Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1999 Jul;77(1):54–69. doi: 10.1016/S0006-3495(99)76872-4

De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.

D Mohanty 1, A Kolinski 1, J Skolnick 1
PMCID: PMC1300312  PMID: 10388740

Abstract

Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4-lz) in the context of a reduced model. Using the calculated partition functions for the monomer and dimer, and taking into account the equilibrium between the monomer and dimer, the average helix content of the GCN4-lz was computed over a range of temperatures and chain concentrations. The predicted helix contents for the native and denatured states of GCN4-lz agree with the experimental values. Similar to experimental results, our helix content versus temperature curves show a small linear decline in helix content with an increase in temperature in the native region. This is followed by a sharp transition to the denatured state. van't Hoff analysis of the helix content versus temperature curves indicates that the folding transition can be described using a two-state model. This indicates that knowledge-based potentials can be used to describe the properties of the folded and unfolded states of proteins.

Full Text

The Full Text of this article is available as a PDF (210.8 KB).

Selected References

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

  1. Alber T. Structure of the leucine zipper. Curr Opin Genet Dev. 1992 Apr;2(2):205–210. doi: 10.1016/s0959-437x(05)80275-8. [DOI] [PubMed] [Google Scholar]
  2. Berg BA, Neuhaus T. Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys Rev Lett. 1992 Jan 6;68(1):9–12. doi: 10.1103/PhysRevLett.68.9. [DOI] [PubMed] [Google Scholar]
  3. Brooks C. L., 3rd Methodological advances in molecular dynamics simulations of biological systems. Curr Opin Struct Biol. 1995 Apr;5(2):211–215. doi: 10.1016/0959-440x(95)80078-6. [DOI] [PubMed] [Google Scholar]
  4. Cohen C., Parry D. A. Alpha-helical coiled coils and bundles: how to design an alpha-helical protein. Proteins. 1990;7(1):1–15. doi: 10.1002/prot.340070102. [DOI] [PubMed] [Google Scholar]
  5. DeLano W. L., Brünger A. T. Helix packing in proteins: prediction and energetic analysis of dimeric, trimeric, and tetrameric GCN4 coiled coil structures. Proteins. 1994 Oct;20(2):105–123. doi: 10.1002/prot.340200202. [DOI] [PubMed] [Google Scholar]
  6. DiDonato J. A., Hayakawa M., Rothwarf D. M., Zandi E., Karin M. A cytokine-responsive IkappaB kinase that activates the transcription factor NF-kappaB. Nature. 1997 Aug 7;388(6642):548–554. doi: 10.1038/41493. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Fraser R. D., MacRae T. P. Structure of alpha-keratin. Nature. 1971 Sep 10;233(5315):138–140. doi: 10.1038/233138a0. [DOI] [PubMed] [Google Scholar]
  9. Harbury P. B., Zhang T., Kim P. S., Alber T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science. 1993 Nov 26;262(5138):1401–1407. doi: 10.1126/science.8248779. [DOI] [PubMed] [Google Scholar]
  10. Harrison S. C. A structural taxonomy of DNA-binding domains. Nature. 1991 Oct 24;353(6346):715–719. doi: 10.1038/353715a0. [DOI] [PubMed] [Google Scholar]
  11. Hirst J. D., Brooks C. L., 3rd Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry. 1995 Jun 13;34(23):7614–7621. doi: 10.1021/bi00023a007. [DOI] [PubMed] [Google Scholar]
  12. Hodges R. S., Saund A. K., Chong P. C., St-Pierre S. A., Reid R. E. Synthetic model for two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization of an 86-residue analog of tropomyosin. J Biol Chem. 1981 Feb 10;256(3):1214–1224. [PubMed] [Google Scholar]
  13. Holtzer M. E., Holtzer A. Alpha-helix to random coil transitions: interpretation of the CD in the region of linear temperature dependence. Biopolymers. 1992 Nov;32(11):1589–1591. doi: 10.1002/bip.360321116. [DOI] [PubMed] [Google Scholar]
  14. Holtzer M. E., Lovett E. G., d'Avignon D. A., Holtzer A. Thermal unfolding in a GCN4-like leucine zipper: 13C alpha NMR chemical shifts and local unfolding curves. Biophys J. 1997 Aug;73(2):1031–1041. doi: 10.1016/S0006-3495(97)78136-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hvidt S., Rodgers M. E., Harrington W. F. Temperature-dependent optical rotatory dispersion properties of helical muscle proteins and homopolymers. Biopolymers. 1985 Sep;24(9):1647–1662. doi: 10.1002/bip.360240902. [DOI] [PubMed] [Google Scholar]
  16. Johnson F., Smillie L. B. Rabbit skeletal alpha-tropomyosin chains are in register. Biochem Biophys Res Commun. 1975 Jun 16;64(4):1316–1322. doi: 10.1016/0006-291x(75)90836-0. [DOI] [PubMed] [Google Scholar]
  17. Kenar K. T., García-Moreno B., Freire E. A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper. Protein Sci. 1995 Sep;4(9):1934–1938. doi: 10.1002/pro.5560040929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kolinski A., Galazka W., Skolnick J. On the origin of the cooperativity of protein folding: implications from model simulations. Proteins. 1996 Nov;26(3):271–287. doi: 10.1002/(SICI)1097-0134(199611)26:3<271::AID-PROT4>3.0.CO;2-H. [DOI] [PubMed] [Google Scholar]
  19. Kolinski A., Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins. 1994 Apr;18(4):338–352. doi: 10.1002/prot.340180405. [DOI] [PubMed] [Google Scholar]
  20. Krystek S. R., Jr, Bruccoleri R. E., Novotny J. Stabilities of leucine zipper dimers estimated by an empirical free energy method. Int J Pept Protein Res. 1991 Sep;38(3):229–236. doi: 10.1111/j.1399-3011.1991.tb01433.x. [DOI] [PubMed] [Google Scholar]
  21. Landschulz W. H., Johnson P. F., McKnight S. L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
  22. Lee J. New Monte Carlo algorithm: Entropic sampling. Phys Rev Lett. 1993 Jul 12;71(2):211–214. doi: 10.1103/PhysRevLett.71.211. [DOI] [PubMed] [Google Scholar]
  23. Lehrer S. S., Stafford W. F., 3rd Preferential assembly of the tropomyosin heterodimer: equilibrium studies. Biochemistry. 1991 Jun 11;30(23):5682–5688. doi: 10.1021/bi00237a007. [DOI] [PubMed] [Google Scholar]
  24. Lovejoy B., Choe S., Cascio D., McRorie D. K., DeGrado W. F., Eisenberg D. Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science. 1993 Feb 26;259(5099):1288–1293. doi: 10.1126/science.8446897. [DOI] [PubMed] [Google Scholar]
  25. Lovett E. G., D'Avignon D. A., Holtzer M. E., Braswell E. H., Zhu D., Holtzer A. Observation via one-dimensional 13Calpha NMR of local conformational substates in thermal unfolding equilibria of a synthetic analog of the GCN4 leucine zipper. Proc Natl Acad Sci U S A. 1996 Mar 5;93(5):1781–1785. doi: 10.1073/pnas.93.5.1781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lumb K. J., Carr C. M., Kim P. S. Subdomain folding of the coiled coil leucine zipper from the bZIP transcriptional activator GCN4. Biochemistry. 1994 Jun 14;33(23):7361–7367. doi: 10.1021/bi00189a042. [DOI] [PubMed] [Google Scholar]
  27. Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987 Sep;26(9):1601–1620. doi: 10.1002/bip.360260911. [DOI] [PubMed] [Google Scholar]
  28. McLachlan A. D., Stewart M. Tropomyosin coiled-coil interactions: evidence for an unstaggered structure. J Mol Biol. 1975 Oct 25;98(2):293–304. doi: 10.1016/s0022-2836(75)80119-7. [DOI] [PubMed] [Google Scholar]
  29. Monera O. D., Zhou N. E., Lavigne P., Kay C. M., Hodges R. S. Formation of parallel and antiparallel coiled-coils controlled by the relative positions of alanine residues in the hydrophobic core. J Biol Chem. 1996 Feb 23;271(8):3995–4001. doi: 10.1074/jbc.271.8.3995. [DOI] [PubMed] [Google Scholar]
  30. Nilges M., Brünger A. T. Automated modeling of coiled coils: application to the GCN4 dimerization region. Protein Eng. 1991 Aug;4(6):649–659. doi: 10.1093/protein/4.6.649. [DOI] [PubMed] [Google Scholar]
  31. Nilges M., Brünger A. T. Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: comparison to the X-ray structure. Proteins. 1993 Feb;15(2):133–146. doi: 10.1002/prot.340150205. [DOI] [PubMed] [Google Scholar]
  32. O'Neil K. T., Hoess R. H., DeGrado W. F. Design of DNA-binding peptides based on the leucine zipper motif. Science. 1990 Aug 17;249(4970):774–778. doi: 10.1126/science.2389143. [DOI] [PubMed] [Google Scholar]
  33. O'Shea E. K., Klemm J. D., Kim P. S., Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 1991 Oct 25;254(5031):539–544. doi: 10.1126/science.1948029. [DOI] [PubMed] [Google Scholar]
  34. O'Shea E. K., Lumb K. J., Kim P. S. Peptide 'Velcro': design of a heterodimeric coiled coil. Curr Biol. 1993 Oct 1;3(10):658–667. doi: 10.1016/0960-9822(93)90063-t. [DOI] [PubMed] [Google Scholar]
  35. Phillips G. N., Jr, Fillers J. P., Cohen C. Tropomyosin crystal structure and muscle regulation. J Mol Biol. 1986 Nov 5;192(1):111–131. doi: 10.1016/0022-2836(86)90468-7. [DOI] [PubMed] [Google Scholar]
  36. Privalov P. L., Gill S. J. Stability of protein structure and hydrophobic interaction. Adv Protein Chem. 1988;39:191–234. doi: 10.1016/s0065-3233(08)60377-0. [DOI] [PubMed] [Google Scholar]
  37. Smeal T., Angel P., Meek J., Karin M. Different requirements for formation of Jun: Jun and Jun: Fos complexes. Genes Dev. 1989 Dec;3(12B):2091–2100. doi: 10.1101/gad.3.12b.2091. [DOI] [PubMed] [Google Scholar]
  38. Sosnick T. R., Jackson S., Wilk R. R., Englander S. W., DeGrado W. F. The role of helix formation in the folding of a fully alpha-helical coiled coil. Proteins. 1996 Apr;24(4):427–432. doi: 10.1002/(SICI)1097-0134(199604)24:4<427::AID-PROT2>3.0.CO;2-B. [DOI] [PubMed] [Google Scholar]
  39. Su J. Y., Hodges R. S., Kay C. M. Effect of chain length on the formation and stability of synthetic alpha-helical coiled coils. Biochemistry. 1994 Dec 27;33(51):15501–15510. doi: 10.1021/bi00255a032. [DOI] [PubMed] [Google Scholar]
  40. Talanian R. V., McKnight C. J., Kim P. S. Sequence-specific DNA binding by a short peptide dimer. Science. 1990 Aug 17;249(4970):769–771. doi: 10.1126/science.2389142. [DOI] [PubMed] [Google Scholar]
  41. Thomas P. D., Dill K. A. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol. 1996 Mar 29;257(2):457–469. doi: 10.1006/jmbi.1996.0175. [DOI] [PubMed] [Google Scholar]
  42. Vieth M., Kolinski A., Brooks C. L., 3rd, Skolnick J. Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. J Mol Biol. 1995 Aug 18;251(3):448–467. doi: 10.1006/jmbi.1995.0447. [DOI] [PubMed] [Google Scholar]
  43. Vieth M., Kolinski A., Brooks C. L., 3rd, Skolnick J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol. 1994 Apr 8;237(4):361–367. doi: 10.1006/jmbi.1994.1239. [DOI] [PubMed] [Google Scholar]
  44. Vieth M., Kolinski A., Skolnick J. Method for predicting the state of association of discretized protein models. Application to leucine zippers. Biochemistry. 1996 Jan 23;35(3):955–967. doi: 10.1021/bi9520702. [DOI] [PubMed] [Google Scholar]
  45. Zhang L., Hermans J. Molecular dynamics study of structure and stability of a model coiled coil. Proteins. 1993 Aug;16(4):384–392. doi: 10.1002/prot.340160407. [DOI] [PubMed] [Google Scholar]
  46. Zhang L., Skolnick J. How do potentials derived from structural databases relate to "true" potentials? Protein Sci. 1998 Jan;7(1):112–122. doi: 10.1002/pro.5560070112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zitzewitz J. A., Bilsel O., Luo J., Jones B. E., Matthews C. R. Probing the folding mechanism of a leucine zipper peptide by stopped-flow circular dichroism spectroscopy. Biochemistry. 1995 Oct 3;34(39):12812–12819. doi: 10.1021/bi00039a042. [DOI] [PubMed] [Google Scholar]

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

RESOURCES