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Speeding along the protein folding highway, are we reading the signs correctly?

Abstract

Detailed studies of submillisecond burst phase signals in non-folding proteins indicate that the observed optical changes may reflect the population of different ensembles of unfolded polypeptides rather than the presence of intermediate species.

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Figure 1: Schematic free energy diagrams illustrating the point that burst phase signals may reflect very different transitions.

References

  1. Daughdrill, G.W., Chadsey, M.S., Karlinsey, J.E., Hughes, K.T. & Dahlquist, F.W. Nature Struct. Biol. 4, 285–291 (1997).

    CAS  PubMed  Google Scholar 

  2. Daughdrill, G.W., Hanely, L.J. & Dahlquist, F.W. Biochemistry 37, 1076– 1082 (1998).

    CAS  PubMed  Google Scholar 

  3. Kriwacki, R., Hengst, L., Tennant, L., Reed, S.I. & Wright, P.E. Proc. Natl. Acad. Sci. USA 93, 11504–11509 (1996).

    CAS  PubMed  Google Scholar 

  4. Baldwin, R.L. J. Biomol. NMR 5, 103–109 (1995).

    CAS  PubMed  Google Scholar 

  5. Baldwin, R.L. Folding & Design 1, R1–R8 (1996).

    CAS  Google Scholar 

  6. Bryngelson, J.D. & Wolynes, P.G. Proc. Natl. Acad. Sci. USA 84, 7524–7528 (1987).

    CAS  PubMed  Google Scholar 

  7. Bryngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. Proteins 21, 167–195 ( 1995).

    CAS  PubMed  Google Scholar 

  8. Creighton, T.E. Nature Struct. Biol. 1, 135–138 (1994).

    CAS  PubMed  Google Scholar 

  9. Creighton, T.E. Curr. Biol. 7, R380–R383 (1997).

    CAS  PubMed  Google Scholar 

  10. Dill, K.A. & Chan, H.S. Nature Struct. Biol. 4, 10–19 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Dobson, C.M. Curr. Biol. 4, 636–640 ( 1994).

    CAS  PubMed  Google Scholar 

  12. Fersht, A.R. Curr. Opin. Struct. Biol. 7, 3–9 (1997).

    CAS  PubMed  Google Scholar 

  13. Khorasanizadeh, S., Peters, I.D. & Roder, H. Nature Struct. Biol. 3, 193– 205 (1996).

    CAS  PubMed  Google Scholar 

  14. Socci, N.D. & Onuchic, J.N. J. Chem. Phys. 103 , 4732–4744 (1995).

    CAS  Google Scholar 

  15. Pande, V.S., Grosberg, A.Y., Tanaka, T. & Rokhsar, D.S. Curr. Opin. Struct. Biol. 8, 68–79 (1998).

    CAS  PubMed  Google Scholar 

  16. Sosnick, T.R., Mayne, L., Hiller, R. & Englander, S.W. Nature Struct. Biol. 1, 149–156 ( 1994).

    CAS  PubMed  Google Scholar 

  17. Raschke, T.M. & Marqusee, S. Nature Struct. Biol. 4, 298–304 (1997).

    CAS  PubMed  Google Scholar 

  18. Jennings, P.A. & Wright, P.E. Science 262, 892–896 (1993).

    CAS  PubMed  Google Scholar 

  19. Jennings, P.A., Dyson, H.J. & Wright, P.E. In Statistical mechanics, protein structure, and protein substrate interactions(ed. Doniach, S.) 7–18 (Plenum Press, New York; 1994)

    Google Scholar 

  20. Ballew, R.M., Sabelko, J. & Gruebele, M. Nature Struct. Biol. 3, 923– 926 (1996).

    CAS  PubMed  Google Scholar 

  21. Burton, R.E., Huang, G.S., Dougherty, M.A., Fulbright, P.W. & Oas, T.G. J. Mol. Biol. 263, 311–322 (1996).

    CAS  PubMed  Google Scholar 

  22. Gladwin, S.T. & Evans, P.A. Folding & Design 1, 407–417 (1996).

    CAS  Google Scholar 

  23. Houry, W.A. & Scheraga, H.A. Biochemistry 35, 11734–11746 (1996).

    CAS  PubMed  Google Scholar 

  24. Jacob, M., Schindler, T., Balbach, J. & Schmid, F.X. Proc. Natl. Acad. Sci. USA 94, 5622– 5627 (1997).

    CAS  PubMed  Google Scholar 

  25. Schindler, T., Herrler, M., Marahiel, M.A. & Schmid, F.X. Nature Struct. Biol. 2, 663–673 (1995).

    CAS  PubMed  Google Scholar 

  26. Shastry, M.C.R. & Roder, H. Nature Struct. Biol. 5, 385–392 ( 1998).

    CAS  PubMed  Google Scholar 

  27. Thompson, P.A., Eaton, W.A. & Hofrichter, J. Biochemistry 36, 9200– 9210 (1997).

    CAS  PubMed  Google Scholar 

  28. Sosnick, T.R., Shtilerman, M.D., Mayne, L. & S.W., E., Proc. Natl. Acad. Sci. USA 94, 8545– 8550 (1997).

    CAS  PubMed  Google Scholar 

  29. Wolynes, P.G., Luthey-Schulten, Z. & Onuchic, J.N. Chem. & Biol. 3, 425– 432 (1996).

    CAS  Google Scholar 

  30. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z. & Socci, N.D. Proc. Natl. Acad. Sci. USA 92, 3626– 3630 (1995).

    CAS  PubMed  Google Scholar 

  31. Wolynes, P.G., Onuchic, J.N. & Thirumalai, D. Science 267, 1619– 1620 (1995).

    CAS  PubMed  Google Scholar 

  32. Sosnick, T.R., Mayne, L. & Englander, S.W. Proteins 24, 413– 426 (1996).

    CAS  PubMed  Google Scholar 

  33. Hosszu, L.L. Nature Struct. 4, 801–804 (1997).

    CAS  Google Scholar 

  34. Parker, M.J., Dempsey, C.E., Lorch, M. & Clarke, A.R. Biochemistry 36, 13396–13405 ( 1997).

    CAS  PubMed  Google Scholar 

  35. Roder, H. & Colon, W. Curr. Opin. Struct. Biol. 7, 15–28 (1997).

    CAS  PubMed  Google Scholar 

  36. Qi, P.X., Sosnick, T.R. & Englander, S.W. Nature Struct. Biol. 5, 882 –884 (1998).

    CAS  PubMed  Google Scholar 

  37. Udgaonkar, J.B. & Baldwin, R.L. Proc. Natl. Acad. Sci. USA 87, 8197–8201 (1990).

    CAS  PubMed  Google Scholar 

  38. Udgaonkar, J.B. & Baldwin, R.L. Nature 335, 694–699 (1988).

    CAS  PubMed  Google Scholar 

  39. Schultz, D.A. & Baldwin, R.L. Prot. Sci. 1, 910–916 (1992).

    CAS  Google Scholar 

  40. Baldwin, R.L. Curr. Opin Struct. Biol. 3, 84–91 (1993).

    CAS  Google Scholar 

  41. Schultz, D.A., Schmid, F.X. & Baldwin, R.L. Prot. Sci. 1, 917– 924 (1992).

    CAS  Google Scholar 

  42. Xu, X & Scheraga, H.A. Biochemistry 37, 7561–7571 (1998).

    CAS  PubMed  Google Scholar 

  43. Iwaoka, M. Juminga, D. & Scheraga, H.A. Biochemistry 37, 4490– 4501 (1998).

    CAS  PubMed  Google Scholar 

  44. Robertson, A.D. & Baldwin, R.L. Biochemistry 41, 9907–9914 ( 1991).

    Google Scholar 

  45. Xu, X., Rothwarf, D.M. & Scheraga, H.A. Biochemistry 35, 6406– 6417 (1996).

    CAS  PubMed  Google Scholar 

  46. Levinthal, C. In Mossbauer Spectroscopy in Biological Systems (eds DeBrunner, P., Tsibris, J. & Munck, E.) 22–24 (University of Illinois Press, Urbana;1969).

    Google Scholar 

  47. Bai, Y., Milne, J.S., Mayne, L. & Englander, S.W. Proteins 17, 75–86 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. van Nuland, N.A. et al. Biochemistry 37, 622– 637 (1998).

    CAS  PubMed  Google Scholar 

  49. Fersht, A.R. Curr. Opin. Struct. Biol. 5, 79–84 (1995).

    CAS  PubMed  Google Scholar 

  50. Onuchic, J.N., Socci, N.D., Luthey-Schulten, Z. & Wolynes, P.G. Folding & Design 1, 441–450 (1996).

    CAS  Google Scholar 

  51. Roder, H. Nature Struct. Biol. 2, 817–820 (1995).

    CAS  PubMed  Google Scholar 

  52. Jackson, S.E. Folding & Design 3, R81–R91 (1998).

    CAS  Google Scholar 

  53. Yao, J.T.J., Kao, Y.H. & Cocco, M.J. FEBS Lett. 419, 285– 289 (1997).

    PubMed  Google Scholar 

  54. Wright, P.E., Dyson, H.J. & Lerner, R.A. Biochemistry 27, 7167– 7175 (1988).

    CAS  PubMed  Google Scholar 

  55. Eliezer, D., Yao, J., Dyson, H.J. & Wright, P.E. Nature Struct. Biol. 5, 148–155 ( 1998).

    CAS  PubMed  Google Scholar 

  56. Dill, K.A. & Shortle, D. Annu. Rev. Biochem. 60, 795–825 (1991).

    CAS  PubMed  Google Scholar 

  57. Gillespie, J.R. & Shortle, D. J. Mol. Biol. 268, 170–184 ( 1997).

    CAS  PubMed  Google Scholar 

  58. Neri, D., Billeter, M., Wider, G. & Wüthrich, K. Science 257, 1559–1563 ( 1992).

    CAS  PubMed  Google Scholar 

  59. Shin, H.-C., Merutka, G., Waltho, J.P., Wright, P.E. & Dyson, H.J. Biochemistry 32, 6348–6355 (1993).

    CAS  PubMed  Google Scholar 

  60. Shin, H.-C. et al. Biochemistry 32, 6356– 6364 (1993).

    CAS  PubMed  Google Scholar 

  61. Waltho, J.P., Feher, V.A., Merutka, G., Dyson, H.J. & Wright, P.E. Biochemistry 32, 6337– 6347 (1993).

    CAS  PubMed  Google Scholar 

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Correspondence to Patricia A. Jennings.

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Jennings, P. Speeding along the protein folding highway, are we reading the signs correctly?. Nat Struct Mol Biol 5, 846–848 (1998). https://doi.org/10.1038/2286

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