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. 1994 Oct 25;91(22):10430–10434. doi: 10.1073/pnas.91.22.10430

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

A Li 1, V Daggett 1
PMCID: PMC45034  PMID: 7937969

Abstract

Temperature-induced unfolding of chymotrypsin inhibitor 2 in water was investigated by molecular dynamics simulations. The major transition state of unfolding was identified on the basis of structural and conformational changes in the protein during the unfolding reaction. The native tertiary contacts in the hydrophobic core were considerably disrupted in the transition state, whereas the secondary structure was partially intact. The extent of structural change of the protein around a particular residue was represented quantitatively by the ratio of the number of contacts the residue makes in the transition state relative to the native state, phi MD, which allows quantitative comparison with the experimentally determined phi F values. For the region of the unfolding trajectory that is identified as the transition state, the phi MD and phi F values are in good agreement, suggesting that the transition state identified in the unfolding simulation corresponds to that probed with protein engineering methods. Although speculative, the transition state identified in the simulation is consistent with available experimental data and provides an in-depth view of what the transition state of unfolding may look like.

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Selected References

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  1. Clore G. M., Gronenborn A. M., James M. N., Kjaer M., McPhalen C. A., Poulsen F. M. Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2. Protein Eng. 1987 Aug-Sep;1(4):313–318. doi: 10.1093/protein/1.4.313. [DOI] [PubMed] [Google Scholar]
  2. Clore G. M., Gronenborn A. M., Kjaer M., Poulsen F. M. The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics. Protein Eng. 1987 Aug-Sep;1(4):305–311. doi: 10.1093/protein/1.4.305. [DOI] [PubMed] [Google Scholar]
  3. Daggett V., Kollman P. A., Kuntz I. D. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 1991 Aug;31(9):1115–1134. doi: 10.1002/bip.360310911. [DOI] [PubMed] [Google Scholar]
  4. Daggett V., Levitt M. Molecular dynamics simulations of helix denaturation. J Mol Biol. 1992 Feb 20;223(4):1121–1138. doi: 10.1016/0022-2836(92)90264-k. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. Goldenberg D. P., Creighton T. E. Energetics of protein structure and folding. Biopolymers. 1985 Jan;24(1):167–182. doi: 10.1002/bip.360240114. [DOI] [PubMed] [Google Scholar]
  8. Harpaz Y., Elmasry N., Fersht A. R., Henrick K. Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):311–315. doi: 10.1073/pnas.91.1.311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hurle M. R., Michelotti G. A., Crisanti M. M., Matthews C. R. Characterization of a slow folding reaction for the alpha subunit of tryptophan synthase. Proteins. 1987;2(1):54–63. doi: 10.1002/prot.340020107. [DOI] [PubMed] [Google Scholar]
  10. Jackson S. E., Fersht A. R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry. 1991 Oct 29;30(43):10428–10435. doi: 10.1021/bi00107a010. [DOI] [PubMed] [Google Scholar]
  11. Jackson S. E., Fersht A. R. Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding. Biochemistry. 1991 Oct 29;30(43):10436–10443. doi: 10.1021/bi00107a011. [DOI] [PubMed] [Google Scholar]
  12. Jackson S. E., Moracci M., elMasry N., Johnson C. M., Fersht A. R. Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. Biochemistry. 1993 Oct 26;32(42):11259–11269. doi: 10.1021/bi00093a001. [DOI] [PubMed] [Google Scholar]
  13. Jackson S. E., elMasry N., Fersht A. R. Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis. Biochemistry. 1993 Oct 26;32(42):11270–11278. doi: 10.1021/bi00093a002. [DOI] [PubMed] [Google Scholar]
  14. Levitt M. Molecular dynamics of native protein. II. Analysis and nature of motion. J Mol Biol. 1983 Aug 15;168(3):621–657. doi: 10.1016/s0022-2836(83)80306-4. [DOI] [PubMed] [Google Scholar]
  15. Ludvigsen S., Shen H. Y., Kjaer M., Madsen J. C., Poulsen F. M. Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals. J Mol Biol. 1991 Dec 5;222(3):621–635. doi: 10.1016/0022-2836(91)90500-6. [DOI] [PubMed] [Google Scholar]
  16. Matouschek A., Kellis J. T., Jr, Serrano L., Fersht A. R. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 1989 Jul 13;340(6229):122–126. doi: 10.1038/340122a0. [DOI] [PubMed] [Google Scholar]
  17. McPhalen C. A., James M. N. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry. 1987 Jan 13;26(1):261–269. doi: 10.1021/bi00375a036. [DOI] [PubMed] [Google Scholar]
  18. Otzen D. E., Itzhaki L. S., elMasry N. F., Jackson S. E., Fersht A. R. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10422–10425. doi: 10.1073/pnas.91.22.10422. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Perry K. M., Onuffer J. J., Touchette N. A., Herndon C. S., Gittelman M. S., Matthews C. R., Chen J. T., Mayer R. J., Taira K., Benkovic S. J. Effect of single amino acid replacements on the folding and stability of dihydrofolate reductase from Escherichia coli. Biochemistry. 1987 May 19;26(10):2674–2682. doi: 10.1021/bi00384a004. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Serrano L., Matouschek A., Fersht A. R. The folding of an enzyme. VI. The folding pathway of barnase: comparison with theoretical models. J Mol Biol. 1992 Apr 5;224(3):847–859. doi: 10.1016/0022-2836(92)90566-3. [DOI] [PubMed] [Google Scholar]

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