Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 2002 Dec;83(6):3525–3532. doi: 10.1016/S0006-3495(02)75352-6

Direct molecular dynamics observation of protein folding transition state ensemble.

Feng Ding 1, Nikolay V Dokholyan 1, Sergey V Buldyrev 1, H Eugene Stanley 1, Eugene I Shakhnovich 1
PMCID: PMC1302427  PMID: 12496119

Abstract

The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50% probability to convert rapidly to the folded state and 50% chance to rapidly unfold, constitutes the basis of the modern interpretation of protein engineering experiments. It has been conjectured that conformations constituting the TSE in many proteins are the expanded and distorted forms of the native state built around a specific folding nucleus. This view has been supported by a number of on-lattice and off-lattice simulations. Here we report a direct observation and characterization of the TSE by molecular dynamic folding simulations of the C-Src SH3 domain, a small protein that has been extensively studied experimentally. Our analysis reveals a set of key interactions between residues, conserved by evolution, that must be formed to enter the kinetic basin of attraction of the native state.

Full Text

The Full Text of this article is available as a PDF (533.7 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abkevich V. I., Gutin A. M., Shakhnovich E. I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 1994 Aug 23;33(33):10026–10036. doi: 10.1021/bi00199a029. [DOI] [PubMed] [Google Scholar]
  2. Abkevich V. I., Shakhnovich E. I. What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. J Mol Biol. 2000 Jul 21;300(4):975–985. doi: 10.1006/jmbi.2000.3893. [DOI] [PubMed] [Google Scholar]
  3. Alm E., Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11305–11310. doi: 10.1073/pnas.96.20.11305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Clementi C., Nymeyer H., Onuchic J. N. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol. 2000 May 19;298(5):937–953. doi: 10.1006/jmbi.2000.3693. [DOI] [PubMed] [Google Scholar]
  5. Dinner A. R., Karplus M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J Mol Biol. 1999 Sep 17;292(2):403–419. doi: 10.1006/jmbi.1999.3051. [DOI] [PubMed] [Google Scholar]
  6. Dokholyan N. V., Buldyrev S. V., Stanley H. E., Shakhnovich E. I. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des. 1998;3(6):577–587. doi: 10.1016/S1359-0278(98)00072-8. [DOI] [PubMed] [Google Scholar]
  7. Dokholyan N. V., Buldyrev S. V., Stanley H. E., Shakhnovich E. I. Identifying the protein folding nucleus using molecular dynamics. J Mol Biol. 2000 Mar 10;296(5):1183–1188. doi: 10.1006/jmbi.1999.3534. [DOI] [PubMed] [Google Scholar]
  8. Duan Y., Kollman P. A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 1998 Oct 23;282(5389):740–744. doi: 10.1126/science.282.5389.740. [DOI] [PubMed] [Google Scholar]
  9. Fersht A. R. Nucleation mechanisms in protein folding. Curr Opin Struct Biol. 1997 Feb;7(1):3–9. doi: 10.1016/s0959-440x(97)80002-4. [DOI] [PubMed] [Google Scholar]
  10. Finkelstein A. V. Can protein unfolding simulate protein folding? Protein Eng. 1997 Aug;10(8):843–845. doi: 10.1093/protein/10.8.843. [DOI] [PubMed] [Google Scholar]
  11. Galzitskaya O. V., Finkelstein A. V. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11299–11304. doi: 10.1073/pnas.96.20.11299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Go N., Abe H. Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers. 1981 May;20(5):991–1011. doi: 10.1002/bip.1981.360200511. [DOI] [PubMed] [Google Scholar]
  13. Goldenberg D. P. Finding the right fold. Nat Struct Biol. 1999 Nov;6(11):987–990. doi: 10.1038/14866. [DOI] [PubMed] [Google Scholar]
  14. Grantcharova V. P., Baker D. Circularization changes the folding transition state of the src SH3 domain. J Mol Biol. 2001 Feb 23;306(3):555–563. doi: 10.1006/jmbi.2000.4352. [DOI] [PubMed] [Google Scholar]
  15. Grantcharova V. P., Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 1997 Dec 16;36(50):15685–15692. doi: 10.1021/bi971786p. [DOI] [PubMed] [Google Scholar]
  16. Grantcharova V. P., Riddle D. S., Baker D. Long-range order in the src SH3 folding transition state. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7084–7089. doi: 10.1073/pnas.97.13.7084. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Grantcharova V. P., Riddle D. S., Santiago J. V., Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol. 1998 Aug;5(8):714–720. doi: 10.1038/1412. [DOI] [PubMed] [Google Scholar]
  18. Guerois R., Serrano L. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol. 2000 Dec 15;304(5):967–982. doi: 10.1006/jmbi.2000.4234. [DOI] [PubMed] [Google Scholar]
  19. Gutin A. M., Abkevich V. I., Shakhnovich E. I. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Fold Des. 1998;3(3):183–194. doi: 10.1016/S1359-0278(98)00026-1. [DOI] [PubMed] [Google Scholar]
  20. Itzhaki L. S., Otzen D. E., Fersht A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol. 1995 Nov 24;254(2):260–288. doi: 10.1006/jmbi.1995.0616. [DOI] [PubMed] [Google Scholar]
  21. Jackson S. E. How do small single-domain proteins fold? Fold Des. 1998;3(4):R81–R91. doi: 10.1016/S1359-0278(98)00033-9. [DOI] [PubMed] [Google Scholar]
  22. Klimov D. K., Thirumalai D. Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins. 2001 Jun 1;43(4):465–475. doi: 10.1002/prot.1058. [DOI] [PubMed] [Google Scholar]
  23. Larson S. M., Davidson A. R. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci. 2000 Nov;9(11):2170–2180. doi: 10.1110/ps.9.11.2170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Li A., Daggett V. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10430–10434. doi: 10.1073/pnas.91.22.10430. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Li A., Daggett V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J Mol Biol. 1998 Jan 30;275(4):677–694. doi: 10.1006/jmbi.1997.1484. [DOI] [PubMed] [Google Scholar]
  26. Martinez J. C., Pisabarro M. T., Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol. 1998 Aug;5(8):721–729. doi: 10.1038/1418. [DOI] [PubMed] [Google Scholar]
  27. Matouschek A., Kellis J. T., Jr, Serrano L., Bycroft M., Fersht A. R. Transient folding intermediates characterized by protein engineering. Nature. 1990 Aug 2;346(6283):440–445. doi: 10.1038/346440a0. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Muñoz V., Eaton W. A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11311–11316. doi: 10.1073/pnas.96.20.11311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Muñoz V., Thompson P. A., Hofrichter J., Eaton W. A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 1997 Nov 13;390(6656):196–199. doi: 10.1038/36626. [DOI] [PubMed] [Google Scholar]
  31. Nymeyer H., Socci N. D., Onuchic J. N. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):634–639. doi: 10.1073/pnas.97.2.634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Ozkan S. B., Bahar I., Dill K. A. Transition states and the meaning of Phi-values in protein folding kinetics. Nat Struct Biol. 2001 Sep;8(9):765–769. doi: 10.1038/nsb0901-765. [DOI] [PubMed] [Google Scholar]
  33. Plaxco K. W., Simons K. T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol. 1998 Apr 10;277(4):985–994. doi: 10.1006/jmbi.1998.1645. [DOI] [PubMed] [Google Scholar]
  34. Sali A., Shakhnovich E., Karplus M. How does a protein fold? Nature. 1994 May 19;369(6477):248–251. doi: 10.1038/369248a0. [DOI] [PubMed] [Google Scholar]
  35. Vendruscolo M., Paci E., Dobson C. M., Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature. 2001 Feb 1;409(6820):641–645. doi: 10.1038/35054591. [DOI] [PubMed] [Google Scholar]
  36. Zhou Y., Karplus M. Folding thermodynamics of a model three-helix-bundle protein. Proc Natl Acad Sci U S A. 1997 Dec 23;94(26):14429–14432. doi: 10.1073/pnas.94.26.14429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Zhou Y., Karplus M. Interpreting the folding kinetics of helical proteins. Nature. 1999 Sep 23;401(6751):400–403. doi: 10.1038/43937. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES