Abstract
Recent studies of the refolding of reduced bovine pancreatic trypsin inhibitor (BPTI) have shown that a previously unidentified intermediate with a single disulfide is formed much more rapidly than any other one-disulfide species. This intermediate contains a disulfide that is present in the native protein (between Cys14 and 38), but it is thermodynamically less stable than the other two intermediates with single native disulfides. To characterize the role of the [14-38] intermediate and the factors that favor its formation, detailed kinetic and mutational analyses of the early disulfide-formation steps were carried out. The results of these studies indicate that the formation of [14-38] from the fully reduced protein is favored by both local electrostatic effects, which enhance the reactivities of the Cys14 and 38 thiols, and conformational tendencies that are diminished by the addition of urea and are enhanced at lower temperatures. At 25 degrees C and pH 7.3, approximately 35% of the reduced molecules were found to initially form the 14-38 disulfide, but the majority of these molecules then undergo intramolecular rearrangements to generate non-native disulfides, and subsequently the more stable intermediates with native disulfides. Amino acid replacements, other than those involving Cys residues, were generally found to have only small effects on either the rate of forming [14-38] or its thermodynamic stability, even though many of the same substitutions greatly destabilized the native protein and other disulfide-bonded intermediates. In addition, those replacements that did decrease the steady-state concentration of [14-38] did not adversely affect further folding and disulfide formation. These results suggest that the weak and transient interactions that are often detected in unfolded proteins and early folding intermediates may, in some cases, not persist or promote subsequent folding steps.
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- Amir D., Haas E. Reduced bovine pancreatic trypsin inhibitor has a compact structure. Biochemistry. 1988 Dec 13;27(25):8889–8893. doi: 10.1021/bi00425a003. [DOI] [PubMed] [Google Scholar]
- Amir D., Krausz S., Haas E. Detection of local structures in reduced unfolded bovine pancreatic trypsin inhibitor. Proteins. 1992 Apr;13(2):162–173. doi: 10.1002/prot.340130210. [DOI] [PubMed] [Google Scholar]
- Barbar E., Barany G., Woodward C. Dynamic structure of a highly ordered beta-sheet molten globule: multiple conformations with a stable core. Biochemistry. 1995 Sep 12;34(36):11423–11434. doi: 10.1021/bi00036a015. [DOI] [PubMed] [Google Scholar]
- Barbar E., Barany G., Woodward C. Unfolded BPTI variants with a single disulfide bond have diminished non-native structure distant from the crosslink. Fold Des. 1996;1(1):65–76. doi: 10.1016/S1359-0278(96)00013-2. [DOI] [PubMed] [Google Scholar]
- Barbar E., LiCata V. J., Barany G., Woodward C. Local fluctuations and global unfolding of partially folded BPTI detected by NMR. Biophys Chem. 1997 Feb 28;64(1-3):45–57. doi: 10.1016/s0301-4622(96)02210-7. [DOI] [PubMed] [Google Scholar]
- Bulaj G., Kortemme T., Goldenberg D. P. Ionization-reactivity relationships for cysteine thiols in polypeptides. Biochemistry. 1998 Jun 23;37(25):8965–8972. doi: 10.1021/bi973101r. [DOI] [PubMed] [Google Scholar]
- Butler P. J., Harris J. I., Hartley B. S., Lebeman R. The use of maleic anhydride for the reversible blocking of amino groups in polypeptide chains. Biochem J. 1969 May;112(5):679–689. doi: 10.1042/bj1120679. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Creighton T. E., Bagley C. J., Cooper L., Darby N. J., Freedman R. B., Kemmink J., Sheikh A. On the biosynthesis of bovine pancreatic trypsin inhibitor (BPTI). Structure, processing, folding and disulphide bond formation of the precursor in vitro and in microsomes. J Mol Biol. 1993 Aug 20;232(4):1176–1196. doi: 10.1006/jmbi.1993.1470. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Effects of urea and guanidine-HCl on the folding and unfolding of pancreatic trypsin inhibitor. J Mol Biol. 1977 Jun 25;113(2):313–328. doi: 10.1016/0022-2836(77)90144-9. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Electrophoretic analysis of the unfolding of proteins by urea. J Mol Biol. 1979 Apr 5;129(2):235–264. doi: 10.1016/0022-2836(79)90279-1. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Energetics of folding and unfolding of pancreatic trypsin inhibitor. J Mol Biol. 1977 Jun 25;113(2):295–312. doi: 10.1016/0022-2836(77)90143-7. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Experimental studies of protein folding and unfolding. Prog Biophys Mol Biol. 1978;33(3):231–297. doi: 10.1016/0079-6107(79)90030-0. [DOI] [PubMed] [Google Scholar]
- Creighton T. E., Goldenberg D. P. Kinetic role of a meta-stable native-like two-disulphide species in the folding transition of bovine pancreatic trypsin inhibitor. J Mol Biol. 1984 Nov 5;179(3):497–526. doi: 10.1016/0022-2836(84)90077-9. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Interactions between cysteine residues as probes of protein conformation: the disulphide bond between Cys-14 and Cys-38 of the pancreatic trypsin inhibitor. J Mol Biol. 1975 Aug 25;96(4):767–776. doi: 10.1016/0022-2836(75)90151-5. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. On the relevance of non-random polypeptide conformations for protein folding. Biophys Chem. 1988 Aug;31(1-2):155–162. doi: 10.1016/0301-4622(88)80021-8. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. Protein folding pathways determined using disulphide bonds. Bioessays. 1992 Mar;14(3):195–199. doi: 10.1002/bies.950140310. [DOI] [PubMed] [Google Scholar]
- Creighton T. E. The single-disulphide intermediates in the refolding of reduced pancreatic trypsin inhibitor. J Mol Biol. 1974 Aug 15;87(3):603–624. doi: 10.1016/0022-2836(74)90106-5. [DOI] [PubMed] [Google Scholar]
- Creighton T. Reactivities of the cysteine residues of the reduced pancreatic trypsin inhibitor. J Mol Biol. 1975 Aug 25;96(4):777–782. doi: 10.1016/0022-2836(75)90152-7. [DOI] [PubMed] [Google Scholar]
- Dadlez M. Hydrophobic interactions accelerate early stages of the folding of BPTI. Biochemistry. 1997 Mar 11;36(10):2788–2797. doi: 10.1021/bi962407f. [DOI] [PubMed] [Google Scholar]
- Dadlez M., Kim P. S. A third native one-disulphide intermediate in the folding of bovine pancreatic trypsin inhibitor. Nat Struct Biol. 1995 Aug;2(8):674–679. doi: 10.1038/nsb0895-674. [DOI] [PubMed] [Google Scholar]
- Dadlez M., Kim P. S. Rapid formation of the native 14-38 disulfide bond in the early stages of BPTI folding. Biochemistry. 1996 Dec 17;35(50):16153–16164. doi: 10.1021/bi9616054. [DOI] [PubMed] [Google Scholar]
- Daggett V., Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol. 1993 Jul 20;232(2):600–619. doi: 10.1006/jmbi.1993.1414. [DOI] [PubMed] [Google Scholar]
- Darby N. J., Creighton T. E. Dissecting the disulphide-coupled folding pathway of bovine pancreatic trypsin inhibitor. Forming the first disulphide bonds in analogues of the reduced protein. J Mol Biol. 1993 Aug 5;232(3):873–896. doi: 10.1006/jmbi.1993.1437. [DOI] [PubMed] [Google Scholar]
- Darby N. J., Morin P. E., Talbo G., Creighton T. E. Refolding of bovine pancreatic trypsin inhibitor via non-native disulphide intermediates. J Mol Biol. 1995 Jun 2;249(2):463–477. doi: 10.1006/jmbi.1995.0309. [DOI] [PubMed] [Google Scholar]
- Ferrer M., Barany G., Woodward C. Partially folded, molten globule and molten coil states of bovine pancreatic trypsin inhibitor. Nat Struct Biol. 1995 Mar;2(3):211–217. doi: 10.1038/nsb0395-211. [DOI] [PubMed] [Google Scholar]
- Freedman R. B., Hirst T. R., Tuite M. F. Protein disulphide isomerase: building bridges in protein folding. Trends Biochem Sci. 1994 Aug;19(8):331–336. doi: 10.1016/0968-0004(94)90072-8. [DOI] [PubMed] [Google Scholar]
- Frieden C. Numerical integration of rate equations by computer. Trends Biochem Sci. 1993 Feb;18(2):58–60. doi: 10.1016/0968-0004(93)90056-s. [DOI] [PubMed] [Google Scholar]
- Fritz H., Schult H., Meister R., Werle E. Herstellung und Eigenschaften von aktiven Derivaten des Trypsin-Kallikrein-Inhibitors aus Rinderorganen. Hoppe Seylers Z Physiol Chem. 1969 Dec;350(12):1531–1540. [PubMed] [Google Scholar]
- Goldenberg D. P., Berger J. M., Laheru D. A., Wooden S., Zhang J. X. Genetic dissection of pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):5083–5087. doi: 10.1073/pnas.89.11.5083. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goldenberg D. P., Frieden R. W., Haack J. A., Morrison T. B. Mutational analysis of a protein-folding pathway. Nature. 1989 Mar 9;338(6211):127–132. doi: 10.1038/338127a0. [DOI] [PubMed] [Google Scholar]
- Goldenberg D. P. Kinetic analysis of the folding and unfolding of a mutant form of bovine pancreatic trypsin inhibitor lacking the cysteine-14 and -38 thiols. Biochemistry. 1988 Apr 5;27(7):2481–2489. doi: 10.1021/bi00407a034. [DOI] [PubMed] [Google Scholar]
- Goldenberg D. P. Native and non-native intermediates in the BPTI folding pathway. Trends Biochem Sci. 1992 Jul;17(7):257–261. doi: 10.1016/0968-0004(92)90405-x. [DOI] [PubMed] [Google Scholar]
- Goldenberg D. P., Zhang J. X. Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor. Proteins. 1993 Mar;15(3):322–329. doi: 10.1002/prot.340150309. [DOI] [PubMed] [Google Scholar]
- Helland R., Otlewski J., Sundheim O., Dadlez M., Smalås A. O. The crystal structures of the complexes between bovine beta-trypsin and ten P1 variants of BPTI. J Mol Biol. 1999 Apr 16;287(5):923–942. doi: 10.1006/jmbi.1999.2654. [DOI] [PubMed] [Google Scholar]
- Ittah V., Haas E. Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry. 1995 Apr 4;34(13):4493–4506. doi: 10.1021/bi00013a042. [DOI] [PubMed] [Google Scholar]
- Kemmink J., Creighton T. E. Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J Mol Biol. 1993 Dec 5;234(3):861–878. doi: 10.1006/jmbi.1993.1631. [DOI] [PubMed] [Google Scholar]
- Kemmink J., van Mierlo C. P., Scheek R. M., Creighton T. E. Local structure due to an aromatic-amide interaction observed by 1H-nuclear magnetic resonance spectroscopy in peptides related to the N terminus of bovine pancreatic trypsin inhibitor. J Mol Biol. 1993 Mar 5;230(1):312–322. doi: 10.1006/jmbi.1993.1144. [DOI] [PubMed] [Google Scholar]
- Kosen P. A., Creighton T. E., Blout E. R. Circular dichroism spectroscopy of bovine pancreatic trypsin inhibitor and five altered conformational states. Relationship of conformation and the refolding pathway of the trypsin inhibitor. Biochemistry. 1981 Sep 29;20(20):5744–5754. doi: 10.1021/bi00523a017. [DOI] [PubMed] [Google Scholar]
- Kosen P. A., Marks C. B., Falick A. M., Anderson S., Kuntz I. D. Disulfide bond-coupled folding of bovine pancreatic trypsin inhibitor derivatives missing one or two disulfide bonds. Biochemistry. 1992 Jun 30;31(25):5705–5717. doi: 10.1021/bi00140a004. [DOI] [PubMed] [Google Scholar]
- Krokoszynska I., Dadlez M., Otlewski J. Structure of single-disulfide variants of bovine pancreatic trypsin inhibitor (BPTI) as probed by their binding to bovine beta-trypsin. J Mol Biol. 1998 Jan 23;275(3):503–513. doi: 10.1006/jmbi.1997.1460. [DOI] [PubMed] [Google Scholar]
- Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Levitt M., Warshel A. Computer simulation of protein folding. Nature. 1975 Feb 27;253(5494):694–698. doi: 10.1038/253694a0. [DOI] [PubMed] [Google Scholar]
- Lumb K. J., Kim P. S. Formation of a hydrophobic cluster in denatured bovine pancreatic trypsin inhibitor. J Mol Biol. 1994 Feb 18;236(2):412–420. doi: 10.1006/jmbi.1994.1153. [DOI] [PubMed] [Google Scholar]
- Pan H., Barany G., Woodward C. Reduced BPTI is collapsed. A pulsed field gradient NMR study of unfolded and partially folded bovine pancreatic trypsin inhibitor. Protein Sci. 1997 Sep;6(9):1985–1992. doi: 10.1002/pro.5560060919. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pan H., Barbar E., Barany G., Woodward C. Extensive nonrandom structure in reduced and unfolded bovine pancreatic trypsin inhibitor. Biochemistry. 1995 Oct 31;34(43):13974–13981. doi: 10.1021/bi00043a002. [DOI] [PubMed] [Google Scholar]
- Snyder G. H., Cennerazzo M. J., Karalis A. J., Field D. Electrostatic influence of local cysteine environments on disulfide exchange kinetics. Biochemistry. 1981 Nov 10;20(23):6509–6519. doi: 10.1021/bi00526a001. [DOI] [PubMed] [Google Scholar]
- Staley J. P., Kim P. S. Complete folding of bovine pancreatic trypsin inhibitor with only a single disulfide bond. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1519–1523. doi: 10.1073/pnas.89.5.1519. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staley J. P., Kim P. S. Formation of a native-like subdomain in a partially folded intermediate of bovine pancreatic trypsin inhibitor. Protein Sci. 1994 Oct;3(10):1822–1832. doi: 10.1002/pro.5560031021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weissman J. S., Kim P. S. A kinetic explanation for the rearrangement pathway of BPTI folding. Nat Struct Biol. 1995 Dec;2(12):1123–1130. doi: 10.1038/nsb1295-1123. [DOI] [PubMed] [Google Scholar]
- Weissman J. S., Kim P. S. Kinetic role of nonnative species in the folding of bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9900–9904. doi: 10.1073/pnas.89.20.9900. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weissman J. S., Kim P. S. Reexamination of the folding of BPTI: predominance of native intermediates. Science. 1991 Sep 20;253(5026):1386–1393. doi: 10.1126/science.1716783. [DOI] [PubMed] [Google Scholar]
- Yu M. H., Weissman J. S., Kim P. S. Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis. J Mol Biol. 1995 Jun 2;249(2):388–397. doi: 10.1006/jmbi.1995.0304. [DOI] [PubMed] [Google Scholar]
- Zhang J. X., Goldenberg D. P. Amino acid replacement that eliminates kinetic traps in the folding pathway of pancreatic trypsin inhibitor. Biochemistry. 1993 Dec 28;32(51):14075–14081. doi: 10.1021/bi00214a001. [DOI] [PubMed] [Google Scholar]
- Zhang J. X., Goldenberg D. P. Mutational analysis of the BPTI folding pathway: I. Effects of aromatic-->leucine substitutions on the distribution of folding intermediates. Protein Sci. 1997 Jul;6(7):1549–1562. doi: 10.1002/pro.5560060719. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang J. X., Goldenberg D. P. Mutational analysis of the BPTI folding pathway: II. Effects of aromatic-->leucine substitutions on folding kinetics and thermodynamics. Protein Sci. 1997 Jul;6(7):1563–1576. doi: 10.1002/pro.5560060720. [DOI] [PMC free article] [PubMed] [Google Scholar]
- van Mierlo C. P., Darby N. J., Keeler J., Neuhaus D., Creighton T. E. Partially folded conformation of the (30-51) intermediate in the disulphide folding pathway of bovine pancreatic trypsin inhibitor. 1H and 15N resonance assignments and determination of backbone dynamics from 15N relaxation measurements. J Mol Biol. 1993 Feb 20;229(4):1125–1146. doi: 10.1006/jmbi.1993.1108. [DOI] [PubMed] [Google Scholar]
- van Mierlo C. P., Darby N. J., Neuhaus D., Creighton T. E. (14-38, 30-51) double-disulphide intermediate in folding of bovine pancreatic trypsin inhibitor: a two-dimensional 1H nuclear magnetic resonance study. J Mol Biol. 1991 Nov 20;222(2):353–371. doi: 10.1016/0022-2836(91)90216-s. [DOI] [PubMed] [Google Scholar]
- van Mierlo C. P., Darby N. J., Neuhaus D., Creighton T. E. Two-dimensional 1H nuclear magnetic resonance study of the (5-55) single-disulphide folding intermediate of bovine pancreatic trypsin inhibitor. J Mol Biol. 1991 Nov 20;222(2):373–390. doi: 10.1016/0022-2836(91)90217-t. [DOI] [PubMed] [Google Scholar]
- van Mierlo C. P., Kemmink J., Neuhaus D., Darby N. J., Creighton T. E. 1H NMR analysis of the partly-folded non-native two-disulphide intermediates (30-51,5-14) and (30-51,5-38) in the folding pathway of bovine pancreatic trypsin inhibitor. J Mol Biol. 1994 Jan 21;235(3):1044–1061. doi: 10.1006/jmbi.1994.1056. [DOI] [PubMed] [Google Scholar]
