Abstract
The refolding of barstar, the intracellular inhibitor of barnase, is dominated by the slow formation of a cis peptidyl prolyl bond in the native protein. The triple mutant C40/82A P27A in which two cysteine residues and one trans proline were replaced by alanine was used as model system to investigate the kinetics and structural consequences of the trans/cis interconversion of Pro48. One- and two-dimensional real-time NMR spectroscopy was used to follow the trans/cis interconversion after folding was initiated by rapid dilution of the urea denatured protein. Series of 1H, 15N HSQC spectra acquired with and without the addition of peptidyl prolyl isomerase unambiguously revealed the accumulation of a transient trans-Pro48 intermediate within the dead time of the experiment. Subtle chemical shift differences between the native state and the intermediate spectra indicate that the intermediate is predominantly native-like with a local rearrangement in the Pro48 loop and in the beta-sheet region including residues Tyr47, Ala82, Thr85, and Val50.
Full Text
The Full Text of this article is available as a PDF (240.9 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Akasaka K., Naito A., Nakatani H. Temperature-jump NMR study of protein folding: ribonuclease A at low pH. J Biomol NMR. 1991 May;1(1):65–70. doi: 10.1007/BF01874569. [DOI] [PubMed] [Google Scholar]
- Balbach J., Forge V., Lau W. S., van Nuland N. A., Brew K., Dobson C. M. Protein folding monitored at individual residues during a two-dimensional NMR experiment. Science. 1996 Nov 15;274(5290):1161–1163. doi: 10.1126/science.274.5290.1161. [DOI] [PubMed] [Google Scholar]
- Balbach J., Forge V., van Nuland N. A., Winder S. L., Hore P. J., Dobson C. M. Following protein folding in real time using NMR spectroscopy. Nat Struct Biol. 1995 Oct;2(10):865–870. doi: 10.1038/nsb1095-865. [DOI] [PubMed] [Google Scholar]
- Buckle A. M., Schreiber G., Fersht A. R. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution. Biochemistry. 1994 Aug 2;33(30):8878–8889. doi: 10.1021/bi00196a004. [DOI] [PubMed] [Google Scholar]
- Dobson C. M., Hore P. J. Kinetic studies of protein folding using NMR spectroscopy. Nat Struct Biol. 1998 Jul;5 (Suppl):504–507. doi: 10.1038/744. [DOI] [PubMed] [Google Scholar]
- Fersht A. R., Matouschek A., Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol. 1992 Apr 5;224(3):771–782. doi: 10.1016/0022-2836(92)90561-w. [DOI] [PubMed] [Google Scholar]
- Guillet V., Lapthorn A., Hartley R. W., Mauguen Y. Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar. Structure. 1993 Nov 15;1(3):165–176. doi: 10.1016/0969-2126(93)90018-c. [DOI] [PubMed] [Google Scholar]
- Kautz R. A., Fox R. O. NMR analysis of staphylococcal nuclease thermal quench refolding kinetics. Protein Sci. 1993 May;2(5):851–858. doi: 10.1002/pro.5560020514. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kiefhaber T., Labhardt A. M., Baldwin R. L. Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A. Nature. 1995 Jun 8;375(6531):513–515. doi: 10.1038/375513a0. [DOI] [PubMed] [Google Scholar]
- Killick T. R., Freund S. M., Fersht A. R. Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2. FEBS Lett. 1998 Feb 13;423(1):110–112. doi: 10.1016/s0014-5793(98)00075-1. [DOI] [PubMed] [Google Scholar]
- Koide S., Dyson H. J., Wright P. E. Characterization of a folding intermediate of apoplastocyanin trapped by proline isomerization. Biochemistry. 1993 Nov 23;32(46):12299–12310. doi: 10.1021/bi00097a005. [DOI] [PubMed] [Google Scholar]
- Kuwajima K., Okayama N., Yamamoto K., Ishihara T., Sugai S. The Pro117 to glycine mutation of staphylococcal nuclease simplifies the unfolding-folding kinetics. FEBS Lett. 1991 Sep 23;290(1-2):135–138. doi: 10.1016/0014-5793(91)81243-2. [DOI] [PubMed] [Google Scholar]
- Liu X., Siegel D. L., Fan P., Brodsky B., Baum J. Direct NMR measurement of folding kinetics of a trimeric peptide. Biochemistry. 1996 Apr 9;35(14):4306–4313. doi: 10.1021/bi952270d. [DOI] [PubMed] [Google Scholar]
- Lubienski M. J., Bycroft M., Freund S. M., Fersht A. R. Three-dimensional solution structure and 13C assignments of barstar using nuclear magnetic resonance spectroscopy. Biochemistry. 1994 Aug 2;33(30):8866–8877. [PubMed] [Google Scholar]
- Martínez J. C., Filimonov V. V., Mateo P. L., Schreiber G., Fersht A. R. A calorimetric study of the thermal stability of barstar and its interaction with barnase. Biochemistry. 1995 Apr 18;34(15):5224–5233. doi: 10.1021/bi00015a036. [DOI] [PubMed] [Google Scholar]
- Matouschek A., Serrano L., Fersht A. R. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure. J Mol Biol. 1992 Apr 5;224(3):819–835. doi: 10.1016/0022-2836(92)90564-z. [DOI] [PubMed] [Google Scholar]
- Nölting B., Golbik R., Neira J. L., Soler-Gonzalez A. S., Schreiber G., Fersht A. R. The folding pathway of a protein at high resolution from microseconds to seconds. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):826–830. doi: 10.1073/pnas.94.3.826. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roder H., Elöve G. A., Englander S. W. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature. 1988 Oct 20;335(6192):700–704. doi: 10.1038/335700a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schreiber G., Fersht A. R. The refolding of cis- and trans-peptidylprolyl isomers of barstar. Biochemistry. 1993 Oct 19;32(41):11195–11203. doi: 10.1021/bi00092a032. [DOI] [PubMed] [Google Scholar]
- Serrano L., Matouschek A., Fersht A. R. The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure. J Mol Biol. 1992 Apr 5;224(3):805–818. doi: 10.1016/0022-2836(92)90563-y. [DOI] [PubMed] [Google Scholar]
- Shastry M. C., Udgaonkar J. B. The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates. J Mol Biol. 1995 Apr 14;247(5):1013–1027. doi: 10.1006/jmbi.1994.0196. [DOI] [PubMed] [Google Scholar]
- Sugawara T., Kuwajima K., Sugai S. Folding of staphylococcal nuclease A studied by equilibrium and kinetic circular dichroism spectra. Biochemistry. 1991 Mar 12;30(10):2698–2706. doi: 10.1021/bi00224a018. [DOI] [PubMed] [Google Scholar]
- Wintrode P. L., Griko Y. V., Privalov P. L. Structural energetics of barstar studied by differential scanning microcalorimetry. Protein Sci. 1995 Aug;4(8):1528–1534. doi: 10.1002/pro.5560040810. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wong K. B., Fersht A. R., Freund S. M. NMR 15N relaxation and structural studies reveal slow conformational exchange in barstar C40/82A. J Mol Biol. 1997 May 2;268(2):494–511. doi: 10.1006/jmbi.1997.0989. [DOI] [PubMed] [Google Scholar]
- Wong K. B., Freund S. M., Fersht A. R. Cold denaturation of barstar: 1H, 15N and 13C NMR assignment and characterisation of residual structure. J Mol Biol. 1996 Jun 21;259(4):805–818. doi: 10.1006/jmbi.1996.0359. [DOI] [PubMed] [Google Scholar]
