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1999 | 46 | 3 |

Tytuł artykułu

Folding initiation sites and protein folding

Autorzy

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
The paper discusses the role of local structural preferences of protein segments in the folding of proteins. First a short overview of the local, secondary structures detected in peptides, protein fragments, denatured proteins and early folding intermediates is given. Next the discussion of their role in protein folding is presented based on recent literature and data obtained in our laboratory. In conclusion it is pointed out that, during folding, local structures populated at low levels in denatured state may facilitate the crossing of the folding transition state barrier, and consequently accelerate the rate limiting step in folding. However, the data show that this effect does not follow simple rules.

Wydawca

-

Rocznik

Tom

46

Numer

3

Opis fizyczny

p.487-508,fig.

Twórcy

autor
  • Polish Academy of Sciences, A.Pawinskiego 5A, 02-106 Warsaw, Poland

Bibliografia

  • 1. Hardesty, B., Tsalkova, T. & Kramer, G. (1999) Co-translational folding. Curr. Opin. Struct Biol 9, 111-114.
  • 2. Ellis, R.J. & Hemmingsen, S.M. (1989) Molec­ular chapennes: Proteins essential for the biogenesis of some macromolecular struc­tures. Trends Biochem. Sci. 14, 339-342.
  • 3. Radford, S.E. (1998) What's new in protein folding? Folding & Design 3, R59-R63.
  • 4. Thulasiraman, V., Yang, C.-F. & Frydman, J. (1999) In vivo newly translated polypeptides are sequestered in a protected folding environ­ment. EMBO J. 18, 85-95.
  • 5. Sifers, R.N. (1995) Defective protein folding as a cause of disease. Nature Struct Biol. 2, 355-357.
  • 6. Wetzel, R. (1996) For protein misassembly this is the I decade. Cell 86, 699-701.
  • 7. CarreU, RW. & Lomas, DA. (1997) Conformational disease. Lancet 350, 134- 138.
  • 8. Baum, J. & Brodsky, B. (1999) Folding of pep­tide models of collagen and misfolding in dis­ease. Curr. Opin. Struct Biol 9, 122-128.
  • 9. Harrison, P.M., Bamborough, P., Dagget, V., Prusiner, S B. & Cohen, F. (1997) The prion folding problem. Curr. Opin. Struct Biol 7, 53-59.
  • 10. Daughdrill, G.W., Chadsey, M.S., Karlinsey, J.E., Hughes, K.T. & Dahlquist, F.W. (1997) The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28. Nature Struct Biol. 4, 285-291.
  • 11. Kriwacki, R., Hengst, L., Tennant, L., Reed, S.I. & Wright, P.E. (1996) Structural studies of p21Wafl/Cipl/Sdil in the free and Cdk2-bound state: Conformational disorder mediates binding diversity. Proc. Natl Acad. Sci. U.S.A 93, 11504-11509.
  • 12.Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. & Thornton, J.M. (1997) CATH — a hierarchic classification of protein domain structures. Structure 5, 1093-1098.
  • 13. Bryngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. (1995) Funnels, pathways, and the energy landscape of protein folding: A syn­thesis. Proteins: Struct Fund. Genet 21, 167- 195.
  • 14. Karplus, M. & Sali, A. (1995) Theoretical stud­ies of protein folding and unfolding. Curr. Opin. Struct Biol 5, 58-73.
  • 15. Dill, K.A. & Chan, H.S. (1995) Principles of protein folding. A perspective from simple ex­act models. Protein Sci 4, 561-602.
  • 16. Dill, K.A. & Chan, H.S. (1997) From Levinthal to pathways to funnels. Nature Struct. Biol 4, 10-19.
  • 17. Shakhnovich, E. (1997) Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct Biol 7, 29-40.
  • 18. Dobson, C.M., Sali, A., Karplus, M. (1998) Pro­tein folding: A perspective from theory and ex­periment. Angew. Chem. Int Ed. 7, 29-40.
  • 19. Brown, J.E. & Klee, W.A. (1971) Helix-coil transition of the isolated terminus of ribonuclease. Biochemistry 10, 470-476.
  • 20. Bierzynski, A., Kim, P.S. & Baldwin, R.L. (1982) A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A. Proc. Natl Acad. ScL U.S.A. 79, 2470-2474.
  • 21. Osterhout, J., Jr., Baldwin, R.L., York, E.J., Stewart, J.M., Dyson, H.J. & Wright, P.E. (1989) 1H NMR studies of the solution confor­mations of an analogue of the C-peptide of ribonuclease A. Biochemistry 28, 7059-7064.
  • 22. Waltho, J.P., Feher, V.A., Merutka, G., Dyson, H.J. & Wright, P.E. (1993) Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides correspond­ing to the G- and H-helices of myoglobin. Bio­chemistry 32, 6337-6347.
  • 23. Marqusee, S. & Sauer, R.T. (1994) Contribu­tions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary struc­ture in lambda repressor. Protein Sci. 12, 2217-2225.
  • 24. Goedken, E.R., Raschke, T.M. & Marqusee, S. (1997) Importance of the C-terminal helix to the stability and enzymatic activity of Esche­richia coli ribonuclease H. Biochemistry 36, 7256-7263.
  • 25. Luisi, D.L., Wu, W.J. & Raleigh, D.P. (1999) Conformational analysis of a set of peptides corresponding to the entire primary sequence of the N-terminal domain of the ribosomal pro­tein L9: Evidence for stable native-like second­ary structure in the unfolded state. J. Mol. Biol 287, 395-407.
  • 26. Baldwin, R.L. (1995) Alpha-helix formation by peptides of defined sequence. Biophys. Chem. 55, 127-135.
  • 27. Chakrabartty, A. & Baldwin, R.L. (1995) a-He- lix stability Adv. Protein Chem. 46, 141-176.
  • 28. Munoz, V. & Serrano, L. (1995) Helix design, prediction and stability. Cutt. Opin. Biotechnol. 6, 382-386.
  • 29. Munoz, V. & Serrano, L. (1994) Elucidating the folding problem of helical peptides using empirical parameters. Nature Struct. Bicl. 1, 399-409.
  • 30. Creamer, T.P. & Rose, G.D. (1992) Side-chain entropy opposes a-helix formation but ratio­nalizes experimentally determined he­lix-forming propensities. Proc. Natl Acad. Sci. U.S.A. 89,5937-5941.
  • 31. Marqusee, S., Robbins, V.H. & Baldwin, R.L. (1989) Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad ScL U.S.A. 86, 5286-5290.
  • 32. Creamer, T.P. & Rose, G.D. (1994) a-Helix forming propensities in peptides and proteins. Proteins: Struct. Fund. Genet. 19, 85-97.
  • 33. Chakrabartty, A., Kortemme, T. & Baldwin, R.L. (1994) Helix propensities of the ammo- acids measured in alanine-based peptides without helix-stabilizing side chain interac­tions. Protein ScL 3, 843-852.
  • 34. Blaber, M., Zang, X. & Matthews, B. (1993) Structural basis of amino acid a-helix propen­sity. Science 260, 1637-1640.
  • 35.O'Neill, K.T. & DeGrado, W.F. (1990) A ther­modynamic scale for the helix forming tenden­cies of the commonly occurring amino acids. Science 250, 646-650.
  • 36. Huyghues-Despointes, B.M., Scholtz, J.M. & Baldwin, R.L. (1993) Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein ScL 2, 80-85.
  • 37. Padmanabhan, S. & Baldwin, R.L. (1994) Tests for helix-stabilizing interactions be­tween various nonpolar side chains in alanine- based peptides. Protein Sci. 3, 1992-1997.
  • 38. Creamer, T.P. & Rose, G.D. (1995) Interac­tions between hydrophobic side chains within alpha-helices. Protein Sci. 4, 1305-1314.
  • 39. Armstrong, K.M., Fairman, R. & Baldwin, R.L. (1993) The (i, i + 4) Phe-His interaction studied in an alanine-based alpha-helix. J. Mol Biol 230, 284-291.
  • 40. Dadlez, M., Bierzyriski A., Godzik A., Sobocińska, M. & Kupryszewski, G. (1988) Conformational role of His-12 in C-peptide of ribonuclease A. Biophys. Chem. 31,175-181.
  • 41. Huyghues-Despointes, B.M., Klingler, T.M. & Baldwin, R.L. (1995) Measuring the strength of side-chain hydrogen bonds in peptide heli­ces: The Gln.Asp (i, i + 4) interaction. Biochem­istry 34, 13267-13271.
  • 42. Baldwin, R.L & Rose, D.G. (1999) Is protein folding hierarchic? I. Local structure and pep­tide folding. Trends Biochem. Sci. 24, 26-33.
  • 43. Jimenez, M.A., Munoz, V., Rico, M. & Serrano, L. (1994) Helix stop signals in proteins and peptides: The capping box does not necessarily prevent helix elongation. J. Mol Biol. 242, 487-496.
  • 44. Aurora, R. & Rose, G.D. (1998) Helix capping. Protein Sci. 7, 21-38.
  • 45. Williams, S., Causgrove, T.P., Gilmanshin, R., Fang, K.S., Callender, R.H., Woodruff, W.H. & Dyer, R.B. (1996) Fast events in protein folding: Helix melting and formation in a small peptide. Biochemistry 35, 691-697.
  • 46. Thompson, P.A., Eaton, W.A. & Hofrichter, J. (1997) Laser temperature jump study of the helix-coil kinetics of an alanine peptide inter­preted with a "kinetic zipper" model. Biochem­istry 36, 9200-9210.
  • 47. Gilmanshin, R.S., Williams, R.H., Callender, W.H., Woocruff, W.H. & Dyer, R.B. (1997) Fast events in protein folding: Relaxation dy­namics of secondary and tertiary structure in native apomyoglobin. Proc. Natl Acad. Sci U.S.A. 94, S709-3713.
  • 48.Scholtz, J.M., Marqusee, S., Baldwin, R.L., York, E.J., Stewart, J.M. Santoro, M. & Bolen, D.W. (1991) Calorimetric determination of the enthalpy change for the a-helix to coil tran­sition of an alanine peptide in water. Proc. Natl. Acad Sci U.S.A. 88, 2854-2858.
  • 49. Myers, J.K., Pace, C.N. & Scholtz, J.M. (1997) A direct comparison of helix propensity in pro­teins and peptides. Proc. Natl. Acad. Sci U.S.A. 94, 2833-2837.
  • 50. Baldwin, R.L. & Rose, D.G. (1999) Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24, 77-83.
  • 51. Luo, P. & Baldwin, R.L. (1999) Interaction be­tween water and polar groups of the helix backbone: An important determinant of helix propensities. Proc. NatL Acad. Sci U.S.A. 96, 4930-4935.
  • 52. Yang, A.-S., Sharp, K.A. & Honig, B. (1992) Analysis of the heat capacity dependence of protein folding. J. MoL Biol 227, 889-900.
  • 53. Scholtz, J.M., Barrick, D., York, E., Stewart, J.M. & Baldwin, R.L. (1995) Urea unfolding of peptide helices as a model for interpreting pro­tein unfolding. Proc. Natl Acad Sci U.S.A 92, 185-189.
  • 54. Luo, P. & Baldwin, R.L. (1997) Mechanism of helix induction by trifluoroethanol: A frame­work for extrapolating the helix-forming prop­erties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 36, 8413-8421.
  • 55. Kentsis, A. & Sosnick, T.R. (1998) Trifluoro­ethanol promotes helix formation by destabi­lising backbone exposure; Desolvation rather than native hydrogen bonding defines the ki­netic pathway of dimeric coiled coil folding. Biochemistry 37, 14613-14622.
  • 56. Blanco, F., Ramirez-Alvarado, M. & Serrano, L. (1998) Formation and stability of beta-hair­pin structures in polypeptides. Curr. Opin. Struct Biol. 8, 107-111.
  • 57. Blanco, F J., Jimenez, M.A., Herranz, J., Rico, M., Santoro, J. & Nieto, J.L. (1993) NMR evi­dence of a short linear peptide that folds into a ^-hairpin in aqueous solution. J. Am. Chem. Soc. 115, 5887-5888.
  • 58. Blanco, F.J., Rivas, G. & Serrano, L. (1994) A short linear peptide that folds into a native sta­ble beta-hairpin in aqueous solution. Nature Struct Biol. 1, 584-590.
  • 59. Searle, M.S., Williams, D.H. & Packman, L.C. (1995) A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin. Nature Struct Biol 2, 999-1006.
  • 60. de Alba, E., Jimenez, M.A., Rico, M. & Nieto, J.L. (1996) Conformational investigation of designed short linear peptides able to fold into beta-hairpir. structures in aqueous solution. Folding & Design 1, 133-144.
  • 61. Sieber, V. & Moe, G.R. (1996) Interactions contributing to the formation of a beta-hair­pin-like structure in a small peptide. Biochem­istry 181-188.
  • 62. Ramirez-Alvarado, M., Blanco, F. & Serrano, L. (1996) De novo design and structural analy­sis of a models-hairpin peptide system. Nature Struct. Biol. 3, 604-611.
  • 63. Munoz, V., Thompson, V.A., Hofrichter, J. & Eaton, W.A. (1997) Folding dynamics and mechanism of beta-hairpin formation. Nature 390, 196-199.
  • 64. Zdanowski, K. & Dadlez, M. (1999) Stability of the residual structure in unfolded BPTI in dif­ferent conditions of temperature and solvent composition measured by disulphide kinetics and double mutant cycle analysis. J. Mol Biol. 287, 433-445.
  • 65. Blasie, C.A. & Berg, J.M. (1997) Electrostatic interactions across a^-sheet. Biochemistry 36, 6218-6222.
  • 66. Friedrichs, M.S., Storch, T.R., Bruccoleri, R.E., Mueller, L. & Constantine, K.L. (1995) Structural and dynamic properties of a /3-hair- pin forming linear peptide. 2. C relaxation analysis. J. Am. Chem. Soc. 117, 10864- 10885.
  • 67. Ramirez-Alvarado, M., Daragan, V., Serrano, L. & Mayo, K.H. (1998) Motional dynamics of residues in a ^-hairpin peptide measured by l3C-NMR relaxation. Protein SciI 7, 720-729.
  • 68. de Alba, E., Blanco, F.J., Jimenez, M.A., Rico, M. & Nieto J.L. (1995) Interactions responsi­ble for the pH dependence of the /J-hairpin conformational population formed by a de­signed linear peptide. Eur. J. Biochem. 233, 283-292.
  • 69. Munoz, V. & Serrano, L. (1994) Intrinsic sec­ondary structure propensities of the amino ac­ids, using statistical -W matrices: Compari­son with experimental scales. Proteins: Struct Funct Genet. 20, 301-311.
  • 70. Regan, L. (1994) Protein structure. Born to be beta. Curr. Biol. 4, 656-658.
  • 71. Minor, D.L. & Kim, P.S. (1994) Measurement of the /9-sheet-forming propensities of amino acids. Nature 367, 660-663.
  • 72. Smith, C.K., Withka, J.M. & Regan, L. (1994) A thermodynamic scale for /?-sheet forming tendencies of the amino-acids. Biochemistry 5510-5517.
  • 73. Kim, C.A. & Berg, J.M. (1993) Thermody­namic /9-sheet propensities measured using a zinc finger host peptide. Nature 362, 267-270.
  • 74. Serrano, L. (1995) Comparison between the distribution of the amino acids in the protein database and NMR data indicates that amino acids have various propensities in the ran­dom coil conformation. J. Mol Biol 254, 322-333.
  • 75.Otzen, D.E. & Fersht, A.R. (1995) Sidechain determinants of /?-sheet stability. Biochemistry 5718-5724.
  • 76. Minor, D.L. & Kim, P.S. (1994) Context is a major determinant of beta-sheet propensity. Nature 371, 264-267.
  • 77. Ramirez-Alvarado, M., Blanco, F.J., Niemann, H. & Serrano, L. (1997) Role of/?-turn residues in /?-hairpin formation and stability in de­signed peptides. J. Mol Biol. 273, 898-912.
  • 78. Bai, Y. & Englander, S.W. (1994) Hydrogen bond strength and fi-sheet propensities: The role of a side chain blocking effect Proteins: Struct Funct Genet 18, 262-266.
  • 79. Yao, J., Dyson, H.J. & Wright, P.E. (1994) Three-dimensional structure of a type VI turn in a linear peptide in water solution. Evidence for stacking of aromatic rings as a major stabi­lising factor. J. Mol Biol. 243, 754-766.
  • 80. Yao, J., Feher, V.A., Rspejo, R.F., Raymond, M.T., Wright, P.E. & Dyson, H J. (1994) Sta­bilisation of a type VI turn in a family of linear peptides in water solution. J. Mol Biol 243, 736-753.
  • 81. Dyson, H.J., Cross, K.J., Houghten, R.A., Wil­son, I.A., Wright, P.E. & Lerner, R.A. (1985) The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn. Nature 318, 480-483.
  • 82. Ramakrishna, V. & Sasidhar, Y.U. (1997) A pentapeptide model for an early folding step in the refolding of staphylococcal nuclease: The role of its turn propensity. Biopolymers 41, 181-191.
  • 83. Haque, T.S. & Gellman, S.H. (1997) Insights on /Miairpin stability in aqueous solution from peptides with enforced type I' and type II' £-turns. J. Am. Chem. Soc. 119, 2303-2304.
  • 84. de Alba, E., Jimenez, M.A. & Rico, M. (1997) Turn residue sequence determines /Miairpin conformation in designed peptides. J. Am. Chem. Soc. 119, 898-912.
  • 85.Stroup, A.N. & Gierash, L.M. (1990) Reduced tendency to form a p turn in peptides from the P22 tailspike protein correlates with a temper­ature-sensitive folding defect. Biochemistry 29, 9765-9771.
  • 86. Predki, P.F., Agrawal, V., Brunger, A.T. & Regan, L. (1996) Amino-acid substitutions in a surface turn modulate protein stability. Nar ture Struct Biol 3, 54-58.
  • 87. Munoz, V. & Serrano, L. (1996) Local versus nonlocal interactions in protein folding and stability — an experimentalist's point of view. Folding & Design 1, R71-R77.
  • 88. McGregor, M.J., Islam, S.A. & Sternberg, M.J.E. (198?) Analysis of the relationship be­tween side-chain conformation and secondary structure in globular proteins. J. Mol Biol 198, 295-310.
  • 89. Griffiths Jones, SR., Sharman, G.J., Maynard, A.J. & Searle, M.S. (1998) Modula­tion of intrinsic phi,psi propensities of amino acids by neighboring residues in the coil re­gions of protein structures: NMR analysis and dissection of a beta-hairpin peptide. J. Mol Biol 284, 1597-1609.
  • 90. Honig, B. & Cohen, F. (1996) Adding backbone to protein folding: Proteins are polypeptides. Folding & Design 1, R17-R20.
  • 91. Chou, P. & Fasman, G.D. (1978) Empirical predictions of protein conformation. Annu. Rev. Biochem. 47, 251-276.
  • 92. Dill, K.A. & Shortle, D. (1991) Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825.
  • 93. Dyson, H.J. & Wright, P.E. (1993) Peptide conformation and protein folding. Curr. Opin. Struct Biol 3, 60-65.
  • 94. Dyson, H.J., Sayre, J.R., Merutka, G., Shin, H.-C., Lerner, R.A. & Wright, P.E. (1992) Folding of peptide fragments comprising the complete sequence of proteins. II. Plasto- cyanin. J. Mol Biol 226, 819-835.
  • 95.Segawa, S.-I., Fukuno, T., Fujiwara, K. & Noda, Y. (1991) Local structures in unfolded lysozyme and correlation with secondary structures in the native conformation: He­lix-forming or -breaking propensity of peptide segments. Biopolymers 31, 497-509.
  • 96. Yang, J.J., Buck, M., Pitkeathly, M., Kotik, M., Haynie, D.T., Dobson, C.M. & Radford, S.E. (1995) Conformational properties of four pep­tides spanning the sequence of hen lysozyme. J. Mol Biol. 252, 483-491.
  • 97. Sancho, J., Neira, J.L. & Fersht, A.R. (1993) An N-terminal fragment of barnase has resid­ual helical structure similar to that in refolding intermediate. J. Mol Biol 224, 749-758.
  • 98. Kemmink, J. & Creighton, T.E. (1993) Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J. Mol Biol. 234, 861-878.
  • 99. Wu, L.C., Laub, P.B., Elove, G.A., Carey, J. & Roder, H. (1993) A non-covalent peptide com­plex as a model for an early folding intermedi­ate of cytochrome c. Biochemistry 32, 10271- 10276.
  • 100. Jtzhaki, L.S., Neira, J.L., Ruiz-Sanz, J., de PratrGay, G. & Fersht, A.R. (1995) Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2. J. Mol Biol 254, 289-304.
  • 101. Blanco, F & Serrano, L. (1995) Folding of protein GBl domain studied by confor­mational characterisation of fragments com­prising its secondary structure elements. Eur. J. Biochem. 230, 634-649.
  • 102. Reymond, M.T., Merutka, G., Dyson, H.J. & Wright, P.E. (1997) Folding propensities of peptide fragments of myoglobin. Protein Sci. 6, 706-716.
  • 103. Muñoz, V., Serrano, L., Jiménez, M.A. & Rico, M. (1995) Structural analysis of pep­tides encompassing all a-helices of three a/fi parallel proteins: Che-Y, flavodoxin and P21-ras: Implications for a-helix stability and the folding of a/fi parallel proteins. J. Mol Biol 247, 648-669.
  • 104. Viguera, A.R., Jimenez, M.A., Rico, M. & Serrano, L. (1996) Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire se­quence of the alpha-spectrin SH3 domain. J. Mol Biol 255, 507-521.
  • 105 Alexandrescu, A.T. & Shortle, D. (1994) Back­bone dynamics of a highly disordered 131 res­idue fragment of staphylococcal nuclease. J. Mol Biol 242, 527-546.
  • 106.Wang, Y. & Shortle, D. (1995) The equilib­rium folding pathway of staphylococcal nuclease: Identification of the most stable chain-chain interactions by NMR and CD spectroscopy. Biochemistry 34,15895-15905.
  • 107.Zhang, O., Kay, L.E., Shortle, D., Forman- Kay, J.D. (1997) Comprehensive NOE charac­terisation of a partially folded large fragment of stapliylucoccal nuclease D131D, using NMR J. Mol Biol 272, 9-20.
  • 108. Sosnick, T.R., Shtilerman, M.D., Mayne, L. & Englander, S.W. (1997) Ultrafast signals in protein folding and the polypeptide con­tracted state. Proc. Natl Acad Sci. U.S.A. 94, 8545-8550.
  • 109.Neira, J.L., Itzhaki, L.S., Ladurner, A.G., Da­vis, B., de PratrGay, G. & Fersht, A.R. (1997) Following co-operative formation of second­ary and tertiary structure in a single protein module. J. Mol Biol 268, 185-197.
  • 110.Fersht, A.R. (1995) Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications. Proc. Natl Acad Sci. U.S.A. 92, 10869-10873.
  • 111. Evans, P.A., Topping, K.D., Woolfson, D.N. & Dobson, C.M. (1991) Hydrophobic clustering in normative states of a protein: Interpreta­tion of chemical shifts in NMR spectra of de­natured states of lysozyme. Proteins 9, 248-266.
  • 112. Neri, D., Billeter, M., Wider, G. & Wuthrich, K. (1992) NMR determination of residual structure in urea denatured protein, the 434 repressor. Science 257, 1559-1563.
  • 113. Logan, T.M., Theriault, Y. & Fesik, S.W. (1994) Structural characterization of the FK506 binding protein unfolded in urea and guanidine hydrochloride. J. Mol Biol 236, 637-648.
  • 114. Arcus, V.L., Vuilleumier, S., Freund, S.M., Bycroft, M. & Fersht, A.R. (1995) A compari­son of the pH, urea, and temperature- dena­tured states of barnase by heteronuclear NMR: Implications for the initiation of pro­tein folding. J. Mol Biol 254, 305-321.
  • 115. Pan, H., Barbar, E., Barany, G. & Woodward, C. (1995) Extensive non-random structure in reduced and unfolded bovine pancreatic trypsin inhibitor. Biochemistry 34, 13974- 13981.
  • 116.Wong, K.B., Freund, S.M. & Fersht, A.R. (1996) Cold denaturation of barstar: 1H, 15N 13 and C NMR assignment and characterisa­tion of residual structure. J. Mol Biol 259, 805-818.
  • 117.Schwalbe, H., Fiebig, K.M., Buck, M., Jones, J.A., Grimshaw, S.B., Spencer, A., Glaser, S.J., Smith, L.J. & Dobson, C.M. (1997) Struc­tural and dynamical properties of a dena­tured protein. Heteronuclear 3D NMR experi­ments and theoretical simulations of lyso- zyme in 8 M urea. Biochemistry 36, 8977- 8991.
  • 118. Bond, C.J., Wong, K.-B., Clarke, J., Fersht, A.R. & Dagget, V. (1997) Characterization of residual structure in the thermally denatured state of barnase by simulation and experi­ment: Description of the folding pathway. Proc. Natl Acad. Sei. U.S.A. 94, 13409- 13413.
  • 119. Wuthrich, K. (1994) NMR assignments as a basis for structural characterisation of dena­tured states of globular proteins. Curr. Opin. Struct. Biol 4, 93-99.
  • 120. Eliezer, D., Yao, J., Dyson, H.J. & Wright, P.E. (1998) Structural and dynamic charac­terization of partially folded states of myoglobin and implications for protein fold­ing. Nature Struct. Biol 5, 148-155.
  • 121. Meekhof, A.E. & Freund, S.M. (1999) Probing residual structure and backbone dynamics an the milli- and picosecond timescale in a urea- denatured fibronectin type III domain. J. Mol Biol 286, 579-592.
  • 122. Sosnick, T.R., Mayne, L. & Englander, S.W. (1996) Molecular collapse: The rate limiting step in two-state cytochrome c folding. Pro­teins: Struct Funct. Genet. 24, 413-426.
  • 123. Sosnick, T.R., Jackson, S., Wilk, R., Eng­lander, S.W. & DeGrado, W.F. (1996) The role of helix formation in the folding of a fully «-helical coiled-coil. Proteins: Struct. Funct. Genet. 24, 427-432.
  • 124.Qi, P.X., Sosnick, T.R. & Englander, S.W. (1998) The burst phase in ribonuclease A fold­ing and solvent dependence of the unfolded state. Nature Struct. Biol 5, 882-884.
  • 125.Roder, H. & Colon, W. (1997) Kinetic role of early intermediates in protein folding. Curr. Opin. Struct Biol. 7, 15-28.
  • 126. Dadlez, M. & Kim, P.S. (1995) A third native one-disulphide intermediate in the folding of bovine pancreatic trypsin inhibitor. Nature Struct Biology 2, 674-678.
  • 127. Dadlez, M. & Kim, P.S. (1996) Rapid forma­tion of the native 14-38 disulphide bond in the early stages of BPTI folding. Biochemistry 35, 16153-16164.
  • 128. Dadlez, M. (1997) Hydrophobic interactions accelerate early stages of the folding of BPTI. Biochemistry 36, 2788-2797.
  • 129 Krokoszynska, I., Dadlez, M. & Otlewski, J. (1998) Structure of single-disulphide variants of bovine pancreatic trypsin inhibitor (BPTI) as probed by their binding to bovine beta- trypsin. J. Mol Biol 275, 503-513.
  • 130. Creighton, T.E. (1997) Protein folding cou­pled to disulphide bond formation. Biol Chem. 378, 731-744.
  • 131. Barbar, E., LiCata, V.J., Barany, G. & Wood­ward, C. (1997) Local fluctuations and global unfolding of partially folded BPTI detected by NMR. Biophys. Chem. 64, 45-57.
  • 132. Ferrer, M., Barany, G. & Woodward, C. (1995) Partially folded, molten globule and molten coil states of bovine pancreatic trypsin inhibi­tor. Nature Struct Biol. 2, 211-217.
  • 133. Amir, D. & Haas, E. (1988) Reduced bovine pancreatic trypsin inhibitor has a compact structure. Biochemistry 27, 8889-8893.
  • 134. Amir, D., Krausz, S. & Haas, E. (1992) Detec­tion of local structures in reduced unfolded bovine pancreatic trypsin inhibitor. Proteins: Struct. Fund. Genet. 13, 162-173.
  • 135. Ittah, V. & Haas, E. (1995) Nonlocal interac­tions stabilize long range loops in the initial folding intermediates of reduced bovine pan­creatic trypsin inhibitor. Biochemistry 34, 4493-4506.
  • 136. Peng, Z.Y., Wu, C.L. & Kim, P.S. (1995) Local structural preferences in the cc-lactalbumin molten globule. Biochemistry 34,3248-3252.
  • 137. Burgering, M J., Hałd, M., Boelens, R., Breg, J.N. & Kaptein, R. (1995) Hydrogen exchange studies of the Arc repressor: Evidence for a monomerir. folding intermediate. Biopoly- mers 35, 217-226.
  • 138. Agashe, V.R., Shastry, M.C.R. & Udgoankar, J.B. (1995) Initial hydrophobic collapse in the folding of barstar. Nature 377, 754-757.
  • 139. Kuwajima, K. (1996) Stopped-flow circular dichroism; in Circular Dichroism and the Conformational Analysis of Biomolecules (Fasman, G.D., ed.) pp. 159-181, Plenum Press, New York.
  • 140. Gronenborn, A.M. & Clore, G.M. (1994) Ex- perimental support for the "hydrophobic zip­per" hypothesis. Science 263, 536.
  • 141. Lorch, M., Mason, J.M., Clarke, A.R. & Parker, M.J. (1999) Effects of core mutations on the folding of a /9-sheet protein: Implica­tions for backbone organisation in the I-state. Biochemistry 38, 1377-1385.
  • 142 Khorasanizadeh, S., Peters, I.D., Butt, T.R. & Roder, H. (1993) Stability and folding of a tryptophan containing mutant of ubiquitin. Biochemistry 32, 7054-7063.
  • 143. Khorasanizadeh, S., Peters, I.D. & Roder, H. (1996) Evidence for a three state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nature Struct BioL 3, 193-205.
  • 144. Colon, W., Elove, G.A., Wakem, L.P., Sher­man, F. & Roder, H. (1996) Sidechain pack­ing of the N-terminal and C-terminal helices play a critical role in the kinetics of cytochrome c folding. Biochemistry 35, 5538- 5549.
  • 145. Gast, K., Chaffotte, A.F., Zirwer, D., Guillou, Y., Mueller Frohnc, M., Cadieux, C., Hodges, M., Damaschun, G. & Goldberg, M.E. (1997) Lack of coupling between secondary struc­ture formation and collapse in a model polypeptide that mimics early folding inter­mediates, the F2 fragment of the Escherichia coli tryptophan-synthase ($ chain. Protein Sci. 6, 2578-2588.
  • 146. Hamada, D., Segawa, S. & Goto, Y. (1996) Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predomi­nantly beta-sheet protein. Nature Struct BiuL 3, 868-873.
  • 147. Blanco, F.J., Serrano, L. & Forman-Kay, J.D. (1998) High population of non-native struc­tures in the denatured state are compatible with the formation of the native folded state. J. MoL Biol. 284, 1153-1164.
  • 148. Prieto, J., Wilmans, M., Jimenez, M.A., Rico, M. & Serrano, L. (1997) Non-native local in­teractions in protein folding and stability: In­troducing a helical tendency in the all /3-sheet a-spectrin SH3 domain. J. MoL BioL 268, 760-778.
  • 149.Minor, D.L. & Kim, P.S. (1996) Contextrde- pendent secondary structure formation of a designed sequence. Nature 380, 730-734.
  • 150Anfinsen, C.B. (1972) The formation and sta­bilisation of protein structure. Biochem. J. 128, 737-749.
  • 151.Wright, P.E., Dyson, H.J. & Lerner, R.A. (1988) Conformation of peptide fragments of proteins in aqueous solutions: Implications for initiation of protein folding. Biochemistry 27, 7167-7175.
  • 152. Freund, S.M., Wong, K.B., Fersht, A.R. (1996) Initiation sites of protein folding by NMR analysis. Proc. NatL Acad. ScL U.S.A. 93, 10600-10603.
  • 153. Ptitsyn, O.B. (1981) Protein folding: General physical model. FEBS Lett. 131, 197-201.
  • 154. Kaiser, E.T. & Kezdy, F.J. (1984) Amphiphilic secondary structure; Design of peptide hor­mones. Science 223, 249-255.
  • 155. Kim, P.S. & Baldwin, R.I,. (1989.) Specific in­termediates in the folding reactions of small proteins and the mechanism of protein fold­ing. Annu. Rev. Biochem. 51, 459-489.
  • 156. Kim, P.S. & Baldwin, R.L. (1990) Intermedi­ates in the folding reactions of small proteins. Annu. Rev. Biochem. 59, 631-660.
  • 157.Harrison, S.C. & Durbin, R. (1985) Is there a single pathway for the folding of a polypeptide chain? Proc. Natl Acad. Sci. U.S.A. 82, 4028-4030.
  • 158. Karplus, M. & Weaver, D.L. (1994) Protein folding dynamics: The diffusion-collision model and experimental data. Protein Sci. 3, 650-668.
  • 159.Wetlaufer, D.B. (1973) Nucleation, rapid fold­ing, and globular intrachain regions in pro­teins. Proc. NatL Acad Sci. U.S.A 70, 697- 701.
  • 160. Ptitsyn, O.B. (1993) Stage mechanism of the self-organisation of protein molecules. Doki Akad Nauk 210, 1213-1215.
  • 161. Plaxco, K.W., Simons, K.T. & Baker, D. (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol Biol 277, 985-994.
  • 162. Creighton, T.E. (1988) On the relevance of non-random polypeptide conformations for protein folding. Biophys. Chem. 31,155-162.
  • 163. Creighton, T.E. (1983) An empirical approach to protein conformation stability and flexibil­ity. Biopolymers 22, 49-58.
  • 164. Baldwin, RL. (1996) Why is protein folding so fast? Proc. Natl Acad. Sci. U.S.A. 93, 2627-2628.
  • 165. Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I. (1996) How the first biopolymers could have evolved. Proc. Natl Acad SciL U.S.A. 93, 839-844.
  • 166. Govindarajan, S. & Goldstein, R.A. (1995) Op­timal local propensities for model proteins. Proteins 22, 413-418.
  • 167. Doyle, R., Simons, K., Qian, H. & Baker, D. (1997) Local interactions and the optimisa­tion of protein folding. Proteins 29,282-291.
  • 168. Unger, R. & Moult, J. (1996) Local interac­tions dominate folding in a simple protein model. J. Mol Biol 259, 988-994.
  • 169.Stickle, D.F., Presta, L.G., Dill, K.A. & Rose, G.D. (1992) Hydrogen bonding in globular proteins. J. Mol Biol 226, 1143-1159.
  • 170.Plaxco, K.W. & Baker, D. (1998) Limited in­ternal friction in the rate-limiting step of a two-state protein folding reaction. Proc. Natl Acad. Sci. U.S.A 95, 13591-13596.
  • 171. Blanco, FJ., Angrand, I. & Serrano, L. (1999) Exploring the conformational properties of the sequence space between two proteins with different folds: An experimental study. J. Mol Biol 285, 741-753.
  • 172. Cordes, M.H.J., Walsh, N.P., McKnight, J. & Sauer, R. (1999) Evolution of a protein fold in vitro. Science 284, 325-327.
  • 173. Brown, B.M. & Sauer, R.T. (1999) Tolerance of Arc repressor to multiple-alanine substitu­tions. Proc. Natl Acad Sci. U.S.A 96,1983- 1988.
  • 174. Xiong, H., Buckwalter, B.L., Shieh, H.-M. & Hecht, M.H. (1995) Periodicity of polar and nonpolar amino acids is the major determi­nant of secondary structure in self-assem­bling oligomeric peptides. Proc. Natl Acad Sci. U.S.A. 92, 6349-6353.
  • 175. Kamtekar, S., Schiffer, J.M., Xiong, H., Babik, J.M. & Hecht, M.H. (1993) Protein de­sign by binary patterning of polar and non- polar amino acids. Science 262, 1680-1685.
  • 176.O'Shea, E.K., Klemm, J.D., Kim, P.S. & Alber, T. (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled-coil. Science 254, 539-544.
  • 177. Munoz, V., Cronet, P., Lopez-Hernandez, E. & Serrano, L. (1996) Analysis of the effect of lo­cal interactions in protein stability. Folding & Design 1, 167-178.
  • 178. Cavangero, S., Dyson, H.J. & Wright, P.E. (1999) Effect of H helix destabilizing muta­tions on the kinetic and equilibrium folding of apomyoglobin. J. Mol Biol 285, 269-282.
  • 179.Shin, H.-C., Merutka, G., Waltho, J.P., Ten- nant, L.L., Dyson, H.J. & Wright, P. (1993) Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry 32, 6356-6364.
  • 180.Viguera, A.R., Blanco, FJ. & Serrano, L. (1995) The order of secondary structure ele­ments does not determine the structure of a protein but does affect its folding kinetics. J. Mol Biol 247, 670-681.
  • 181.Villegas, V., Viguera, A.R., Aviles, F.X. & Serrano, L. (1996) Stabilisation of proteins by rational design of/3-helix stability using he­lix/coil transition theory. Folding & Design 1, 29-34.
  • 182. Viguera, A.R., Villegas, V., Aviles, F.X. & Serrano, L. (1997) Favorable native-like heli­cal local interactions can accelerate protein folding. Folding & Design 2, 23-33.
  • 183. Ladurner, A.G., Itzhaki, L.S., Dagget, V. & Fersht, A.R. (1998) Synergy between simula­tion and experiment in describing the energy landscape of protein folding. Proc. Natl Acad. Sci. U.S.A. 95, 8473-8478.
  • 184. Chiti, F., Taddei, N., Webster. P., Hamada, D., Fiaschi, T., Ramponi, G. & Dobson, C. (1999) Acceleration of the folding of acylphospha- tase by stabilisation of local secondary struc­ture. Nature Struct Biol 6, 380-387.
  • 185. Viguera, A.-R. & Serrano, L. (1997) Loop length, intramolecular diffusion and protein folding. Nature Struct Biol 4, 939-946.
  • 186. Neira, J.L. & Fersht, A. (1999) Exploring the folding funnel of a polypeptide chain by bio­physical studies on protein fragments. J. Mol Biol. 285, 1309-1333.
  • 187. Brunet, A.P., Huang, E.S, Huffine, M., Loeb, J.E., Weltman, R.J. & Hecht, M.H. (1993) The role of turns in the structure of an alpha-heli­cal protein. Nature 364, 355-358.
  • 188. Zhou, H.X., Hoess, R.H. & DeGrado, W.F. (1996) In vitro evolution of thermodynami- cally stable turns. Nature Struct Biol. 3, 446-451.
  • 189. Castagnoli, L., Vetriani, C. & Cesareni, C. (1994) Linking an easily detectable pheno- type to the folding of a common structural motif. Selection of a rare mutations that pre­vent the folding of Rop. J. Mol. Biol 234, 378-387.
  • 190. Ybe, J.A. & Hecht, M.H. (1996) Sequence re­placements in the central /?-turn of plastocyanin. Protein Sci. 5, 814-824.
  • 191. Villegas, V., Martinez, J.C., Aviles, F.X. & Serrano, L. (1998) Structure of the transition state in the folding process of human procarboxydase A2 activation domain. J. Mol Biol 283, 1027-1936.
  • 192. Goldberg, J.M. & Baldwin, R.L. (1999) A spe­cific transition state for S-peptide combining with folded S-protein and then refolding. Proc. Natl Acad. Sci. U.S.A. 96,2019-2024.
  • 193. Zwanzig, R. (1997) Two^tate models for pro­tein folding kinetics. Proc. Natl Acad. ScL U.S.A. 94, 148-150.

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