Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2002 Aug;83(2):681–698. doi: 10.1016/S0006-3495(02)75200-4

Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data.

Tru Huynh 1, Jeremy C Smith 1, Alain Sanson 1
PMCID: PMC1302178  PMID: 12124256

Abstract

Unfolding transitions of an intrinsically unstable annexin domain and the unfolded state structure have been examined using multiple approximately 10-ns molecular dynamics simulations. Three main basins are observed in the configurational space: native-like state, compact partially unfolded or intermediate compact state, and the unfolded state. In the native-like state fluctuations are observed that are nonproductive for unfolding. During these fluctuations, after an initial loss of approximately 20% of the core residue native contacts, the core of the protein transiently completely refolds to the native state. The transition from the native-like basin to the partially unfolded compact state involves approximately 75% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate state adopts for part of the time in one of the trajectories a novel highly compact salt-bridge stabilized structure that can be identified as a conformational trap. The intermediate-to-unfolded state transition is characterized by a large increase in the radius of gyration. After an initial relaxation the unfolded state recovers a native-like topology of the domain. The simulated unfolded state ensemble reproduces in detail experimental nuclear magnetic resonance data and leads to a convincing complete picture of the unfolded domain.

Full Text

The Full Text of this article is available as a PDF (1.6 MB).

Selected References

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

  1. Boczko E. M., Brooks C. L., 3rd First-principles calculation of the folding free energy of a three-helix bundle protein. Science. 1995 Jul 21;269(5222):393–396. doi: 10.1126/science.7618103. [DOI] [PubMed] [Google Scholar]
  2. Chiti F., Taddei N., White P. M., Bucciantini M., Magherini F., Stefani M., Dobson C. M. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat Struct Biol. 1999 Nov;6(11):1005–1009. doi: 10.1038/14890. [DOI] [PubMed] [Google Scholar]
  3. Cordier-Ochsenbein F., Guerois R., Baleux F., Huynh-Dinh T., Chaffotte A., Neumann J. M., Sanson A. Folding properties of an annexin I domain: a 1H-15N NMR and CD study. Biochemistry. 1996 Aug 13;35(32):10347–10357. doi: 10.1021/bi960747v. [DOI] [PubMed] [Google Scholar]
  4. Cordier-Ochsenbein F., Guerois R., Baleux F., Huynh-Dinh T., Lirsac P. N., Russo-Marie F., Neumann J. M., Sanson A. Exploring the folding pathways of annexin I, a multidomain protein. I. non-native structures stabilize the partially folded state of the isolated domain 2 of annexin I. J Mol Biol. 1998 Jun 26;279(5):1163–1175. doi: 10.1006/jmbi.1998.1829. [DOI] [PubMed] [Google Scholar]
  5. Cordier-Ochsenbein F., Guerois R., Russo-Marie F., Neumann J. M., Sanson A. Exploring the folding pathways of annexin I, a multidomain protein. II. Hierarchy in domain folding propensities may govern the folding process. J Mol Biol. 1998 Jun 26;279(5):1177–1185. doi: 10.1006/jmbi.1998.1828. [DOI] [PubMed] [Google Scholar]
  6. Daura X., van Gunsteren W. F., Mark A. E. Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins. 1999 Feb 15;34(3):269–280. doi: 10.1002/(sici)1097-0134(19990215)34:3<269::aid-prot1>3.0.co;2-3. [DOI] [PubMed] [Google Scholar]
  7. Denisov V. P., Jonsson B. H., Halle B. Hydration of denatured and molten globule proteins. Nat Struct Biol. 1999 Mar;6(3):253–260. doi: 10.1038/6692. [DOI] [PubMed] [Google Scholar]
  8. Dill K. A., Bromberg S., Yue K., Fiebig K. M., Yee D. P., Thomas P. D., Chan H. S. Principles of protein folding--a perspective from simple exact models. Protein Sci. 1995 Apr;4(4):561–602. doi: 10.1002/pro.5560040401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Eaton W. A. Searching for "downhill scenarios" in protein folding. Proc Natl Acad Sci U S A. 1999 May 25;96(11):5897–5899. doi: 10.1073/pnas.96.11.5897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Favier-Perron B., Lewit-Bentley A., Russo-Marie F. The high-resolution crystal structure of human annexin III shows subtle differences with annexin V. Biochemistry. 1996 Feb 13;35(6):1740–1744. doi: 10.1021/bi952092o. [DOI] [PubMed] [Google Scholar]
  12. Ferrara P., Caflisch A. Folding simulations of a three-stranded antiparallel beta -sheet peptide. Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10780–10785. doi: 10.1073/pnas.190324897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins. 1995 Dec;23(4):566–579. doi: 10.1002/prot.340230412. [DOI] [PubMed] [Google Scholar]
  15. Gilquin B., Guilbert C., Perahia D. Unfolding of hen egg lysozyme by molecular dynamics simulations at 300K: insight into the role of the interdomain interface. Proteins. 2000 Oct 1;41(1):58–74. [PubMed] [Google Scholar]
  16. Guerois R., Cordier-Ochsenbein F., Baleux F., Huynh-Dinh T., Neumann J. M., Sanson A. A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: 1H-, 13C-NMR, and mutational analysis. Protein Sci. 1998 Jul;7(7):1506–1515. doi: 10.1002/pro.5560070703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Huber R., Berendes R., Burger A., Schneider M., Karshikov A., Luecke H., Römisch J., Paques E. Crystal and molecular structure of human annexin V after refinement. Implications for structure, membrane binding and ion channel formation of the annexin family of proteins. J Mol Biol. 1992 Feb 5;223(3):683–704. doi: 10.1016/0022-2836(92)90984-r. [DOI] [PubMed] [Google Scholar]
  18. Ibragimova G. T., Wade R. C. Stability of the beta-sheet of the WW domain: A molecular dynamics simulation study. Biophys J. 1999 Oct;77(4):2191–2198. doi: 10.1016/S0006-3495(99)77059-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Inuzuka Y., Lazaridis T. On the unfolding of alpha-lytic protease and the role of the pro region. Proteins. 2000 Oct 1;41(1):21–32. [PubMed] [Google Scholar]
  20. Kataoka M., Kuwajima K., Tokunaga F., Goto Y. Structural characterization of the molten globule of alpha-lactalbumin by solution X-ray scattering. Protein Sci. 1997 Feb;6(2):422–430. doi: 10.1002/pro.5560060219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lazaridis T., Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science. 1997 Dec 12;278(5345):1928–1931. doi: 10.1126/science.278.5345.1928. [DOI] [PubMed] [Google Scholar]
  22. Macquaire F., Baleux F., Huynh-Dinh T., Neumann J. M., Sanson A. 1H-NMR conformational study of a synthetic peptide derived from the consensus sequence of annexins. Int J Pept Protein Res. 1992 Feb;39(2):117–122. doi: 10.1111/j.1399-3011.1992.tb00780.x. [DOI] [PubMed] [Google Scholar]
  23. Macquaire F., Baleux F., Huynh-Dinh T., Rouge D., Neumann J. M., Sanson A. Proton NMR conformational study of an annexin I fragment: influence of a phospholipidic micellar environment. Biochemistry. 1993 Jul 20;32(28):7244–7254. doi: 10.1021/bi00079a022. [DOI] [PubMed] [Google Scholar]
  24. Martínez J. C., Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol. 1999 Nov;6(11):1010–1016. doi: 10.1038/14896. [DOI] [PubMed] [Google Scholar]
  25. Mayor U., Johnson C. M., Daggett V., Fersht A. R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13518–13522. doi: 10.1073/pnas.250473497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nath U., Agashe V. R., Udgaonkar J. B. Initial loss of secondary structure in the unfolding of barstar. Nat Struct Biol. 1996 Nov;3(11):920–923. doi: 10.1038/nsb1196-920. [DOI] [PubMed] [Google Scholar]
  27. Petrescu A. J., Calmettes P., Durand D., Receveur V., Smith J. C. Change in backbone torsion angle distribution on protein folding. Protein Sci. 2000 Jun;9(6):1129–1136. doi: 10.1110/ps.9.6.1129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Petrescu A. J., Receveur V., Calmettes P., Durand D., Smith J. C. Excluded volume in the configurational distribution of a strongly-denatured protein. Protein Sci. 1998 Jun;7(6):1396–1403. doi: 10.1002/pro.5560070616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Prompers J. J., Scheurer C., Brüschweiler R. Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin. J Mol Biol. 2001 Feb 2;305(5):1085–1097. doi: 10.1006/jmbi.2000.4353. [DOI] [PubMed] [Google Scholar]
  30. Riddle D. S., Grantcharova V. P., Santiago J. V., Alm E., Ruczinski I., Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol. 1999 Nov;6(11):1016–1024. doi: 10.1038/14901. [DOI] [PubMed] [Google Scholar]
  31. Sali A., Shakhnovich E., Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J Mol Biol. 1994 Feb 4;235(5):1614–1636. doi: 10.1006/jmbi.1994.1110. [DOI] [PubMed] [Google Scholar]
  32. Segel D. J., Fink A. L., Hodgson K. O., Doniach S. Protein denaturation: a small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c. Biochemistry. 1998 Sep 8;37(36):12443–12451. doi: 10.1021/bi980535t. [DOI] [PubMed] [Google Scholar]
  33. Shakhnovich E. I. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Fold Des. 1998;3(6):R108–R107. doi: 10.1016/s1359-0278(98)00056-x. [DOI] [PubMed] [Google Scholar]
  34. Smith L. J., Dobson C. M., van Gunsteren W. F. Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin. J Mol Biol. 1999 Mar 12;286(5):1567–1580. doi: 10.1006/jmbi.1999.2545. [DOI] [PubMed] [Google Scholar]
  35. Ternström T., Mayor U., Akke M., Oliveberg M. From snapshot to movie: phi analysis of protein folding transition states taken one step further. Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14854–14859. doi: 10.1073/pnas.96.26.14854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tirado-Rives J., Orozco M., Jorgensen W. L. Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry. 1997 Jun 17;36(24):7313–7329. doi: 10.1021/bi970096i. [DOI] [PubMed] [Google Scholar]
  37. Tsai J., Levitt M., Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol. 1999 Aug 6;291(1):215–225. doi: 10.1006/jmbi.1999.2949. [DOI] [PubMed] [Google Scholar]
  38. Walser R., Mark A. E., van Gunsteren W. F. On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations. Biophys J. 2000 Jun;78(6):2752–2760. doi: 10.1016/S0006-3495(00)76820-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Weng X., Luecke H., Song I. S., Kang D. S., Kim S. H., Huber R. Crystal structure of human annexin I at 2.5 A resolution. Protein Sci. 1993 Mar;2(3):448–458. doi: 10.1002/pro.5560020317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wong K. B., Clarke J., Bond C. J., Neira J. L., Freund S. M., Fersht A. R., Daggett V. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J Mol Biol. 2000 Mar 10;296(5):1257–1282. doi: 10.1006/jmbi.2000.3523. [DOI] [PubMed] [Google Scholar]

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

RESOURCES