cracking the folding code. Why do some proteins adopt partially folded conformations, whereas other don't. FEBS Lett. 514, 181-183. https://doi.org/10.1016/S0014-5793(02)02359-1
  31. Wilkinson, K. D. and Mayer, A. N. (1986) Alcohol-induced conformational changes of ubiquitin. Arch. Biochem. Biophys. 250, 390-399. https://doi.org/10.1016/0003-9861(86)90741-1

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